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| Abbreviated Title:   | Molecular Profiling NSCLC   |
|----------------------|-----------------------------|
| CC Protocol #:       | 11-C-0096 V                 |
| Version Date:        | January 7, 2020             |
| NCT Number:          | NCT01306045                 |  
  
TITLE: Pilot Trial of Molecular Profiling and Targeted Therapy for  
Advanced Non-Small Cell Lung Cancer, Small Cell Lung Cancer, and Thymic Malignancies  
Coordinating Center: Center for Cancer Research / National Cancer Institute  
10 Center Drive Bethesda, MD 20892  
NCI Principal Investigator: Arun Rajan, MD  
Thoracic and GI Malignancies Branch / CCR / NCI 9000 Rockville Pike Bldg 10, Rm 4-5332 Bethesda, MD 20892 Telephone: 240-760-6236 Email rajana@mail.nih.gov  
  
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NOTE: Trial administratively completed with CTEP 03/22/2016; trial remains open under NIH Intramural **IRB for molecular profiling arm only**  
| Drug Sponsor:    | CTEP, NCI   |         |           |           |                   |
|------------------|-------------|---------|-----------|-----------|-------------------|
| CTEP Protocol #: | 8639        |         |           |           |                   |
| Study Drug       | AZD6244     | MK-2206 | Lapatinib | Erlotinib | Sunitinib         |
| NSC #            | 748727      | 749607  | 727989    | 718781    | 736511            |
| IND #            | 77782       | 109493  | 70252     | 63383     | Commercial Supply |  
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precis background

- A better understanding of the genetic make-up of the individual tumor may offer potentially improved therapies. This approach may also give rapid access to response data in patients with sometimes rare genetic abnormalities.  
- In addition, it will allow us to test targeted therapies in a select population of patients that is more likely to have a favorable response based on their molecular profile and the specific mechanism of action of the drug being tested.  
- This approach will also speed up drug development and potentially approval, and rescue an otherwise ineffective drug candidate for the specific subgroup that can benefit.
Primary Objectives V
- To determine the feasibility of the use of tumor's molecular profiling and targeted therapies in the treatment of advanced stage non-small cell lung cancer (NSCLC), small cell lung cancer (SCLC) and thymic malignancies.  
- To estimate the response rate of molecular-profile directed treatments in NSCLC, SCLC
and thymic malignancies patients.
Eligibility
- Patients with histologically confirmed advanced lung cancer or thymic malignancies for whom surgical resection with curative intent is not feasible.  
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- Patients must either have biopsiable disease and be willing to undergo biopsy for molecular profiling or have paraffin embedded tissue blocks suitable for molecular profiling analysis.  
- Individuals are eligible for *EGFR* germline mutation testing if they have:
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o a personal history of invasive lung cancer or one of the pre-invasive histologies associated with the development of lung cancer and more than two affected family members with invasive lung cancer or one of the pre-invasive histologies associated with the development of lung cancer; OR
o a first-degree relative with a known *EGFR* germline mutation (*EGFR* exon 20 T790M, exon 21 V843I, exon 21 R831C and exon 20 R776G).
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design

- All patients will have their tumors undergo molecular profiling. Based on these results and on other eligibility criteria, the patients will be offered enrollment into different targeted therapy arms according to the schema shown below.  
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- At the NCI site only, individuals eligible for *EGFR* germline mutation will undergo testing for germline mutations affecting the *EGFR* gene; if a mutation is detected, their first-degree relatives would be invited to undergo testing for the index germline mutation found in the proband and appropriate follow-up on trial.
- Effective with Amendment I, the participating site, OHSU, will discontinue new enrollments and data entry for existing patients on the NOS arm on this protocol in favor of the OHSU protocol L8639, "Personalized Cancer Medicine Registry." The data from these patients will be included with the data from 11-C-0096 (8639) NCI patients at the time of publication. Any OHSU patients who are eligible for a treatment arm will continue to be enrolled and followed per protocol.  
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* See Sections 3.2 and 3.3 for eligibility criteria for the treatment arms. Patients will be allowed to crossover to different treatment arms as long as they meet eligibility criteria.  
† See separate eligibility criteria (Section 3.4) and schema for *EGFR* germline mutation testing. No = No or not available Amp = gene amplification by FISH NOS = non-otherwise specified arm A **= optional re-biopsy for patients that responded to previous line of therapy**  
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1 Consent II: Informed consent for testing for *EGFR* germline mutations of proband. 2 *EGFR* germline mutation panel: *EGFR* exon 20 T790M, exon 21 V843I, exon 21 R831C and exon 20 R776G.  
  
  
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1Between 55 and 74 years of age at enrollment with a history of cigarette smoking of at least 30 pack-years, and, if former smokers, those who quit within the previous 15 years.  
2 Age ≥ 45 years at enrollment with ≥ 20 pack-year smoking history or age within 5 years before the youngest family member was diagnosed with lung cancer.  
3 For lung nodules and incidental lesions detected on CT, follow up is per standard guidelines.  
Consent III: Informed consent for testing for *EGFR* germline mutations in first-degree relatives of individuals with known *EGFR* germline mutations. Abbreviation: LDCT, low-dose screening computed tomography scan.  
Follow-up of lung nodules recommended by Fleischner Society (1) and National Comprehensive Cancer Network(2)(2)(2).  
| Table of Contents                              |                                                                                       |             |
|------------------------------------------------|---------------------------------------------------------------------------------------|-------------|
| PRÉCIS .                                       |                                                                                       |             |
| SCHEMA .                                       |                                                                                       |             |
| TABLE OF CONTENTS.                             |                                                                                       |             |
| TABLE OF TABLES                                |                                                                                       |             |
| l                                              | OBJECTIVES .                                                                          |             |
| 1.1                                            |                                                                                       |             |
| 1.2                                            | SECONDARY PROTOCOL OBJECTIVES                                                         |             |
| 2                                              | BA OR GROUND .                                                                        |             |
| 2.1                                            | BACKGROUND AND RATIONALE                                                              |             |
| 2.2                                            | CTEP-SUPPLIED INVESTIGATIONAL AGENT(S)                                                |             |
| 2.3                                            | OTHER AGENTS .                                                                        |             |
| H I I S                                        |                                                                                       |             |
| 2.4                                            |                                                                                       |             |
| 3                                              | PATIENT SELECTION                                                                     |             |
| 3.1                                            | ELIGIBILITY CRITERIA FOR INITIAL ENROLLMENT                                           |             |
| 3.2                                            | ELIGIBILITY CRITERIA FOR ENROLLMENT INTO THE TREATMENT ARMS (TREATMENT                |             |
| ARMS ARE NO LONGER REGRUITING AS OF 3/22/16) . |                                                                                       |             |
| 3.3                                            | SPECIFIC ELIGIBILITY CRITERIA FOR ENROLLMENT IN TREATMENT ARMS (TREATMENT             |             |
| ARMS ARE NO LONGER RECRUITING AS OF 3/22/16)   |                                                                                       |             |
| 3.4                                            | ELIGIBILITY CRITERIA FOR EGFR GERMLINE MUTATION TESTING (NCI SITE ONLY) ...... 34     |             |
| 3.5                                            | INCLUSION OF WOMEN AND MINORITIES                                                     |             |
| 4                                              | PATIENT REGISTRATION                                                                  |             |
| REGISTRATION PROCESS .                         |                                                                                       |             |
| 4.1                                            | ON-STUDY RESEARCH EVALUATION .                                                        |             |
| 4.2                                            |                                                                                       |             |
| STUDY DESIGN / TREATMENT PLAN                  |                                                                                       |             |
| S                                              | SPECIMEN COLLECTION                                                                   |             |
| 5.1                                            |                                                                                       |             |
| 5.2                                            | MOLECULAR PROFILING                                                                   |             |
| ENROLLMENT IN TREATMENT ARMS .                 |                                                                                       |             |
| 5.3                                            |                                                                                       |             |
| 5.4                                            | T T REATMENT AFTER DISEASE PROGRESSION .                                              |             |
| 5.5                                            | T THE NOS ARM                                                                         |             |
| EGFR GERMLINE MUTATION TESTING .               |                                                                                       |             |
| 5.6                                            |                                                                                       |             |
| 5.7                                            | A A GENT A DMINISTRATION                                                              |             |
| 5.8                                            | GENERAL CONCOMITANT MEDICATION AND SUPPORTIVE CARE GUIDELINES ............... 50      |             |
| 5.9                                            | PROTOCOL EVALUATION  .                                                                |             |
| 5.10                                           | DURATION OF THERAPY / OFF TREATMENT CRITERIA .                                        |             |
| 5.11                                           | D DURATION OF FOLLOW UP                                                               |             |
| OFF STUDY CRITERIA .                           |                                                                                       |             |
| 5.12                                           |                                                                                       |             |
| 5.13                                           | OFF-STUDY PROCEDURE                                                                   |             |
| DOSING DELAYS/DOSE MODIFICATIONS .             |                                                                                       |             |
| 6                                              | 6.1                                                                                   | CTEP AGENTS |
| OTHER AGENTS .                                 |                                                                                       |             |
| 6.2                                            |                                                                                       |             |
| 6.3                                            | TREATMENT DELAYS AND MODIFICATIONS FOR ADMINISTRATIVE NEEDS ...................... 68 |             |  
6.4 TREATMENT DELAYS AND MODIFICATIONS FOR MEDICAL NEEDS ................................... 68 7 SPONSOR SAFETY REPORTING REQUIREMENTS ...... **ERROR! BOOKMARK NOT**
DEFINED.  
| 7.1                                                                   | DEFINITIONS ERROR! BOOKMARK NOT DEFINED.                               |
|-----------------------------------------------------------------------|------------------------------------------------------------------------|
| 7.2                                                                   | ADVERSE EVENTS: LIST AND REPORTING REQUIREMENTS 68                     |
| 7.3                                                                   | COMPREHENSIVE ADVERSE EVENTS AND POTENTIAL RISKS LISTS (CAEPRS) 68     |
| 7.4                                                                   | ADVERSE EVENT CHARACTERISTICS 84                                       |
| 7.5                                                                   | EXPEDITED ADVERSE EVENT REPORTING 85                                   |
| 7.6                                                                   | ROUTINE ADVERSE EVENT REPORTING 88                                     |
| V                                                                     |                                                                        |
| 8                                                                     | NIH REPORTING REQUIREMENTS / DATA AND SAFETY MONITORING PLAN .. 88     |
| 8.1                                                                   | DEFINITIONS 88                                                         |
| 8.2                                                                   | OHSRP OFFICE OF COMPLIANCE AND TRAINING / IRB REPORTING 88             |
| 8.3                                                                   | NCI CLINICAL DIRECTOR REPORTING 88                                     |
| 8.4                                                                   | NIH REQUIRED DATA AND SAFETY MONITORING PLAN 88                        |
| 9                                                                     | PHARMACEUTICAL INFORMATION 89 O                                        |
| 9.1                                                                   | CTEP-SUPPLIED INVESTIGATIONAL AGENT(S) 89                              |
| 9.2                                                                   | OTHER AGENT(S) 95                                                      |
| 9.3                                                                   | AGENT ORDERING 96                                                      |
| 9.4                                                                   | AGENT ACCOUNTABILITY 97                                                |
| 10                                                                    | CORRELATIVE / SPECIAL STUDIES 97                                       |
| 10.1                                                                  | SAMPLE STORAGE, TRACKING AND DISPOSITION 97                            |
| 10.2                                                                  | LARGE SCALE DETECTION OF MUTATIONS IN CANDIDATE GENES 98               |
| 10.3                                                                  | OTHER MOLECULAR PROFILING ANALYSES IN TUMOR SAMPLES 103                |
| 10.4                                                                  | NON-INVASIVE BIOMARKERS STUDIES (ONLY FOR PATIENTS ENROLLED AT THE NCI |
| INTRAMURAL PROGRAM) 104 10.5 SAMPLES FOR GENETIC/GENOMIC ANALYSIS 106 |                                                                        |
| 11                                                                    | DATA COLLECTION AND EVALUATION 107                                     |  
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11.1 DATA COLLECTION ...................................................................................................... 107 11.2 GENOMIC DATA SHARING PLAN .................................................................................. 107 12 STUDY CALENDAR ........................................................................................................ 108 13 MEASUREMENT OF EFFECT......................................................................................... 110  
| D    |                                              |
|------|----------------------------------------------|
| 13.1 | ANTITUMOR EFFECT - SOLID TUMORS 110          |
| 14   | DATA REPORTING / REGULATORY REQUIREMENTS 116 |
| 14.1 | DATA REPORTING 116                           |
| 14.2 | CTEP MULTICENTER GUIDELINES 116              |
| 14.3 | COLLABORATIVE AGREEMENTS LANGUAGE 117        |
| 15   | STATISTICAL CONSIDERATIONS 119               |
| 15.1 | STUDY DESIGN/ENDPOINTS 119                   |
| 15.2 | SAMPLE SIZE/ACCRUAL RATE 120                 |
| 15.3 | STRATIFICATION FACTORS 120                   |
| 15.4 | ANALYSIS OF SECONDARY ENDPOINTS 120          |
| 15.5 | REPORTING AND EXCLUSIONS 121                 |  
| 16   | HUMAN SUBJECTS PROTECTIONS 121                              |
|------|-------------------------------------------------------------|
| 16.1 | RATIONALE FOR SUBJECT SELECTION 121                         |
| 16.2 | JUSTIFICATION FOR EXCLUSIONS 122                            |
| 16.3 | PARTICIPATION OF SUBJECTS UNABLE TO GIVE CONSENT 122        |
| 16.4 | EVALUATION OF BENEFITS AND RISKS/DISCOMFORTS 122            |
| 16.5 | RISK/BENEFIT ANALYSIS 123                                   |
| 16.6 | CONSENT AND ASSENT PROCESS AND DOCUMENTATION 123            |
| 16.7 | DATA AND SAFETY MONITORING PLAN 124                         |
| V    |                                                             |
| 17   | REFERENCES 125                                              |
| 18   | APPENDICES 137                                              |
| 18.1 | APPENDIX A: STUDY AGENT BACKGROUND INFORMATION 137          |
| 18.2 | APPENDIX B: MEDICATION DIARIES 167                          |
| 18.3 | APPENDIX C: PERFORMANCE STATUS CRITERIA 179                 |
| 18.4 | APPENDIX D: NEW YORK HEART ASSOCIATION CLASSIFICATIONS 180  |
| 18.5 | APPENDIX E: MEDICATIONS THAT MAY CAUSE QTC PROLONGATION 181 |
| 18.6 | APPENDIX F: LIST OF CYP3A4 INHIBITORS AND INDUCERS 184      |
| 18.7 | APPENDIX G: INFORMATION ON POSSIBLE INTERACTIONS WITH OTHER |
| AGENTS FOR PATIENTS AND THEIR CAREGIVERS AND NON-STUDY HEALTH CARE TEAM 186 18.8 APPENDIX H: HYPERTENSION MANAGEMENT TOOLS FOR PATIENTS IN SUNITINIB 188 18.9 APPENDIX I: CTEP MULTICENTER GUIDELINES 191 18.10 APPENDIX J: MOLECULAR PROFILING FOLLOW-UP WORKSHEET 193 18.11 APPENDIX K: TOBBACCO USE HISTORY QUESTIONNAIRE 194 18.12 APPENDIX L: ACQUISITION, STORAGE, INTERPRETATION AND REPORTING OF LOWDOSE CT SCANS FOR ENROLLED FIRST-DEGREE RELATIVES 195 O      |                                                             |  
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| Table of Tables                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
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| Table 1. Top 5 mutated genes in SCLC 12 Table 2. EGFR drug-sensitive and resistant mutations 14 Table 3. Frequency of mutated KRAS in selected tumors 16 Table 4. PI3K mutations in NSCLC 18 Table 5. Previously reported germline mutations in lung cancer, clinico-pathologic features of  the patients and their response to TKI 26 V Table 6. Erlotinib Monotherapy Dose Level Reductions 55 Table 7. Dosage Modification Criteria for Erlotinib–related Toxicities 56 Table 8: AZD6244 Monotherapy Dose Level Reductions 57 Table 9: Dosage Modification Criteria for AZD6244–related Toxicities 57 Table 10: MK2206 Monotherapy Dose Level Reductions 59 Table 11: Dosage Modification Criteria for MK2206–related Toxicities 59 O Table 12: Lapatinib Monotherapy Dose Level Reductions 61 Table 13: Dosage Modification Criteria for Lapatinib –related Toxicities 61 Table 14: Sunitinib Monotherapy Dose Level Reductions 63 Table 15. Management of Treatment-Emergent Hypertension 64 Table 16. Dosage Modification Criteria for Sunitinib –related Toxicities 66 Table 17. Management of Other Clinically Significant Sunitinib-related AEs 67 Table 18. Summary of nonclinical pharmacokinetics for MK-2206 139 |  
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1 objectives 1.1 primary protocol

1.1.1 To determine the feasibility of the use of tumor's molecular profiling and targeted therapies in the treatment of advanced stage non-small cell lung cancer (NSCLC), small cell lung cancer (SCLC) and thymic malignancies.  
1.1.2 To estimate the response rate of molecular-profile directed treatments in NSCLC, SCLC
and thymic malignancies patients.
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1.2 secondary protocol objectives

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1.2.1 To determine the progression free survival (PFS), duration of response and overall survival (OS) of patients with NSCLC, SCLC and thymic malignancies who undergo molecular profiling and receive molecular-profile directed treatments.  
1.2.2 To evaluate changes in the tumor's molecular profile on serial biopsies when patients progress after an initial response to treatment.  
1.2.3 To identify molecular profiles in patients with NSCLC, SCLC and thymic malignancies and characterize their natural histories, clinical course and response to treatments.  
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1.2.4 To determine the frequency of *EGFR* germline mutations in families with high susceptibility to lung cancer.
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2 background 2.1 background and

2.1.1 Background and rationale for the use of molecular profiling and molecularly based treatment in NSCLC, SCLC and thymic malignancies.  
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The current management of lung cancer and thymic malignancies is primarily based on the broad classification of tumors into categories based on histopathology and clinical stage at presentation. However, the existing classifications and staging systems have remained largely unchanged for decades and it seems that they have reached their limit in providing critical information that may influence management strategy. This is evident by the small improvement in overall survival of patients with this disease in the last few decades. The heterogeneity of lung cancer and thymic malignancies at each disease stage with respect to outcome and treatment response suggests that additional subclassification and substaging remains possible. Molecular heterogeneity within individual lung cancer diagnostic categories is evident in the variable presence of specific mutations, deletions of tumor suppressor genes, and numerous chromosomal abnormalities found to date (3, 4). Reports that some of these genetic aberrations are prognostic factors for patients provide evidence that additional information on risk of relapse or death from cancer may be defined at molecular levels (4). Molecular-profiling studies indicate that activating mutations in the epidermal growth factor receptor (EGFR) and KRAS genes are generally nonoverlapping and identifiable in approximately 30 to 40% of non– small-cell lung cancers. Rarer oncogene mutations have been reported in less than 5% of lung cancer patients including mutations in ERBB2, ERBB4, MET, MEK, PI3K, AKT, FGFR1-4, and PTEN, among others (3). In addition, a fusion gene, EML4/ALK has been reported in about 6 to 13% of NSCLC patients (5). These mutations, plus others that contribute to tumor progression D  
("driver" mutations), can be found in almost half of non–small-cell lung cancers. Thus, correlations of molecular profiles from individual tumor samples to clinical outcome data hold the promise of a better classification of lung cancer, improved diagnostic and prognostic information and ultimately influence patient management and improve outcomes (6).  
  
Figure 1. Significantly mutated genes in lung adenocarcinomas I
EGFR, ERBB2, TGF and AKT among others (7-10). These abnormalities have been shown to correlate with response to targeted therapies in some cases (8, 11-13). Additionally, oncogene mutations have also been reported in small cell lung cancer patients including mutations in TP53, KDR, KIT, BCL-2, SRC, VHL, PTCH1, VHL, ERBB2, ERBB3, CDKN2A, BRAC2, ERCC1, AKT, PIK3C3, and PTEN (Table 1. Top 5 mutated genes in SCLC ). Table 1. Top 5 mutated genes in SCLC (COSMIC database: www.sanger.ac.uk/genetics/CGP/cosmic)  
| Gene Name   | Sample Number   | Positive Samples   | Percent Mutated   |
|-------------|-----------------|--------------------|-------------------|
| RB1         | 121             | 70                 | 57%               |  
  
| TP53   | 78   | 62   | 79%   |
|--------|------|------|-------|
| PTEN   | 246  | 34   | 13%   |
| EGFR   | 298  | 16   | 5%    |
| PIK3CA | 99   | 11   | 11%   |  
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Evidence that molecular profiling can have a significant impact on patient's management can be found in a recent study of molecular profiling of tumors presented at the AACR 2009 conference (Von Hoff, et al. AACR 2009). This study was conducted in patients with advanced cancers that were progressing despite several previous treatments and was designed to determine whether molecular profiling of patients' tumors at this stage in their disease could provide any clinical benefit. To be eligible, patients had to undergo or have available a tumor biopsy for molecular profiling. Patients' tissue samples were submitted for molecular profiling with oligonucleotide microarray gene expression assays. The primary objective was to compare progression free survival (PFS) using a treatment regimen selected by molecular profiling with the PFS for the most recent regimen on which the patient progressed. Of 86 patients, 66 received treatments based on molecular profiling and a significant number of patients had a clinical benefit with a longer PFS treated by molecular profiling results than the PFS they had on their prior treatment regimen. This prospective study demonstrated that it is feasible to measure molecular targets in patients' tumors and that this approach may provide clinical benefit for some patients.  
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A better understanding of the genetic make-up of the individual tumor may offer potentially improved therapies. This approach may also give rapid access to response data in patients with sometimes rare genetic abnormalities. In addition, it will allow us to test targeted therapies in a select population of patients that is more likely to have a favorable response based on their molecular profile and the specific mechanism of action of the drug being tested. This approach will also speed up drug development and potentially approval, and rescue an otherwise ineffective drug candidate for the specific subgroup that can benefit.  
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2.1.2 Background and rationale for the use of erlotinib in patients with EGFR TKIs sensitizing mutations.  
EGFR is a member of the receptor tyrosine kinases (RTKs) family, known as the ErbB or human epidermal receptor (HER) family of transmembrane receptors. EGFR is activated when specific ligands, such as EGF, bind to its extracellular domain. Ligand binding induces a conformational change that leads to dimerization of the receptor with either another EGFR molecule (homodimerization) or another member of the HER family (heterodimerization). Following receptor dimerization, activation of the intrinsic protein tyrosine kinase and tyrosine autophosphorylation initiates a cascade of intracellular mitogenic signaling. The EGFR can activate several different signaling pathways, including the Ras/Raf/MEK/ERK, phospholipase C, PI3K/Akt, STAT and Src/FAK pathways. These pathways form a network of signals that are important for cell growth and proliferation [7].  
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The development of epidermal growth factor receptor (EGFR) inhibitors has significantly influenced the field of targeted therapeutics. A high sensitivity to EGFR tyrosine kinase inhibitors (TKIs), such as gefitinib or erlotinib, has been reported in patients with EGFR-mutated lung cancers (14-16). Activating mutations in the epidermal growth factor receptor (EGFR) (Table 2. EGFR drug-sensitive and resistant mutations ) have been found in about 15% of NSCLC patients from North America and Europe, and up to 40% of Asian NSCLC patients (15-17).  
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| Exon           | Mutation / Deletion   |         |
|----------------|-----------------------|---------|
| Drug sensitive | 18                    | G719A/C |
| 19             | delE746-A750          |         |
| 21             | L858R                 |         |
| 21             | L861Q                 |         |
| Drug Resistant | 19                    | D761Y   |
| 20             | T790M                 |         |
| 20             | D770_N771insNPG       |         |
| O              |                       |         |  
The specific EGFR tyrosine kinase inhibitors erlotinib and gefitinib have been shown to have activity in patients with activating EGFR mutations and response and survival rates are higher compared with multi-agent chemotherapy in this population. In contrast, chemotherapy is superior in patients with wild type EGFR genes (15, 17, 18). A recent phase III, randomized, controlled clinical trial in an Asian population (IPASS) has demonstrated a considerable benefit in progression free survival with the use of gefitinib as a first-line therapy for the treatment of patients with metastatic NSCLC with an EGFR TKI sensitizing mutation compared to chemotherapy (RR = 71.2% vs 47.3%; P<0.001; hazard ratio for progression, 0.48; 95% CI, 0.36 to 0.64; P<0.001) (18). Additionally, a large, non-randomized clinical trial conducted in a primarily Caucasian population from Spain has shown outstanding results with the use of EGFR TKIs in patients with NSCLC with EGFR TKI sensitizing mutations. In this trial, 217 patients with EGFR TKI sensitizing mutations that were either chemotherapy naïve or previously treated with chemotherapy received erlotinib until disease progression. PFS and OS for these patients (14 months and 27 months, respectively) was significantly higher than historical controls for unselected populations (17).  
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In SCLC, EGFR mutations are a rare event that represents 5% of the samples analyzed (Table 1. Top 5 mutated genes in SCLC). Interestingly, most of these mutations appear in patients with mixed histological features of SCLC and NSCLC or in patients who have never smoked. Remarkably, the EGFR mutations observed in SCLC (L858R, G719A/C and deletions in exon 19) are similar to the active mutations in NSCLC that have been reported to be predictors of a therapeutic response to EGFR-TKIs. Furthermore, anecdotal evidence shows efficacy with the use of TKIs in these patients (19, 20). In thymic malignancies, only one phase II study has been conducted using anti-EGFR targeted therapies. In this study, twenty-six (female = 15, male = 11) previously treated patients with metastatic thymoma (n = 19) or thymic carcinoma (n = 7), with ECOG performance status of 0 or 1, were enrolled. Patients received gefitinib orally at 250 mg daily. There were 0 CRs, 1 PR (response duration = 5 months), and 14 SDs. Six patients had SD for > 4 months. Grade 3/4 adverse events noted were: dyspnea (grade 4, n = 1; grade 3, n = 2), fatigue (grade 4, n = 1), anemia/thrombocytopenia (grade 4, n = 1), and myocardial infarction (n = 1). After completing 3 cycles, the patient with a PR developed presumed gefitinib-induced Grade 2 pneumonitis, which resolved following steroids and discontinuation of treatment. Median time to progression (TTP) was 4 months (range, 1 - 17+). None of the 5 pts (including 1 PR), analyzed by DNA sequencing, had evidence of EGFR or KRAS mutations and there was no EGFR expression analysis.  
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In thymic malignancies EGFR mutations are a rare event that represents < 2% of the thymic tumors analyzed (9, 10). Remarkably, the EGFR mutations (L858R and G863D in exon 21) observed in thymic tumors are similar to the active mutations in NSCLC that have been reported to be predictors of a therapeutic response to EGFR-TKIs. Even though there are no prospective trials to demonstrate the efficacy of EGFR TKIs in patients with thymic malignancies harboring EGFR mutations, anecdotal reports suggest that these patients are in fact sensitive to EGFR TKIs(9).  
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2.1.3 Background and rationale for the use of AZD6244 in patients with Ras/Raf/Mek/Erk pathway mutations.  
The RAS/RAF/MEK/ERK pathway regulates proliferation and survival of normal cells. Hyperactivation of this pathway results in deregulated cell proliferation and malignant transformation (21). In human tumors, RAS/RAF/MEK/ERK pathway activation is a common feature which results from unregulated activation of upstream RTKs, such as EGFR, or mutations in pathway intermediates, such as KRAS, BRAF, NRAS or NF-1 (22).  
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The Ras superfamily of GTP binding proteins consists of more than 150 proteins, and can be grouped into at least five families (Ras, Rho, Rab, Arf, and Ran). The Ras subfamily itself includes at least 21 members (23, 24); however, there are just three closely related human Ras genes, KRAS, HRAS and NRAS, which constitute the founding members of the RAS super family. Ras signaling requires the activation of Ras by exchange of GDP for GTP, followed by interaction of Ras-GTP with Ras-effector molecules, and inactivation of Ras by GTPaseactivating proteins. This signaling pathway requires the anchorage of Ras to the inner leaflet of the plasma membrane through their C-terminal S-farnesylcysteine by either a stretch of lysine residues (KRAS 4B isoform) or S-palmitoyl moieties (NRAS, NRAS and KRAS 4A
isoforms)(25). The farnesyltransferase (FTase) catalyses the post-translational addition of the Cterminal cysteine residue in a process called farnesylation which is critical for the biological function of Ras (26). Ras relays its signal downstream through a high affinity complex with Raf. Activated Raf phosphorylates and activates two MAPK kinases (MEK1 and MEK2) and activated MEK then phosphorylates ERK which in turn activates multiple nuclear transcription factors (27).  
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Mutations in the Ras/Raf/Mek/Erk pathway are some of the most frequently mutated oncogenes in patients with NSCLC. KRAS mutations account for 20 to 38% of NSCLC cases and NRAS and BRAF for less than 3% each (3, 28-30). KRAS mutations occur more frequently in smokers and adenocarcinoma histologies. Up to 90% of the KRAS mutations are activating point mutations localized in codons 12 and 13, and less frequently in codons 61 and 63 (31). Although mutational activation of RAS in human cancer was first demonstrated in 1982, somatic activating mutations in BRAF were only detected in 2002. Mutationally activated BRAF is detected in melanoma (70%), colorectal (15%), papillary thyroid (40%), ovarian (30%), and nonsmall-cell lung cancers (NSCLCs) (3%) (32, 33). Sequence analysis of the BRAF gene associated with human cancers has identified over 30 single site missense mutations, mostly within the kinase domain in exon 15. Most of the mutations of BRAF are clustered to two regions: the glycine-rich P loop of the N lobe and the activation segment and flanking regions. A Glu for Val substitution at residue 599 in the activation segment, adjacent to the conserved DFG motif, accounts for 90% of BRAF mutations in human cancers. The V599E (a.k.a. V600E) mutant of BRAF possesses the hallmarks of a conventional oncogene. The kinase activity of this mutant protein is greatly elevated, it constitutively stimulates ERK activity *in vivo* independent of RAS, and it potently transforms NIH3T3 cells. Interestingly, the conserved regulatory phosphorylation sites within the activation segment of BRAF, Thr598 and Ser601, flank Val599, leading to the suggestion that the Glu substitution at this position functions as a phosphomimetic. Analysis of three other oncogenic mutants of BRAF showed that they stimulate kinase activity in a manner similar to V600E (32, 34, 35). In addition, non-V-600E mutations mostly localized in exon 11 have also been described in NSCLC with different frequencies but in general accounting for less than 3% of tumor or cell line samples (32, 33, 36, 37). Interestingly, both V600E and non-V600E mutations (i.e. G469A, G466V, L597V) have been shown to be sensitive to MEK inhibition in preclinical models (NSCLC cell lines)(33).  
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Mutations of either BRAF, NRAS or KRAS lead to constitutive activation (phosphorylation) of their downstream target, mitogen-activated protein kinase (MAPK), also known as extracellular signal-regulated protein kinase (ERK) (29, 30, 32, 34, 35). Patients with Ras/Raf/Mek/Erk pathway mutated tumors are less likely to respond to EGFR TKIs and no specific targeted therapy has thus far demonstrated activity in this patient population (14).  
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untitled h1
table 3. frequency of mutated

| KRAS Incidence             |        |
|----------------------------|--------|
| Lung Cancer (subtypes)     | 16–38% |
| Adenocarcinoma             | 22%    |
| Broncho-alveolar           | 31%    |
| Carcinoma (BAC) Large Cell | 22%    |
| Squamous Cell              | 1-5%   |  
  
MEK or MAPK/ERK kinase is an attractive therapeutic target because its only known substrate is ERK1/2 (39). MEK inhibitors have shown good preclinical activity in different malignancies and activating mutations in the RAS (K-and N-) and BRAF genes have been reported to identify tumors that may be sensitive to MEK inhibition (32, 34, 35, 40, 41). Additionally, preclinical models have shown that synergistic cytotoxicity is achieved when combining MEK with EGFR inhibitors(42). However, CI-1040 which was the first MEK inhibitor ever tested in humans, showed poor results in clinical trials due to low systemic exposure and rapid metabolism (39). Furthermore, a second-generation more potent oral MEK inhibitor, PD0325901, was prematurely discontinued due to unexpected toxicities (Clinicaltrials.gov identifier: NCT00174369).  
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AZD6244 is a potent, selective, and noncompetitive ATP inhibitor of MEK1/2 that has preclinical activity against many different tumors in both cell lines and xenograft models (40). A recent phase I trial has shown promising results in patients harboring mutations in the Ras or Raf genes(43). Of the 26 patients with samples assessable for mutational status, 10 had a single mutation in KRAS (n=5), NRAS (n=4), or BRAF (n=1). The average length of time on study for patients carrying mutations (median, 3.5 months; range, 1 to 6 months) was greater than for those without a mutation (median, 2 months; range, 1 to 4 months). Several phase II clinical trials are currently underway with an emphasis on determining the efficacy of AZD6244 in tumors harboring mutations in the Ras/Raf/Mek/Erk pathway (44).  
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2.1.4 Background and rationale for the use of MK2206 in patients with PI3K/Akt/mTOR
pathway mutations / alterations.  
The PI3K/Akt/mTOR pathway is a critical regulator of cellular growth and proliferation and is essential for oncogenic transformation. It is activated through a number of tyrosine kinase growth factor receptors such as EGFR, insulin-like growth factor-1 receptor (IGF-1R), G-protein coupled receptors, and through oncogenes such as Ras (45). PI3K stimulation and mammalian target of rapamycin (mTOR) activation as well as PTEN inhibition have been demonstrated to be intimately connected to Akt activation leading to tumor mediated angiogenesis, proliferation, and cell survival. Specifically mTOR is an intracellular serine/threonine kinase that resembles that of the PI3 kinase enzymes. Once activated, mTOR can form complexes with Raptor (mTORC1) or Rictor (mTORC2) (46). The mTORC2 complex phosphorylates and activates Akt/PKB. Concurrently, the mTORC1 complex phosphorylates and activates two key regulators of translation: S6K1 (p70S6 kinase) and 4E-BP1, which both activate ribosomal formation and translation.  
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In a recent study, NSCLC patient samples were evaluated by FISH for PI3K amplification with > 7 copies/cell. This study revealed PI3K amplification in 42% of lung squamous cell carcinomas (47). Addtionally, P-Akt expression and loss of PTEN expression via IHC were shown to occur in NSCLC samples (48). Specifically, P-Akt expression was noted in 49% of squamous cell carcinomas and 33% of adenocarcinomas. Similarly, loss of PTEN expression was seen in 53% of SCC and 61% of adenocarcinomas. Furthermore, these findings were associated with poorer prognosis including poor differentiation, lymph node involvement, distant metastasis, late stages, and lower cumulative survival rates (48).  
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Mutational analyses of the PI3K/Akt/mTOR pathway in lung cancer have revealed the presence of several mutations in this pathway. Eighty-six NSCLC cell lines and 691 NSCLC patient tumor samples were evaluated for PIK3CA mutational analysis in exon 9 and 20 and gene copy nmber via PCR and real-time quantitative PCR respectively.  This study reported PIK3CA
mutations in 4.7% NSCLC cell lines and 1.6% of the NSCLC patient samples.  PIK3CA copy nmber gain were revealed in 9.3% of the NSCLC cell lines and 17.1% of the NSCLC patient samples, where 33.1% were SCC and 6.2% were lung adenocarcinomas.  Furthermore, cell lines expressing these mutations and copy number gains correlated to increased PI3K expression and activity (49).  
  
endogenous kinase carrying the E17K mutation immunoprecipitated by tumour tissue was significantly higher compared with the wildtype kinase immunoprecipitated by the adjacent normal tissue.  Immunostaining or immunoblot analysis on membrane-enriched extracts indicated that the enhanced membrane localization exhibited by the endogenous E17K-AKT1 may account for the observed increased activity of mutant E17K kinase in comparison with the wild-type AKT1 from adjacent normal tissue.  These mulations appear to be limited to patients with SCC subtype ( 50-52 ).  Mutations in the AKT2 gene have also been described.  One was a missense mutation in exon 11 [1130C-A (A377V)] in a 65 year old female with lung adenocarcinoma with an EGFR L858R mutation.  The other one was a deletion in intron 10
( IVS10 + 7delG) in a 66 year old male with NSCLC squamous subtype( 53 ).  Deletions and mutations have also been found on PTEN in patients with NSCLC with a frequency of approximately 9%( 54 , 55 ).  Mutations present in any of the crucial domains of this gene result in reduced phosphatase activity which affects its growth suppression functions ( 54 )
Preclinical studies have demonstrated encouraging results with inhibition of mTOR in NSCLC
( 56 ).  Furthermore, in NSCLC cell lines, everolimus, an oral mTOR inhibitor, plus gefitinib have induced a significant decrease in the activation of MAPK and mTOR signaling pathways and resulted in a growth-inhibitory effect ( 57 ).  In clinical trials RAD001 monotherapy was evaluated in an unselected population of 85 advanced NSCLC patients previously treated with chemotherapy alone (stratum 1) or with chemotherapy and EGFR inhibitors (stratum 2) ( 58 ).  
Both patient strata had to have failed two or fewer chemotherapeutic regimens including a previous platinum agent.  The ORR was 7.3% in stratum 1 and 2.3% in stratum 2, where in total there were 4 patients achieving a PR. No CRs were recorded. Additionally, the PFS was 79 days (95% CI 57-87 days) in stratum 1 and 81 days (95% CI 51-113 days) in stratum 2. A recent study evaluating the AKT/mTOR pathway demonstrated that 50% (15 out of 30) SCLC
patient tumor samples expressed mTOR via IHC analysis. Furthermore, mTOR inhibition via RAD001 was observed to inhibit SCLC tumor growth in an *in vivo* xenograft model utilizing H69 SCLC cells. An additional study investigated the presence of PTEN mutations in SCLC in 34 SCLC cell lines and 10 SCLC tumors. This study revealed that 18% of cell lines and 10% of tumor samples had mutations in the PTEN gene including point mutations, small fragment deletions, and homozygous deletions (59). Overall, PTEN mutations have been identified in 13% of samples according to the COSMIC database (Table 1. Top 5 mutated genes in SCLC
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). In addition, a target-specific mutational search revealed mutation of the PIK3CA gene in three of 13 SCLC cell lines and two of 15 primary SCLCs. In this study, these mutant PIK3CA cDNAs were introduced into cell lines establishing artificial "PIK3CA-addicted" cells and found that Triciribine, a small-molecule inhibitor of AKT signaling that is located downstream from PIK3CA, significantly inhibited the growth and colony formation activity of these cells. Using cancer cell lines, it was further shown that PIK3CA-mutated SCLC cells are more sensitive to Triciribine than PIK3CA wild-type cells. Additionally, it was found that a cisplatin-resistant subclone of PIK3CA-mutant SCLC cells was equally sensitive to Triciribine. This study for the first time uncovered PIK3CA alterations in SCLC, and suggested that anti-AKT molecular therapy could be effective for a subgroup of SCLC, which shows activation of specific genes, such as PIK3CA mutation, and that genetic stratification of SCLC according to the activation status of individual therapeutic target pathways could be clinically beneficial, especially for chemotherapy-resistant/relapsing tumors(60).  
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Temsirolimus is an inhibitor of mTORC1 which binds to an intracellular protein, FKBP12, and the protein-drug complex inhibits the activity of mTOR that controls cell division. The inhibition of mTOR prevents the transcription of mRNAs and translation of proteins required for cell cycle progression from G1 to S phase by mediating the activation of p70S6K and 4E-BP12. Inhibition of mTOR activity results in a G1 growth arrest in treated tumor cells. A randomized phase II study (E1500) utilizing temsirolimus in patients with extensive stage SCLC following induction chemotherapy has been conducted to study the progression-free survival (PFS) and toxicity with 25- or 250-mg doses of temsirolimus (CCI-779). Patients with either stable or responding disease to four to six cycles of cisplatin or carboplatin plus etoposide or irinotecan were randomized between 4 and 8 weeks after completion of induction therapy to receive either 25 or 250 mg of temsirolimus intravenously every week until disease progression. Eighty-seven patients entered between January 2002 and December 2003, of whom 85 were eligible: 44 received 25 mg (arm A), and 41 received 250 mg (arm 13). The overall median follow-up time for all eligible patients was 34.6 months. Median age was 59 years (range, 39-80); 42 (49.4%) were male and 43 (50.6%) female; 12.9% had brain metastases. The overall median and 1-year PFS were 2.2 months (95% confidence interval [CI]: 1.8, 2.9) and 4.7% (95% Cl: 0.2%, 9.2%), respectively. The median PFS (95% CI) for arm A was 1.9 months (1.6, 2.3); for arm B, it was 2.5 months (1.9, 3.4; p = 0.24). The median overall survival from randomization was 8 months (95% Cl: 6.5, 9.5). Among the 86 patients with reported toxicities, 36 (42%) had grade 3 toxicities, the most common of which were thrombocytopenia, hypophosphatemia, and fatigue, and an additional 12 (14%) had grade 4 toxicities, the most common of which was neutropenia.  
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No patients experienced lethal toxicities. In conclusion, temsirolimus given to responding or stable patients with extensive-stage SCLC after induction chemotherapy did not seem to result in any prolongation in PFS compared with what has been reported in the literature. However, it is important to note is that this study was conducted in a molecularly unselected population and that correlative analysis to determine alterations in the PI3K / mTOR pathway were not conducted(61). MK-2206 is the first allosteric AKT inhibitor to enter clinical development. As an AKT inhibitor, it is equally potent towards purified recombinant human AKT1 and AKT2 isoenzymes, and 5-fold less potent against AKT3 (Investigator's Brochure, 2008). It has an advantage of having a higher intrinsic selectivity for AKT compared to the active-site AKT-specific inhibitors, i.e., ATP-competitive AKT inhibitorswhich have been clinically evaluated thus far. *In vitro* and in vivo anticancer efficacy of MK-2206 was demonstrated in breast cancer cell lines and in the A2780 ovarian cancer xenograft model in nude mouse and rat, either as a single agent or in combination with erlotinib, trastuzumab, and docetaxel.  
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Preclinical safety assessment studies in the most sensitive species, dogs, demonstrated NOAEL (no observed adverse effect level) at a 2.5 mg/kg dose (Cmax of 365 nM and AUC0-48h of 8.52 μM∙h) and NOEL for cardiovascular effects at a 1 mg/kg dose (Cmax of 92 nM and AUC0-48h of 1.59 μM. Based on these data, the human equivalent doses are 34 mg (NOEL) and 80 mg (NOAEL) for a 60-kg man.  
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The projected human clearance for MK-2206 is 2-4 mL/min/kg with bioavailability in the range of 50%-75%. Although preclinical safety/tolerability studies identified health risks of prolonged QTc interval and hyperglycemia associated with MK-2206, no significant hyperglycemia has been seen thus far on the phase I trial; and while Grades 1-2 QTc prolongation has been noted with MK-2206 in clinical trials, it has not been thought to be clinically significant. Merck is completing a phase 1 clinical trial with MK-2206 as a single agent in patients with solid tumors. Preliminary data from this study suggest that the dosing regimen of 60 mg orally (PO) every other day (QOD) is well-tolerated and achieves target effects of AKT inhibition. In addition, Merck has completed Phase I testing of a weekly schedule of MK-2206 and has recommended a Phase II dose of 200 mg orally (PO) weekly. Pharmacokinetic data is available for this weekly regimen. This schedule has demonstrated less toxicity than the 60 mg PO QOD schedule, appears to have at least equal antitumor activity, and is favored by Merck for subsequent trials.  
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2.1.5 Background and rationale for the use of lapatinib in patients with ERBB2 mutations or amplification.  
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HER2 (erbB-2/neu) is a member of the erbB receptor tyrosine kinase family that also includes EGFR (HER1/erbB-1), HER3 (erbB-3), and HER4 (erbB-4). Whereas these family members usually dimerize upon ligand binding, HER2, for which no ligand is reported, exists mainly in its active conformation. HER2 readily heterodimerizes with other erbB family members and is considered to be the preferred dimerization partner for EGFR, HER3, and HER4. In addition to ligand binding, receptor dimerization can be induced by a high concentration of receptors at the plasma membrane or by kinase domain mutations, resulting in receptor activation by the transphosphorylation of tyrosine residues in the C terminus of the respective molecules. The phosphorylated residues act as docking sites for an array of downstream signaling molecules activating several biochemical pathways such as the MAPK, the PI3K/Akt/mTOR, the phospholipase C, and the Jak/Stat signaling pathways. These signal transduction cascades in concert regulate cellular processes such as proliferation, apoptosis, angiogenesis, migration, adhesion, and differentiation(62).  
Mutations in the HER2 kinase domain have been reported in lung adenocarcinomas at a relatively low frequency of 2–4%. Thus far, the majority of the HER2 mutations identified in non-small cell lung cancer (NSCLC) samples are in-frame duplications or insertions in a small 8codon region (codons 774–781 or 775–782) on exon 20. These mutations are analogous to the duplications/insertions in the 9-codon region of exon 20 in EGFR, translating to the C terminus of the αC helix in the TK (tyrosine kinase) domain. Based on this similarity, it has been postulated that mutations in HER2 cause a shift in the helical axis that narrows the ATP binding cleft, resulting in both increased TK activity and TK inhibitor sensitivity. These HER2 mutations are independent of HER2 receptor overexpression or KRAS, NRAS, BRAF, or EGFR mutations(63-65).  
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Studies of ERBB2 expression in NSCLC have varied in use of antibodies and immunohistochemical technique as well as the definition of positive cases. In general, positive immunostaining for ERBB2 (IHC ≥1+) in NSCLC has been reported in 2 to 60% of cases and overexpression has been associated with poor prognosis. Discrepancies among the reported frequencies might be due to different factors, including distribution of histological types, tissue processing, criteria for the scoring and interpretation of the staining results. However, strong overexpression defined by3+ IHC or gene amplification by FISH has been reported in less than 5 % of NSCLC patients (62, 66).  
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Molecular characterization of ERBB2 abnormalities in thymic carcinoma has shown a high rate of ERBB2 overexpression (45%) and gene amplification (50%) and a positive correlation (85%) was detected between ERBB2 protein expression and gene amplification (Kuhn E. et al. 1st International Conference on Thymic malignancies 2009).  
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The clinical experience with anti-HER2 directed therapies in the thoracic malignancies such as NSCLC has been disappointing most likely as a result of poor patient selection. The Cancer and Leukemia Group B (CALGB) initiated a trial in February 2000 to determine the single-agent efficacy of trastuzumab in patients with stage IIIB or IV NSCLC who had tumors that overexpressed ERBB2. Of note is that ERBB2 overexpression was defined by 2 or 3 + positivity on immunohistochemistry analysis. Among 209 screened patients, 24 patients (11%) had tumors with 2+ or 3+ expression of HER-2. However, of the 22 patients that were treated, 21 had 2+ IHC and no FISH analysis was performed. Only one patient achieved a partial response and the trial was stopped (67). A randomized phase II trial examined the effect of adding trastuzumab to a standard chemotherapeutic combination (gemcitabine–cisplatin) in patients with HER2positive NSCLC defined by IHC ≥1. Efficacy was similar in the trastuzumab and control arms with a response rate 36% versus 41%; median time to progression 6.3 versus 7.2 months; and median progression-free survival (PFS) 6.1 versus 7 months(68).  
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Lapatinib (GW572016) is an oral reversible, dual tyrosine kinase inhibitor of EGFR (ERBB1) and HER2/neu (ERBB2). A study conducted in chemotherapy naïve patients with NSCLC was stopped for futility after 131 patients were randomized. Median age 66 (range 32–86); female 56%; BAC 20%, No BAC 71%; previously untreated 98.5%; current/former smokers 70%, never smoker 30%. There were no complete responses. Of 56 patients in the target population, 1 (2%) achieved partial response (PR), 11 (20%) had stable disease (SD) of 24 wks; in the non-target population, 1 patient had a PR (1.3%) and 12 (16%) had SD of 24 wks. Three patients had ERBB1 mutations (G719S, S768I, KRAS G12S; L858R and T790M; L858R) but none of them responded. Three of 77 patients evaluated had ERBB1 gene copy increase (none of whom responded) and 2 had ERBB2 gene copy increase (one had a 51% decrease in tumor size). The most common adverse events were grade 1/2 diarrhea, nausea, rash, vomiting and fatigue, and were similar in both groups(69). Despite the lack of efficacy of lapatinib in an unselected population of patients with NSCLC, there is no prospective clinical data on the use of Lapatinib in patients with ERBB2 mutations or amplification. As stated above, these mutations are analogous to the duplications/insertions in the 9-codon region of exon 20 in EGFR, translating to the C terminus of the αC helix in the TK domain. Based on this similarity, it has been postulated that mutations in ERBB2 cause a shift in the helical axis that narrows the ATP binding cleft, resulting in both increased TK activity and TK inhibitor sensitivity(63-65, 70). Furthermore, preclinical studies assessing the *in vivo* effect of a dual EGFR / ERBB2 TKI (BIBW2992) on HER2(YVMA) transgenic mice or H1781 xenografts with documented tumor burden revealed that BIBW2992 has significant activity in regards to signaling and tumor shrinkage(63).  
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Theoretically it might be predicted that the protein expression would be superior for assessing response to trastuzumab therapy because the antibody binds to the cell surface protein. In breast cancer, however, FISH technique has been demonstrated to be a more accurate and reliable method for selecting patients eligible for treatment with anti-HER2 directed therapy(66). In NSCLC HER2 status assessed by IHC has been has been shown to be a method that is not optimal. On the other hand, anecdotal evidence supports the notion that FISH analysis would be a better method to predict the response to anti-HER2 therapies in NSCLC patients (66, 70). Moreover, in a phase II clinical trial of trastuzumab in combination with chemotherapy in NSCLC, the few patients whose tumors had HER2 gene amplification and who were treated with trastuzumab had a better response to trastuzumab compared to other patients. Response rate (83%) and median PFS (8.5 months) are higher in trastuzumab-treated patients with HER2 3+ or fluorescence in situ hybridization (FISH)-positive NSCLC compared to patients without HER2 overexpression (68).  
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2.1.6 Background and rationale for the use of sunitinib in patients with PDGFR-A gene amplification or mutations or KIT mutations.  
The PDGFR/PDGF system includes two receptors (PDGFRA and PDGFRB) and four ligands (PDGFA, PDGFB, PDGFC, and PDGFD). Ligand binding induces receptor dimerization, enabling autophosphorylation of specific tyrosine residues and subsequent recruitment of a variety of signal transduction molecules. PDGFR regulates normal cellular growth and differentiation, and expression of activated PDGFR promotes oncogenic transformation Increased expression of PDGFR has also been associated with poor prognosis in NSCLC (71).  
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Analysis of early stage (I and II) NSCLC samples by IHC revealed a high expression of PDGFRA in 51% of squamous cell carcinoma, 77% in large cell carcinoma, 73% in adenocarcinomas
(73%), and 68% in bronchioalveolar carcinoma (68%) (72). However, a similar study performed in early stage NSCLC patient samples identified strong PDGFR-A staining by IHC in just 2 to 3% of cases (73). In addition, mutations in the PDGFR-A gene have been identified in 3.7% of cases of adenocarcinoma (3). Sunitinib malate is an oral, selective multitargeted tyrosine kinase inhibitor with antiangiogenic and antitumor activities. It inhibits VEGF receptor (VEGFR)-1, -2, and -3 and PDGFR-A and -B activity, as well as the activity of several related tyrosine kinases. It is FDA approved for its use in previously untreated patients with advanced renal cell carcinoma and in imatinib-refractory gastrointestinal stromal tumors (GIST). A recent phase II clinical study has revealed modest efficacy of single-agent sunitinib in advanced NSCLC patients with an ORR of 11.1% (95% CI, 4.6% to 21.6%). An additional 18 patients (28.6%) experienced stable disease of at least 8 weeks in duration. Median progression-free survival was 12.0 weeks (95% CI, 10.0 to 16.1 weeks), median overall survival was 23.4 weeks (95% CI, 17.0 to 28.3 weeks), and therapy was generally well tolerated (74).  
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However, sunitinib has not been tested in selected populations of NSCLC patients who have mutations or overexpression of PDGFR or VEGFR and there is no retrospective analysis correlating the levels of these receptors with clinical outcomes(74). Using a high-throughput cancer cell line screening platform, it has been found that a small fraction of human tumorderived cell lines show significant sensitivity to single-agent sunitinib exposure. These two cell lines [a non–small-cell lung cancer (NSCLC) and a rhabdomyosarcoma] showed expression of highly phosphorylated PDGFRA. In the sunitinib-sensitive adenosquamous NSCLC cell line, PDGFRA expression was associated with focal PFGRA gene amplification, which was similarly detected in a small fraction of squamous cell NSCLC primary tumor specimens. Moreover, in this NSCLC cell line, focal amplification of the gene encoding the PDGFR ligand PDGFC was also detected, and silencing PDGFRA or PDGFC expression by RNA interference inhibited proliferation. These findings suggest that, rare tumors that show PDGFRA activation may be more likely to be responsive to pharmacologic inhibition by sunitinib (75).  
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The c-kit proto-oncogene encodes a Kit transmembrane tyrosine kinase receptor whose ligand is stem cell factor (SCF), a growth factor important in the stimulation and formation of various cell types. Upon SCF binding, the Kit receptor dimerizes and autophosphorylates to in turn activate many downstream signal transduction components including PI3K, PKB/Akt, Src, Janus transcription pathway, and the Ras-Raf-MAPK cascade that all in some form promote cell survival and increase cellular proliferation. Mutations in KIT lead to a constitutive activation of the receptor in a ligand independent fashion. It has been shown through structural analyses of the KIT receptor and related tyrosine kinase receptors that the juxtamembrane domain of this receptor plays an inhibitory role on the regulation of this receptor. Furthermore, this ability to suppress Kit receptor firing is compromised by mutations and deletions seen in the juxtamembrane domain.  
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The presence of KIT mutations has been found in less than 4% of samples from thymic malignancies. In contrast to other mutations, KIT mutations have been found exclusively in thymic carcinomas. One of these mutations is a V560 deletion in exon 11. This mutation is associated with sensitivity to KIT inhibitors based upon multiple lines of evidence: (a) the growth of mutant-bearing Ba/F3 cells *in vitro* is readily inhibited by treatment with imatinib and sunitinib(7); (b) a patient whose tumor harbored this mutation responded to treatment with imatinib(8); and (c) this mutation has also been found in an imatinib-sensitive gastrointestinal stromal tumor (76). Another KIT-mutant case of thymic carcinoma reported in the literature harbored an L576P mutation in exon 11 (10). This mutation has also previously been described in gastrointestinal stromal tumor and melanoma and has been biologically characterized as being sensitive to imatinib (76). The third type of mutation reported is a D820E mutation in exon 17 D
exhibited by a thymic carcinoma responding to sorafenib(13). Finally, the KIT H697Y mutation identified in exon 14 is associated *in vitro* with sensitivity to sunitinib and imatinib (7). 2.1.7 Rationale for the non-otherwise (NOS) specified arm In order to accomplish the primary objective of identifying molecular profiles in patients with NSCLC, SCLC, and thymic malignancies and characterize their natural histories, clinical course and response to treatment, we will follow all patients that undergo molecular profiling from the time that they are enrolled in the trial until the time of death. For this reason, we have created a study arm called the "non otherwise specified" (NOS) arm. In this arm, we will include all patients that undergo molecular profiling under this protocol, but that are otherwise not eligible for any of the active treatment arms in the protocol. This will allow us to link their clinical and mutational analyses, to determine the frequency of each mutation, its association with clinical features, response to treatment and outcome, and its association with other mutations. As future therapeutic protocols specific for these mutations are developed, patients may be notified of their eligibility for these studies, if they consent. Future translational studies may be used to: a) unravel the complex biology of lung cancer; b) identify prognostic markers; c) define predictive markers of response/resistance to new therapies; and d) identify new targets.  
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2.1.8 Background and rationale for *EGFR* germline mutation testing in lung cancer families O
Lung cancer is the leading cause of cancer-related death worldwide, accounting for more than one million deaths every year (2, 77). Cigarette smoke accounts for approximately 85-90% of all lung cancers. Other etiological factors for lung cancer include radon (a radioactive gas produced by decay of radium 226), asbestos, lung inflammation and scarring (78).  
Although the etiological role of genetic factors in lung cancer is poorly understood, several lines of evidence suggest a role for these factors in lung carcinogenesis even after adjustment for age, gender and smoking habits. For example, in the Environment And Genetics in Lung cancer Etiology (EAGLE) study, the relative risk of lung cancer associated with a positive family history, adjusted for age, gender, residence, education, and smoking, was 1.57 (95% CI 1.251.98) (79). Genome-wide association (GWA) studies have suggested lung cancer susceptibility loci at various locations (80). Other studies have identified single nucleotide polymorphisms (SNPs) in enzymes involved in DNA repair and detoxification of xenobiotics and environmental chemicals as well as germline mutations in pro-survival pathways (81-84). However, as cigarette smoking is such an overwhelming and preventable risk factor, the importance of family history and genetic susceptibility to lung cancer risk has often been overlooked and is difficult to discern.  
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Germline testing for inherited predisposition is a well established part of care of individuals who may be at hereditary risk for cancers of the breast, ovary, colon, stomach, uterus, thyroid, and other primary sites(85, 86). In contrast to somatic genetic profiling of tumor tissue, germline testing involves analysis of DNA from blood or saliva for inherited mutations in specific genes that are associated with the type of cancer seen in the individual or family seeking assessment (86).  
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High-penetrance germline mutations usually result in a significant alteration in the function of the corresponding gene product and are associated with large increases in cancer risk. For example, *BRCA1* mutation, which is found at a frequency of 1 in 166 to 1000 in the general population, confers a relative risk for breast cancer of 32 in women aged between 40 and 49.  
Other mutations are associated with less dramatic increases in risk. APC*I1307K and  
 rs10505477 at 8q24 are associated with relative risks of 1.7 (intermediate-penetrance mutations) and 1.2 respectively for colon cancer (low-penetrance variants) (86). Germline testing of several high-penetrance germline mutations are now part of standard clinical practice and identification of these mutations often justifies an adjustment of clinical care through the modification of surveillance or through preventive surgery. Genetic tests for intermediate-penetrance mutations and low-penetrance variants are of uncertain clinical utility because the cancer risk associated with the mutation is generally too small to form an appropriate basis for clinical decision making. V  
  
  
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Table 5. Previously reported germline mutations in lung cancer, clinico-pathologic features of the patients  
and their response to TKI  
| and their response to TKI                           | Concurrent                                                                                                             |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
|-----------------------------------------------------|------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------|--------------|----------------------------------------------------|---------------------------|--------------------------------------------------------------------------------------|-------------|-------------|-------|
| Germline                                            | Author,  year                                                                                                          | Proband                                                 | Ethnicity    | Smoking                                            | Stage                     | at                                                                                   |             |             |       |
| presentation                                        | Histology                                                                                                              | somatic                                                 |              |                                                    |                           |                                                                                      |             |             |       |
| mutation                                            | status                                                                                                                 | mutations                                               | Response     | Germline                                           |                           |                                                                                      |             |             |       |
| Family                                              |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| to EGFR                                             | mutation in                                                                                                            |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| History                                             |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| TKI                                                 | family members                                                                                                         | Follow  up                                              |              |                                                    |                           |                                                                                      |             |             |       |
| EGFR E746-                                          |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| 72F                                                 | European                                                                                                               | NS                                                      | IV           | Adenocarcinoma                                     | A750 in  exon 19          | PR/ PFS 9  months                                                                    | Sister with | Absent in 2 | OS 23 |
| LC                                                  | daughters                                                                                                              | months                                                  |              |                                                    |                           |                                                                                      |             |             |       |
| (below)                                             |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| Carmelo  et al,  2011                               | V                                                                                                                      | Poorly                                                  | PR/          | Absent in 2                                        |                           |                                                                                      |             |             |       |
| 74F                                                 | European                                                                                                               | NS                                                      | IIIBwet      | differentiated                                     | Negative                  | PFS 45                                                                               | sons        | NR          |       |
| carcinoma                                           | months                                                                                                                 | 2 family  members  with lung  cancer in  2  generations |              |                                                    |                           |                                                                                      |             |             |       |
| Asian                                               | Mixed  adenocarcinoma                                                                                                  |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| 66F                                                 | Indian                                                                                                                 | NS                                                      | IV           | (acinar                                            | and                       |                                                                                      |             |             |       |
| bronchioloalveolar)                                 | somatic  EGFR                                                                                                          | NR                                                      |              |                                                    |                           |                                                                                      |             |             |       |
| L858R  mutation                                     | NR                                                                                                                     | NR                                                      |              |                                                    |                           |                                                                                      |             |             |       |
| Girard  et al,  2010                                | 7 family  members  with lung  cancer in  5  generations                                                                |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| Poorly                                              |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| 58M                                                 | Eastern  European                                                                                                      | NS                                                      | IV           | differentiated  adenocarcinoma  (acinar and solid) |                           |                                                                                      |             |             |       |
| EGFR exon 20  T790M                                 | EGFR L858R                                                                                                             | NR                                                      | NR           | NR                                                 |                           |                                                                                      |             |             |       |
| O                                                   | EGFR L858R, del                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| 50M                                                 | European                                                                                                               | Smoker                                                  | IV           | BAC                                                | L747- T751                | 6 family  members  with lung  cancer,  BAC or  pulmonary  nodules in  3  generations |             |             |       |
| PFS 9  months                                       | NR                                                                                                                     |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| Bell et  al, 2005                                   | EGFRT790M  in all 4 siblings                                                                                           |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| 55M                                                 | European                                                                                                               | NR                                                      | IV           | Adenocarcinoma                                     | EGFR                      | No                                                                                   | OS 6        |             |       |
| G719A                                               | response                                                                                                               | months                                                  |              |                                                    |                           |                                                                                      |             |             |       |
| 2 family  members  with lung                        | NR                                                                                                                     | NR                                                      |              |                                                    |                           |                                                                                      |             |             |       |
| cancer in 2  generations                            |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| Prudkin                                             | 72F                                                                                                                    | NR                                                      | NS           | NR                                                 | Adenocarcinoma,           |                                                                                      |             |             |       |
| et al,                                              | BAC, LCNEC                                                                                                             | None                                                    | NR           |                                                    |                           |                                                                                      |             |             |       |
| 2009                                                | I                                                                                                                      | 3 family  members  with lung                            | EGFRL861Q in | PFS 8                                              |                           |                                                                                      |             |             |       |
| cancer in 2                                         | 3 siblings                                                                                                             | months*                                                 |              |                                                    |                           |                                                                                      |             |             |       |
| generations                                         |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| EGFR L861Q                                          |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| Ikeda et  al, 2008                                  | 70F                                                                                                                    | NR                                                      | NR           | IIA, IA                                            | Adenocarcinoma,  BAC, AAH | Not used                                                                             |             |             |       |
| EGFR L858R                                          |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| EGFR exon 21  V843I                                 | EGFRV843I in  4 family  members- 3  with lung  adenocarcinoma  and 1 healthy  person                                   |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| 4  individuals  with lung  cancer in 3  generations |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| Ohtsuka                                             | 48F                                                                                                                    | Japanese                                                | NR           | IV                                                 | Adenocarcinoma            | NR                                                                                   | No          |             |       |
| et al                                               | response                                                                                                               |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| 2010                                                | OS NR                                                                                                                  |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| DSister died  of lung  cancer at  NR 67 years       |                                                                                                                        |                                                         |              |                                                    |                           |                                                                                      |             |             |       |
| EGFR exon 21  R831C                                 | Chung                                                                                                                  | PR                                                      |              |                                                    |                           |                                                                                      |             |             |       |
| 76F                                                 | NR                                                                                                                     | NS                                                      | IIIA         | Adenocarcinoma                                     | EGFR                      |                                                                                      |             |             |       |
| et al,                                              | L861R                                                                                                                  | PFS 14                                                  |              |                                                    |                           |                                                                                      |             |             |       |
| 2010                                                | months                                                                                                                 | One                                                     |              |                                                    |                           |                                                                                      |             |             |       |
| Centeno                                             | EGFR                                                                                                                   | sibling                                                 | NR           | OS 1                                               |                           |                                                                                      |             |             |       |
| et al,                                              | 47M                                                                                                                    | European                                                | Smoker       | IIIA                                               | Adenocarcinoma            | exon 21                                                                              | NR          | died of     | year  |
| 2011                                                | L858R                                                                                                                  | cancer                                                  |              |                                                    |                           |                                                                                      |             |             |       |
| EGFR exon 20  R776G                                 | Abbreviations: EGFR: epidermal growth factor; PFS: progression free survival; NR: not reported; NS: never-smoker; BAC: |                                                         |              |                                                    |                           |                                                                                      |             |             |       |  
Abbreviations: EGFR: epidermal growth factor; PFS: progression free survival; NR: not reported; NS: never-smoker; BAC: bronchioalceolar carcinoma; AAH: atypical adenomatous hyperplasia; LCNEC: large cell neuroendocrine carcinoma; TKI: tyrosine kinase inhibitor OS: overall survival No high penetrance mutations have been described for lung cancer. Germline mutations in *EGFR* and its association with familial lung cancer have been rarely described, but their penetrance and patterns of familial involvement are not known. Previously described germline mutations and clinico-pathologic features of lung cancer patients are shown in Table 5. *EGFR*T790M is the most extensively studied germline mutation in familial lung cancer. The T790M mutation occurs within exon 20, which encodes part of the kinase domain and results in an amino acid substitution at position 790 in EGFR, from a threonine (T) to a methionine (M). It is known to occur as a 'second-site mutation' in more than 50% of patients who develop acquired resistance (progressive disease while on therapy after an initial response) to EGFR tyrosine kinase inhibitor (TKI) therapy (87, 88).  
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Bell *et al* reported a family with multiple cases of lung cancer associated with germline transmission of the *EGFR*T790M mutation (81). Four of the six tumors analyzed showed a secondary somatic activating *EGFR* mutation (either L858R, del L747-T751, or G719A) occurring in cis with the germ line T790M mutation. Although somatic *EGFR*T790M mutations are common in patients with acquired resistance to EGFR inhibitors, germline *EGFR*T790M mutations are rare. Two subsequent studies examined this germline mutation in a larger series of patients: Girard *et al* found *EGFR*T790M germline mutation in two of 369 cases of never smokers with NSCLC- both patients had a family history significant for lung cancer (89). However Vikis *et al* analyzed genomic DNA from 237 probands representing lung cancer families with more than three affected individuals for *EGFR*T790M mutation (90). No mutation was observed in any of the family probands analyzed and in any of 60 random fresh-frozen resected lung tumors suggesting that it may be a minor contributor to genetic susceptibility in familial lung cancers. Furthermore, in the Genetic Epidemiology of Lung Cancer Consortium (GELCC) linkage study, the analysis of 52 families (and family subsets within) did not reveal a significant logarithm of odds (LOD) score on or near 7p11, where the *EGFR* gene is located, which also suggests that the mutation may not be a major contributor to familial predisposition to lung cancer. Prudkin *et al* identified one germ line *EGFR*T790M mutation in a cohort of 240 patients with previously untreated lung adenocarcinoma (91).  
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EGFR exon 21V843I is an additional germline mutation which has been described in two reports, in association with a significant family history of lung cancer (92, 93). One subsequent study found no V843I mutations in 285 NSCLC patients with family history of lung cancer (94). The role if any of these mutations in inherited susceptibility to lung cancer in families with clustering of germline mutation and lung cancer is not completely clear. However early evidence suggests that *EGFR*T790M may provide a proliferative advantage with respect to wild-type (WT) *EGFR*, possibly due to the enhanced kinase activity of the mutant (90, 95-97). In a human bronchial epithelial cell line, overexpression of *EGFR*T790M displayed a growth advantage over WT *EGFR* (90). Moreover, presence of a concurrent L858R mutation, i.e. T790M/L858R double mutation resulted in a substantial increase in phosphorylation, compared with the L858R alone (95). Additionally, even in the absence of additional kinase domain mutations, *EGFR* T790M mice developed tumors, albeit with longer latency than *EGFR* L858R/T790M mice. Enhanced tyrosine autophosphorylation was also observed in cells transfected with the plasmid containing EGFRR776G (a germline *EGFR* mutation identified in Case 3 of Table 5) when compared to those transfected with WT *EGFR* (94).  
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At this time, the clinical utility of identification of these germline mutations in lung cancer is not known. It is likely that these and other intrinsic genetic factors controlling susceptibility to lung  
cancer might be hidden by strong environmental factors like cigarette smoking and air pollution which have been implicated in the mutagenesis of many other genes controlling pathways involved in the development lung cancers (3, 98). However, identification of these germline mutations may benefit individuals by providing deeper self-knowledge and motivation to pursue healthy behaviors (e.g., quit smoking), even if the results may not inform clinical decision making (99). With Amendment F, we will begin testing selected individuals (see Section 3.4) for the presence of *EGFR* germline mutations known to be associated with susceptibility to lung cancer. Only patients who enroll at the NCI will be eligible for this testing.
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2.4 hypothesis

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A better understanding of the genetic make-up of the individual tumor may offer potentially improved therapies. This approach may also give rapid access to response data in patients with sometimes rare genetic abnormalities. In addition, it will allow us to test targeted therapies in a select population of patients that is more likely to have a favorable response based on their molecular profile and the specific mechanism of action of the drug being tested. This approach will also speed up drug development and potentially approval, and rescue an otherwise ineffective drug candidate for the specific subgroup that can benefit.
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3 patient selection 3.1 eligibility

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3.1.1 Patients with histologically confirmed advanced NSCLC, SCLC and thymic malignancies for whom surgical resection or multimodality therapy with curative intent is not feasible. For patients with Stage III NSCLC, who can be encompassed by a radiation port, definitive XRT should have been performed first when possible.  
3.1.2 Individuals who meet the eligibility criteria for *EGFR* germline mutation testing (Section 3.4) but who do not have advanced cancer as defined in 3.1.1 may enroll for *EGFR* germline mutation testing only and will not be eligible for the treatment or NOS arms.  
3.1.3 Patients with advanced cancer must meet one of the following criteria (does not apply to first-degree relatives or individuals with pre-invasive histology enrolling only for *EGFR* germline mutation testing):
- Patients must have biopsiable disease and be willing to undergo biopsy for molecular profiling
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or
- Patients must have enough and adequate archival material from a previous biopsy to perform molecular profiling analyses. The adequacy of the material provided will be determined by the principal investigator in conjunction with the laboratories performing the molecular profiling analyses.  
or  
- Patients must have previously undergone a successful molecular profiling of their tumor with mutation analysis of any of the genes described in section 5.2 or ALK break apart fluorescence in situ hybridization, as part of this protocol (crossover patients) or other molecular profiling protocols such as the Lung Cancer Mutation Consortium protocol among others.
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$$3.1.4$$
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3.2 eligibility criteria for enrollment

Please refer to section 3.3 for eligibility criteria for enrollment in the specific molecular profile / treatment arms of this protocol. 3.2.1 Inclusion Criteria  
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3.2.1.1 Patients must have measurable disease, defined as at least one lesion that can be accurately measured in at least one dimension (longest diameter to be recorded) as >20 mm with conventional techniques or as >10 mm with spiral CT scan. See Section 13 for the evaluation of measurable disease.
Target lesions cannot be selected within previously irradiated areas, if not newly arising or clearly progressing after irradiation as proven by repeat scanning.  
3.2.1.2 Life expectancy of greater than 3 months.  
3.2.1.3 Performance status (ECOG) ≤ 2 (See **Appendix C: Performance Status Criteria**).  
3.2.1.4 Patients must have normal organ and marrow function as defined below:
- leukocytes >1,500/mcL
- absolute neutrophil count >1,000/mcL  
- platelets >100,000/mcL
$\blacksquare$  
  
  
$$>$$1,000/m$$
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- total bilirubin* < 1.5 X institutional upper limit of normal  
$$\Pi$$
$$>$$100,000{\sqrt{\mathrm{m}}}\mathrm{e}\mathrm{L}$$  
For patients with Gilbert's syndrome or levels of indirect bilirubin above the upper limit of normal, direct bilirubin will be used for eligibility and should be < 1.5 X institutional upper limit of normal.  
$$\mathrm{AST}(\mathrm{SGOT})/\mathrm{ALT}(\mathrm{SGPT})$$
$\blacksquare$
- AST(SGOT)/ALT(SGPT) < 3 X institutional upper limit of normal
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$$\mathrm{creatining}$$
- creatinine ≤1.5 X institutional upper limits of normal
* 3 X institutional upper limit of normal
$\leq$1.5 X institutional upper limits of normal
OR creatinine clearance >50 mL/min/1.73 m2 for patients with creatinine levels above 1.5 X institutional normal.  
3.2.1.5 Patients must have recovered from toxicity related to prior therapy (chemotherapy, surgery or radiation) to grade ≤ 1 (defined by CTCAE: The NCI Common Terminology Criteria for Adverse Events Version 4 (CTCAE) will be used for toxicity and adverse event reporting. All appropriate treatment areas have access to a copy of the CTCAE version 4.0. A copy of the CTCAE version 4.0 can be downloaded from the CTEP web site (http://ctep.cancer.gov).  
3.2.1.6 The effects of most of the therapeutic agents used in this trial on the developing human fetus at the recommended therapeutic doses are unknown. For this reason and because some agents are known to be teratogenic, women of child-bearing potential and men must agree to use adequate contraception (hormonal or barrier method of birth control; abstinence) prior to study entry and for the duration of study participation, and continue for at least 16 weeks after completing the study to avoid pregnancy and/or potential adverse effects on the developing embryo. Should a woman become pregnant or suspect she is pregnant while participating in this study, she should inform her treating physician immediately. Because there is an unknown but potential risk for adverse events in nursing infants secondary to treatment of the mother with targeted therapies, breastfeeding should be discontinued if the mother is treated with targeted therapies.  
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3.2.1.7 Ability to understand and the willingness to sign a written informed consent document. 3.2.2 Exclusion Criteria O
3.2.2.1 Patients who have had major surgery, chemotherapy or radiotherapy within 2 weeks prior to entering the study or those who have not recovered from adverse events due to agents administered more than 2 weeks earlier.  
3.2.2.2 Patients may not be receiving any other investigational agents or other medications for the treatment of their malignancy.  
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3.2.2.3 Patients with symptomatic brain metastases should be excluded from this clinical trial because of their poor prognosis and because they often develop progressive neurologic dysfunction that would confound the evaluation of neurologic and other adverse events. However, patients who have had treatment for their brain metastases and whose brain metastatic disease status has remained stable for at least 1 week after the end of brain radiation may be enrolled to undergo molecular profiling at the discretion of the principal investigator. In addition, brain metastatic disease should be stable for at least 4 weeks, before the patients can be enrolled in any of the experimental treatment arms.  
3.2.2.4 Patients with any condition (e.g., gastrointestinal tract disease resulting in an inability to take oral medication or a requirement for IV alimentation, prior surgical procedures affecting absorption, or active peptic ulcer disease) that impairs their ability to swallow and retain tablets are excluded.  
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3.2.2.5 Any uncontrolled medical illness that precludes the patient from undergoing a biopsy for molecular profiling and / or receiving treatment under one of the experimental arms of the study should be excluded. These conditions include but are not limited to:
- Ongoing or uncontrolled, symptomatic congestive heart failure (Class III or IV as defined by the NYHA functional classification system (see **Appendix D**).  
- Uncontrolled hypertension
- Unstable angina pectoris  
- Cardiac arrhythmia
- Uncontrolled diabetes
- Uncontrolled psychiatric illness/social situations that would limit compliance with study requirements.
3.2.2.6 Patients with QTc prolongation (defined as a QTc interval equal to or greater than 500 msec) or other significant ECG abnormalities are excluded.  
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3.2.2.7 Caution should be used if patients are required to use a concomitant medication that can prolong the QT interval and efforts should be made to switch to a different medication before the patient begins treatment under an experimental arm. See **Appendix E** for a table of medications with the potential to prolong the QTc interval. A comprehensive list of agents with the potential to cause QTc prolongation can be found at: http://www.azcert.org/medical-pros/drug-lists/bycategory.cfm
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3.2.2.8 The eligibility of patients taking medications that are potent inducers or inhibitors of that enzyme will be determined following a review of their case by the Principal Investigator. (A list of potent CYP3A4 inducers or inhibitors can be found in Appendix F). Every effort should be made to switch patients taking such agents or substances to other medications before they begin treatment with one of the experimental drug included in this protocol, particularly patients with gliomas or brain metastases who are taking enzyme-inducing anticonvulsant agents. A comprehensive list of medications and substances known or with the potential to alter the pharmacokinetics of sunitinib through CYP3A4 is provided in **Appendix F**.  
3.2.2.9 Patients with tumor amenable to potentially curative therapy as assessed by the investigator.  
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3.2.2.10 Pregnant women are excluded from this study because many of the FDA approved agents and investigational agents in this trial have the potential for teratogenic or abortifacient effects. Because there is an unknown but potential risk for adverse events in nursing infants secondary to treatment of the mother with these agents, breastfeeding should be discontinued if the mother is treated in this protocol. These potential risks may also apply to other agents used in this study.
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3.3 specific eligibility criteria for

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The following is a description of the eligibility criteria required to be enrolled in the specific molecular profile-based treatment arms of this study which include: Erlotinib, AZD6244, MK2206, Lapatinib and Sunitinib arms. This is in addition to the general eligibility and exclusion criteria described in sections 3.1 and 3.2.  
3.3.1 Erlotinib arm 3.3.1.1 Inclusion criteria  
3.3.1.1.1 Patients must have an EGFR TKI sensitizing mutation as determined by analysis of the primary tumor or a metastatic site in a CLIA certified laboratory.  
3.3.1.1.2 Patients with SCLC or thymic malignancies must have been treated with at least 1 previous standard of care chemotherapy regimen or refuse to be treated with conventional chemotherapy agents.  
3.3.1.2 Exclusion criteria
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3.3.1.2.1 previous anti-egfr tki therapy

3.3.1.2.2 Patients with a known EGFR TKI resistant mutation.  
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3.3.1.2.3 History of allergic reactions attributed to compounds of similar chemical or biologic composition to Erlotinib.
3.3.2 AZD6244 arm  
3.3.2.1 Inclusion criteria 3.3.2.1.1 Patients must have one of the following as determined by analysis of the primary tumor or a metastatic site in a CLIA certified laboratory:
- KRAS mutation or
- NRAS mutation or  
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- HRAS mutation or
- BRAF mutation  
3.3.2.1.2 Patients must have been treated with at least 1 previous standard of care chemotherapy regimen or refuse to be treated with conventional chemotherapy agents.  
3.3.2.2 Exclusion criteria
3.3.2.2.1 Any prior exposure to MEK, Ras, or Raf inhibitors.  
3.3.2.2.2 History of allergic reactions attributed to compounds of similar chemical or biologic composition to AZD6244.  
3.3.2.2.3 Cardiac conditions as follows:
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- Uncontrolled hypertension (BP ≥150/95 despite optimal therapy)
- Heart failure NYHA Class II or above (**See Appendix D: New York Heart**
Association Classifications)
- Prior or current cardiomyopathy
- Baseline LVEF ≤ 50%.  
- Atrial fibrillation with heart rate >100 bpm - Unstable ischaemic heart disease (MI within 6 months prior to starting treatment, or angina requiring use of nitrates more than once weekly).
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3.3.2.2.4 Laboratory values as listed below (SI units):  
- Absolute Neutrophil Count (ANC) <1.5x109/L (1500 per mm3) - Platelets <100x109/L (100,000 per mm3) - Hemoglobin (Hgb) <9.0 g/dL
- Serum bilirubin >1.5 x upper limit of normal (ULN)
- Aspartate aminotransferase (AST/SGOT) or alanine aminotransferase
(ALT/SGPT) >2.5 x ULN (≥5 ULN in presence of liver metastases).
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3.3.3 mk2206 arm

3.3.3.1 Inclusion criteria 3.3.3.1.1 Patients must have one of the following as determined by analysis of the primary tumor or a metastatic site in a CLIA certified laboratory:
- PI3KCA mutation or  
  
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- AKT mutation or
- PTEN mutation
- PI3KCA gene amplification by FISH (gene to chromosome ration >2) or 3.3.3.1.2 Patients must have been treated with at least 1 previous standard of care chemotherapy regimen or refuse to be treated with conventional chemotherapy agents.  
3.3.3.2 Exclusion criteria 3.3.3.2.1 Previous AKT inhibitor therapy. 3.3.3.2.2 History of allergic reactions attributed to compounds of similar chemical or biologic composition to MK-2206.  
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3.2.3.2.3 Preclinical studies demonstrated the potential of MK-2206 for induction of hyperglycemia in all preclinical species tested. Patients with diabetes or in risk for hyperglycemia should not be excluded from trials with MK-2206, but the hyperglycemia should be well controlled on oral agents before the patient enters the trial.  
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3.3.4 Lapatinib arm 3.3.4.1 Inclusion criteria 3.3.4.1.1 Patients must have one of the following as determined by analysis of the primary tumor or a metastatic site in a CLIA certified laboratory:
- ERBB2 mutation or
- ERBB2 gene amplification by FISH (gene to chromosome ration >2)
3.3.4.1.2 Patients must have been treated with at least 1 previous standard of care chemotherapy regimen or refuse to be treated with conventional chemotherapy agents.  
3.3.4.2 Exclusion criteria  
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3.3.4.2.1 Previous Lapatinib therapy.  
3.3.4.2.2 History of allergic reactions attributed to compounds of similar chemical or biologic composition to lapatinib.  
3.3.4.2.3 LVEF < 50%
3.3.5 Sunitinib arm 3.3.5.1 Inclusion criteria  
3.3.5.1.1 Patients must have one of the following as determined by analysis of the primary tumor or a metastatic site in a CLIA certified laboratory:
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- PDGFR-A mutation or  
  
- PDGFR-A gene amplification by FISH (gene to chromosome ratio >2) or
- KIT mutation  
3.3.5.1.2 Patients must have been treated with at least 1 previous standard of care chemotherapy regimen or refuse to be treated with conventional chemotherapy agents.  
3.3.5.2 Exclusion criteria 3.3.5.2.1 Previous sunitinib therapy 3.3.5.2.2 History of allergic reactions attributed to compounds of similar chemical or biologic composition to sunitinib.  
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3.3.5.2.3 Patients who require use of therapeutic doses of coumarin-derivative anticoagulants such as warfarin are excluded. Note: Low molecular weight heparin is permitted provided the patient's PT INR is <1.5.  
3.3.5.2.4 Patients with any of the following conditions are excluded:
- Serious or non-healing wound, ulcer, or bone fracture.  
- History of abdominal fistula, gastrointestinal perforation, or intra-abdominal abscess within 28 days of treatment.  
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- Any history of cerebrovascular accident (CVA) or transient ischemic attack within 12 months prior to study entry.  
- History of myocardial infarction, cardiac arrhythmia, stable/unstable angina, symptomatic congestive heart failure, or coronary/peripheral artery bypass graft or stenting within 12 months prior to study entry.  
- History of pulmonary embolism within the past 12 months.  
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3.3.5.2.5 Patients with a pre-existing thyroid abnormality who are unable to maintain thyroid function in the normal range with medication are ineligible.
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3.4 eligibility criteria for egfr

3.4.1 Age ≥ 18 years with one of the following criteria: 3.4.2 Personal history of invasive lung cancer or one of the pre-invasive histologies associated with the development of lung cancer [adenocarcinoma in situ (AIS), minimally invasive
adenocarcinomas (MIA) or atypical adenomatous hyperplasia (AAH)] and more than two affected family members with invasive lung cancer or one of the pre-invasive histologies associated with the development of lung cancer; OR  
3.4.3 First-degree relatives of an individual enrolled in the study with a known *EGFR* germline mutation; OR
3.4.4 Detection of de-novo (prior to any treatment with TKI) T790M mutation in the tumor specimen of a lung cancer patient; OR
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3.4.5 A family history of lung cancer not possibly related to smoking history, defined as at least one family member within the 3rd degree of consanguinity with lung cancer who was a never or oligo-smoker* or at least two family members in either the maternal or paternal side with a history of lung cancer; OR
3.4.6 Documented germline lung cancer associated mutation (such as EGFR T790M) tested elsewhere.
*An oligo-smoker is defined as an individual with ≤ 15 pack-year history of smoking.
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3.5 inclusion of women and

Both men and women of all races and ethnic groups are eligible for this trial. The following are our accrual targets based on race and gender for allhistology groups combined (i.e. NSCLC, SCLC, and thymic malignancies):  
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| Accrual Targets Ethnic Category                   | Sex/Gender Females   | Males   | Total   |    |     |
|---------------------------------------------------|----------------------|---------|---------|----|-----|
| I                                                 |                      |         |         |    |     |
| Hispanic or Latino                                | 42                   | +       | 42      | =  | 84  |
| Not Hispanic or Latino                            | 258                  | +       | 258     | =  | 516 |
| Ethnic Category: Total of all subjects            | 300                  | +       | 300     | =  | 600 |
| Racial Category American Indian or Alaskan Native | 12                   | +       | 12      | =  | 24  |
| Asian                                             | 90                   | +       | 90      | =  | 180 |
| Black or African American                         | 42                   | +       | 42      | =  | 84  |
| Native Hawaiian or other Pacific                  | 12                   | +       | 12      | =  | 24  |
| Islander                                          | D                    |         |         |    |     |
| White                                             | 144                  | +       | 144     | =  | 288 |
| Racial Category: Total of all subjects            | 300                  | +       | 300     | =  | 600 |
| Accrual Rate: 10 patients/month                   |                      |         |         |    |     |  
Total Expected Accrual: 600 patients from all participating sites and in all diseases combined.
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4 patient registration 4.1 registration

Authorized staff must register an eligible candidate with NCI Central Registration Office (CRO) within 24 hours of signing consent. A registration Eligibility Checklist from the web site (http://home.ccr.cancer.gov/intra/eligibility/welcome.htm) must be completed and sent via encrypted email to: NCI Central Registration Office (HOIS) ncicentralregistrationl@mail.nih.gov . After confirmation of eligibility at Central Registration Office, CRO staff will call pharmacy to advise them of the acceptance of the treatment-eligible patient on the protocol prior to the release of any investigational agents. Verification of Registration will be forwarded electronically via e-mail to the research team. Please note, it is very important for all registrars to acquire encrypted e-mail from NIH Help Desk, since the verification of registration includes patient's information. A recorder is available during non-working hours.  
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Patients will retain their number throughout their time on the protocol but will be given a letter designation to identify which arm they have been enrolled to, or re-enrolled to in accordance with Section 5.4. The letters that correspond to the treatment arms are as follows:
A - Arm A (Erlotinib)  
B - Arm B (AZD6244) C - Arm C (MK-2206) D - Arm D (Lapatinib) E - Arm E (Sunitinib) F - Arm F (NOS)
Version M 04/08/14 NOTE: The treatment arms are closed to accrual, but patients are still being accrued for germline testing. 4.1.2 For Participating Site Registration NOTE: The participating site closed on 02/05/2015. This section is no longer applicable, but is being retained for historical purposes.  
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All patients must be registered through the NCI Central Registration Office (CRO). The CRO is open from 8:30am to 5:30pm EST Monday through Friday, excluding federal holidays. The protocol registration form and cover memo will be supplied by the Coordinating Center, NCI CCR, and updates will be provided as needed. Subject eligibility and demographic information is required for registration. To initially register a subject after the participant has signed consent, complete the top portion of the form and fax to the CRO at 301-480-0757. Once eligibility is confirmed, complete the remainder of the form which is the eligibility checklist and, fax the completed registration checklist and cover memo to the CRO at 301-480-0757.  
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The CRO will notify the registering site personnel either by e-mail or fax that the protocol registration form has been received. The CRO will assign a unique patient/subject ID number for each subject that will be used to enter data into the C3D database. Questions about eligibility should be directed to the Coordinating Center's Research Nurse:
Arlene Berman, RN  
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9000 Rockville Pike Bldg 10, Rm 12N226 Bethesda, MD 20892 Telephone: 301.435.5609 Fax: 301.480.2590 Email: arleneb@mail.nih.gov Technical questions about the form should be directed to the Central Registration: Office (301402-1732).
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4.2 on-study research evaluation

This section applies only to patients enrolled into any of the treatment arms of the protocol.  
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4.2.1 Complete history and physical examination (including height, weight, vital signs and ECOG performance score) with documentation of 1) measurable disease, 2) narcotic use and pain assessment, and 3) prior therapies (surgical, radio therapeutic and cytotoxic) will be conducted prior to on-study. A complete medication history will be obtained prior to starting, including medications at base line, over the counter medications, homeopathic remedies, vitamins, and alternative therapies.  
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4.2.2 Imaging Studies (Baseline) - Every patient should have a baseline clinical evaluation with CT scan of chest, abdomen and/or pelvis for areas of known or suspected disease involvement prior to receiving treatment. In some patients an MRI may be more appropriate. FDG-PET scans are recommended but not mandatory. Baseline scans must be completed within 28 days prior to enrollment.  
4.2.3 Laboratory Evaluation [baseline labs must be obtained within one week prior to enrollment].
4.2.4 Hematological Profile: CBC with differential and platelet count, prothrombin time, activated partial thromboplastin time.  
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4.2.5 Biochemical Profile: Sodium, potassium, chloride, CO2, BUN, creatinine, glucose, AST,
ALT, alkaline phosphatase, bilirubin, albumin, total protein, LDH, calcium, phosphorous, magnesium, and urinalysis.
4.2.6 PT and PTT 4.2.7 EKG (baseline) 4.2.8 Pregnancy test for female patients of childbearing age and anatomic ability.
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5 study design / treatment

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The purpose of this trial is to perform molecular profiling analysis in patients with advanced NSCLC, SCLC and thymic malignancies and offer enrollment into targeted therapy arms based on their molecular profiles. We will also be studying the frequency of *EGFR* germline mutations by enrolling patients from families with high susceptibility to lung cancer and their first-degree relatives (at the NCI only).
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5.1 specimen collection

Individuals who meet the eligibility criteria for *EGFR* germline mutation testing but who do not have advanced cancer as defined in Section 3.1.1 will not undergo tumor biopsy for molecular profiling.  
Patients with advanced cancer (as defined in Section 3.1.1) who meet eligibility criteria will undergo biopsy of the primary tumor or any metastatic site for molecular profiling analyses (with the exception of patients who have available archival material or patients that have previously undergone successful molecular profiling). All attempts will be made to obtain fresh tissue biopsies but if this is not feasible, archived paraffin blocks will be acceptable as long as there is enough and adequate material to perform the molecular profiling analyses described below. The adequacy of the archival tissue provided by the patient will be determined by the principal investigator at each participating institution in conjunction with the molecular pathology laboratories performing the molecular analyses. The following techniques will be used to obtain tissue samples for molecular profiling according to the location and size of the lesions:
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- Core needle biopsy
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- excisional biopsies

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Sample collection will be performed either by the interventional radiology or the surgery departments at the participating institution. Biopsies will be performed according to the standard operating procedures in place at the performing institution. Samples will be formalin fixed and sent to the local pathology department for further processing and confirmation of the histologic diagnosis. If possible, one of the samples will be immediately frozen to perform some of the correlative analyses described in Section 10.
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5.2 molecular profiling

After the tumor samples are obtained, molecular profiling analyses will be performed to determine enrollment in specific treatment arms (with the exception of patients who have previously undergone successful molecular profiling). Since these analyses will be used for treatment decisions, they will be performed in a CLIA certified laboratory at the participating institutions. The following is a list of the molecular profiling analyses to be performed:
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| Approved  Gene  Symbol   | Approved Gene Name                                                                                    | Location   | Sequence  Accession  IDs   | Previous   | Aliases   |
|--------------------------|-------------------------------------------------------------------------------------------------------|------------|----------------------------|------------|-----------|
| Symbols D                |                                                                                                       |            |                            |            |           |
| AKT1                     | v-akt murine thymoma viral                                                                            | 14q32.32-  | M63167                     |            | RAC, PKB, |
| oncogene homolog 1       | q32.33                                                                                                | NM_005163  | PRKBA, AKT                 |            |           |
| AKT2                     | v-akt murine thymoma viral                                                                            | 19q13.1-   | NM_001626                  |            |           |
| oncogene homolog 2       | q13.2                                                                                                 |            |                            |            |           |
| BRAF                     | v-raf murine sarcoma viral                                                                            | 7q34       | M95712                     |            | BRAF1     |
| oncogene homolog B1      | NM_004333                                                                                             |            |                            |            |           |
| EGFR                     | epidermal growth factor  receptor (erythroblastic  leukemia viral (v-erb-b)  oncogene homolog, avian) | 7p12       | NM_005228                  | ERBB       | ERBB1     |  
5.2.1 Gene mutation analyses for treatment decisions  
| ERBB2                        | v-erb-b2 erythroblastic leukemia  viral oncogene homolog 2,  neuro/glioblastoma derived  oncogene homolog (avian)   | 17q11.2-   | X03363    | NGL   | NEU, HER-2,   |
|------------------------------|---------------------------------------------------------------------------------------------------------------------|------------|-----------|-------|---------------|
| q12                          | CD340, HER2                                                                                                         |            |           |       |               |
| HRAS                         | v-Ha-ras Harvey rat sarcoma                                                                                         | 11p15.5    | AJ437024  | HRAS1 |               |
| viral oncogene homolog       | NM_176795                                                                                                           |            |           |       |               |
| KIT                          | v-kit Hardy-Zuckerman 4 feline  sarcoma viral oncogene  homolog                                                     | 4q11-q12   | S67773    | PBT   | CD117, SCFR, CKit               |
| V                            |                                                                                                                     |            |           |       |               |
| KRAS                         | v-Ki-ras2 Kirsten rat sarcoma                                                                                       | 12p12.1    | BC010502  | KRAS2 | KRAS1         |
| viral oncogene homolog       | NM_033360                                                                                                           |            |           |       |               |
| NRAS                         | neuroblastoma RAS viral (v-ras)                                                                                     | 1p13.2     | BC005219  |       |               |
| oncogene homolog             | NM_002524                                                                                                           |            |           |       |               |
| PDGFRA                       | platelet-derived growth factor                                                                                      | 4q12       | D50001    |       | CD140a,       |
| receptor, alpha polypeptide  | NM_006206                                                                                                           | PDGFR2     |           |       |               |
| PIK3CA                       | phosphoinositide-3-kinase,                                                                                          | 3q26.3     | NM_006218 |       | p110-alpha,   |
| catalytic, alpha polypeptide | MGC142161,  PI3K,  MGC142163                                                                                        |            |           |       |               |
| PTEN                         | phosphatase and tensin homolog                                                                                      | 10q23      | U92436    | BZS,  | MMAC1, TEP1,  |
| NM_000314                    | MHAM                                                                                                                | PTEN1      |           |       |               |
| O                            |                                                                                                                     |            |           |       |               |
| 5.2.2                        | ERBB2 amplification by FISH                                                                                         |            |           |       |               |
| 5.2.3                        | PDGFRA amplification by FISH                                                                                        |            |           |       |               |
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5.3 enrollment in treatment arms

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Due to the rapidly progressing course of the thoracic malignancies in this study, treatment decisions will be made in approximately 2 weeks from the time that the tumor samples were obtained. Based on the molecular profiling results, the patients will be offered enrollment into a specific treatment arm according to the decision tree shown in Figure 2 and the eligibility criteria described in Section 3. Individuals who meet the eligibility criteria for *EGFR* germline mutation testing (Section 3.4) but who do not have advanced cancer as defined in Section 3.1.1 are not eligible for the treatment arms.  
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allowed to crossover to different treatment arms as long as they meet eligibility criteria.
† See separate eligibility criteria (Section 3.4) and schema for *EGFR* germline mutation testing. No = No or not available Amp = gene amplification by FISH NOS = non-otherwise specified arm A = optional **re-biopsy for patients that responded to previous line of therapy**
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Each study arm is independent from the other arms; it has its own eligibility criteria (Section 3) and statistical considerations (Section 15), and will be analyzed independently. Additionally, it is not our intention to compare the outcomes among treatment arms since the patients enrolled in each arm will have different molecular characteristics. Patients enrolled in one of the treatment arms of this protocol, with the exception of the NOS arm and individuals enrolled for *EGFR* germline mutation testing only, will be treated and  
followed with clinical visits at least every 3, 4, or 6 weeks, as defined for each treatment arm; i.e., every 3 weeks for the Erlotinib, AZD6244, and Lapatinib arms; every 4 weeks for the MK2206 arm; and every 6 weeks for the Sunitinib arm. The time between clinic visits may be extended at the PI's discretion by up to 1 full cycle, for a maximum of 2 cycles between clinic visits (i.e., clinic visits may be extended to every 6 weeks for the Erlotinib, AZD6244, and Lapatinib arms; every 8 weeks for the MK-2206 arm; and every 12 weeks for the Sunitinib arm). If the frequency of clinic visits is extended, laboratory tests will not be required nor samples collected until the next clinic visit. Re-staging imaging will be performed at the end of every two cycles as defined for each treatment arm; i.e., every 6, 8, or 12 weeks +/- 1 week. See Section 5.9.2 for details. The patients will continue on the selected arms until disease progression.  
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5.4 treatment after disease progression

Patients who initially had a response to treatment or a prolongued stabilization of the tumor (>6 months) but that eventually develop progressive disease, will be offered the option to have a repeat biopsy for molecular profiling analyses. This biopsy will have the intention to study potential mechanisms of resistance to specific targeted therapies. This will also be potentially used for treatment decisions or enrollment in other molecularly targeted protocols. However, if the patient refuses this option, we will use the most recent results of the molecular profiling analyses to verify eligibility for enrollment in an alternative treatment arm on this study (crossover).  
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At the time of disease progression, the patients will be allowed to re-register onto another treatment arm that is available in this protocol, according to the schema, and as long as they still meet the eligibility criteria described in Section 3. In this case, patients will be re-registered onto the treatment arm, but not re-consented. The patient will count as a new patient to that specific arm, keeping their original patient ID number.
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5.5 the nos arm

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All patients that undergo molecular profiling but that are not enrolled into any of the investigational treatment arms will be enrolled into the NOS arm, which is considered to be a natural history arm. These patients do not have to meet any particular eligibility criteria. Individuals who meet the eligibility criteria for *EGFR* germline mutation testing (Section 3.4) but who do not have advanced cancer as defined in Section 3.1.1 are not eligible for the NOS arm. This will allow data collection on these patients, linking their clinical information with their molecular profiling analyses. Frequency determination of each mutation, its association with clinical features, response to other standard and experimental treatments and overall outcome data will be collected. As future therapeutic protocols or treatment arms specific for their molecular profiles are developed at NIH or elsewhere, patients may be notified of their eligibility for these studies.  
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The NOS arm will consist of the following mixture of patients:  
- Patients that do not meet the eligibility criteria for enrollment in the available treatment arms of this protocol.  
- Patients that meet eligibility criteria for a particular arm but cannot be enrolled on it because of other reasons such as patient preference or drug availability issues, among others.
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The NOS arm is considered a natural history arm in which the patients are allowed to receive a standard of care or experimental therapy of their choice, including but not limited to the following modalities:  
- Patients will be allowed to participate on any available treatment clinical trial at NIH or elsewhere.  
- Patients will be allowed to receive standard of care treatment at NIH under protocol 04-
C-0165 ("Care of the Adult Oncology Patient, Center for Cancer Research, NCI;" Principal Investigator: James Gulley, M.D.) or elsewhere.  
- Patients will be allowed to receive best supportive care at NIH or elsewhere.
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Patients on this arm will be followed either with clinic visits, phone interviews, or medical records review every 4 months (+/- 2 months). The patients will continue to be followed in this arm indefinitely, until death or until the patient decides to withdraw from the protocol.
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5.6 egfr germline mutation testing

Patients at the NCI site meeting the eligibility criteria in Section 3.4 will be enrolled in *EGFR*
germline mutation arm of the study (100, 101). Guidelines set forth by American Society of Clinical Oncology (ASCO) in 2003 and updated in 2010 will be followed in obtaining consent, genetic counseling, testing and follow up (86, 102). Evaluation and follow-up of eligible patients and family members are outlined in Figure 3 and Figure 4.  
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Figure 3. Flow chart depicting evaluation and follow-up of eligible patients who undergo *EGFR*
germline mutation testing.  
  
1 Consent II: Informed consent for testing for *EGFR* germline mutations.
2 *EGFR* germline mutation panel: *EGFR* exon 20 T790M, exon 21 V843I, exon 21 R831C and exon 20 R776G.
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Figure 4. Flow chart depicting evaluation and follow-up of first-degree relatives who undergo  
  
smokers, those who quit within the previous 15 years.  
2 Age ≥ 45 years at enrollment with ≥ 20 pack-year smoking history or age within 5 years before the youngest family member was diagnosed with lung cancer.  
3 For lung nodules and incidental lesions detected on CT, follow up is per standard guidelines.  
Consent III: Informed consent for testing for *EGFR* germline mutations in first-degree relatives of individuals with known EGFR germline mutations. Abbreviation: LDCT, low-dose screening computed tomography scan.  
Follow-up of lung nodules recommended by Fleischner Society (1) and National Comprehensive Cancer Network(2)(2)(2).  
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5.6.1 Consent The proband as well as all family members undergoing germline genetic testing will sign informed consent after undergoing genetic counseling and prior to any germline genetic testing. Consents I, II and III will be used as follows: Consent I: Patients who are eligible for the molecular profiling protocol will sign the standard consent for molecular profiling protocol. Consent II: Individuals with lung cancer or a pre-invasive histology who meet the eligibility criteria for *EGFR* germline mutation testing (i.e., meets criteria **3.4.1** and **3.4.2**) will sign consent II (i.e., consent for germline mutation testing of proband). Consent II will be obtained from the next of kin for deceased family members of the proband with a history of lung cancer for whom tissue is available.  
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Consent III: First-degree relatives of individuals with *EGFR* germline mutations (with no known lung cancer and/or germline mutations, i.e., meets criteria **3.4.1** and **3.4.3**) will sign consent III
(i.e., consent for germline mutation testing of unaffected family member).
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5.6.2 pre-test genetic counseling

Genetic counseling will be provided for the individual and family members both before and after germline mutation analysis as detailed below: The proband and family members who undergo genetic testing will meet a genetics healthcare provider (GHP) (either in clinic or via phone conference) prior to signing consent for germline testing and undergoing germline genetic testing. The GHP will explain the specific testing to be performed, the timeframe for analysis, follow-up testing that may be required, and the types of information that may be obtained and potential healthcare recommendations which could result based on potential results. Ample time will be given to ensure that all questions are answered. At each step in the process the GHP will be available to answer questions and assist the individual in the decision process regarding testing and results.  
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5.6.3 genetic testing

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Step 1: The proband (patient who presents to our clinic with lung cancer or a pre-invasive histology with more than two affected family members with invasive lung cancer or one of the pre-invasive histologies associated with the development of lung cancer) will be tested for *EGFR* germline mutations (on peripheral blood mononuclear cells) that have been associated with familial clustering of lung cancer (*EGFR* exon 20 T790M, exon 21 V843I, exon 21 R831C and exon 20 R776G). The following information will be documented for the proband: mutational status of the tumor, treatment history and response to EGFR TKI, age, sex, ethnicity, detailed family history with documentation of any malignencies in the family, smoking survey based on the Centers for Disease Control and Prevention Behavioral Risk Factor Surveillance System Survey Questionnaire (**Appendix K: Tobbacco Use History Questionnaire**), environmental exposure and previous malignancies. Once a specific mutation is confirmed in the proband, all adult first-degree relatives (parents, offspring, and siblings) will be invited to participate in this study.  
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Step 2: Recruitment of first-degree relatives If the proband consents to do so, all first-degree relatives (of the proband) will be contacted by a letter followed by phone call.  
Step 3: Consenting family members of the proband will be asked to undergo germline mutation testing of the index mutation, which was identified in the proband. For all family members, a history and physical exam will be performed and the following information documented: age, sex, ethnicity, detailed family history with documentation of any malignencies, smoking survey based on the Centers for Disease Control and Prevention Behavioral Health Factor Surveillance System Survey Questionnaire (**Appendix K: Tobbacco Use History Questionnaire**),
environmental exposure and previous malignancies. In many cases, due to the high case-fatality rate of lung cancer, the family member with lung cancer may be deceased. In these cases, archived FFPE tissue may be used for germline mutation testing (after genetic counseling and obtaining consent from next of kin), if normal tissue can be isolated using laser capture microdissection. 5.6.4 Result disclosure and post-test counseling V
Results of *EGFR* germline mutation testing will be available in Clinical Research Information System (CRIS) in ≤ 2 weeks after date of sample collection. Disclosure of test results will be performed by a study investigator and GHP, who will provide any management recommendations as well as recommendations for testing family members as applicable. Study participants and their designated local health care provider(s) will also receive these recommendations in writing as a counseling letter.
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5.6.5 follow-up

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The follow up of individuals who undergo germline mutation testing will follow the schema in Figure 3. After result disclosure and post-test counseling, whether an *EGFR* germline mutation is found or not, mangement of invasive carcinoma/pre-invasive histology will follow standard guidelines. The follow up of first-degree relatives of the proband who undergo germline mutation testing will follow the schema in Figure 4. Mutation negative individual: These individuals will be will be risk stratified based on smoking history into "high-risk" (individuals between 55 and 74 years of age at enrollment with a history of cigarette smoking of at least 30 pack-years, and, if former smokers, those who quit within the previous 15 years) and "not high-risk" (individuals not meeting the high-risk criteria) groups (103). In the high-risk group, annual low-dose computed tomography (LDCT) screening (CT
screening techniques will follow NCCN guidelines; an example of the latest guideline is in Appendix L) will be rcommended for at least 3 years and until age 74 (103). No further intervention will be recommended for the not high-risk group.  
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Mutation positive individual: These individuals will be will be risk stratified based on smoking history and age of youngest family member with lung cancer into "high-risk" (age ≥ 45 at enrollment with ≥ 20 pack-year smoking history or age within 5 years before the youngest family member was diagnosed with lung cancer) and "not high-risk" (individuals not meeting the highrisk criteria) groups. In the high-risk group, annual LDCT screening will be rcommended for at least 3 years and until age 74 (103). The not-high risk individuals will be further risk-stratified based on smoking history into 2 groups and followed as described: ≥ 20 pack-year history of smoking [Baseline CT followed by LDCT at 1 year intervals for 3 years starting 5 years before the youngest family member was diagnosed with lung cancer or age 45 (whichever one earlier)] and ≤20 pack year history of smoking [LDCT at 1 year intervals for 3 years starting 5 years before the youngest family member was diagnosed with lung cancer or age 45 (whichever one earlier)].  
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All probands as well as family members who are enrolled in the protocol will be counseled regarding smoking cessation and will be offered pharmacologic assistance if needed at NIH. All consented individuals (probands and first-degree relatives) will remain on study until death or withdrawal of consent to participate. Survival data, adherence to screening recommendations and details of incident cancers (date of diagnosis, stage at diagnosis) will be documented in firstdegree relatives using a phone call once a year. The proband will be followed using a phone call once a year to collect survival data.
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5.6.6 laboratory and specimen information

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Peripheral blood samples (3-5 mL) will be submitted in sodium citrate anticoagulated "light blue top" tubes to the Molecular Diagnostics Laboratory of the Laboratory of Pathology, NCI for analysis of the following germline mutations affecting the *EGFR* gene: exon 20 T790M, exon 21 V843I, exon 21 R831C and exon 20 R776G. DNA extraction is performed on a PSS Biosystems (Pleasanton, CA) robotic device using the company's proprietary bead-based DNA extraction kit. Targeted analysis for potential germline *EGFR* mutations will be performed by pyrosequencing on a PyroMark Q24 instrument (Qiagen, Valencia, CA) after initial PCR of the targeted regions. Primers for all PCR and pyrosequencing reactions are designed and validated by the Molecular Diagnostics Laboratory (MDU) of the Laboratory of Pathology, Center for Cancer Research, NCI, NIH, and are available upon request. The MDU is a CLIA-regulated and CAP-inspected high-complexity clinical molecular diagnostics laboratory (CLIA\# 21D0716664; Exp. 7/16/2012). The report will be issued within 2 weeks from the date of collection and will be available in Clinical Research Information System (CRIS).  
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5.6.7 data collection

A full pedigree will be collected on each family enrolled in this aspect of the study. This study will utilize the genetic database Progeny for collection and storage of pedigree data. Progeny is an online multi-user clinical data management system used to track family history, phenotype, and genotype data. The Progeny database is stored on a secure NCI server that is password protected. The database itself is also password protected with the options to restrict each class of users to specifically defined access and read/write privileges based on their role on the study. The database also has the capability to track passwords, logins, previous entry, new entry and user information with a date/time stamp. Families and individual subjects within families are tracked by distinct identification labels that include a unique numeric family and individual identifier.  
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5.6.8 Description of how privacy and confidentiality of medical information/biological specimens will be maximized Biospecimens will be collected and processed using validated SOPs that will ensure both specimen quality and patient confidentiality pursuant to informed consent provisions.  
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Using a computerized inventory system and a backup hardcopy process, all specimen collection and processing steps will be documented and the specific location of each specimen will be tracked. Each new specimen collected will be assigned a unique barcode identifier that can be linked to the original specimen collected and other relevant information within the inventory system. To ensure patient confidentiality, only containers used for the initial specimen collections will be labeled with patient identifiers. Coded, linked labels will be applied to all subsequent specimen containers. When specimens are processed and aliquoted, no patient  
information will be included on the new containers. Original specimen containers will be discarded. Only de-linked specimens will be shipped for analysis and/or storage. Coded, linked specimen labels will indicate: protocol number, order in which the patient was enrolled in the trial, type of sample, collection time, and total volume collected, as appropriate. The inventory process contains other security provisions sufficient to safeguard patient privacy and confidentiality. Access to the inventory system and associated documents will be restricted to appropriate personnel only. The only patient information available in the inventory system will be the patient sex, diagnosis, and level of informed consent provided. SOPs ensure that any changes in the informed consent made by a patient and relayed to the PI will be reflected in the inventory system to ensure that specimens are destroyed as appropriate. All laboratory personnel will be trained to adhere to SOPs and will be monitored for high-quality performance.  
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If, at any time, a patient withdraws from the study and does not wish for their existing samples to be utilized, the individual must provide a written request. Following receipt of this request, the samples will be destroyed (or returned to the patient, if so requested). The PI will record any loss or unanticipated destruction of samples as a deviation. Reports will be made per the requirements of section 8.2.  
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A Certificate of Confidentiality will be obtained from the Department of Health and Human Services before germline mutation testing begins. The investigators will use the Certificate to protect against the compelled disclosure of personally identifiable information and to support and defend the authority of the Certificate against legal challenges. Personnel involved in the conduct of the research will comply with all the requirements of 45 CFR Part 46 "Protection of Human Subjects." All research participants will be informed that a Certificate has been issued, and they will be given a description of the protection provided by the Certificate.
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5.7 agent administration

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Treatment will be administered on an outpatient basis. Reported adverse events and potential risks from the agents used in this protocol are described in Section 7. Appropriate dose modifications for these agents are described in Section 6. No investigational or commercial agents or therapies other than those described below may be administered with the intent to treat the patient's malignancy. Patients in all treatment arms (Erlotinib, AZD6244, MK2206, Lapatinib and Sunitinib) will be provided with a Medication Diary (**Appendix B**). They will be instructed in its use and asked to bring the diary with them to each appointment. A new copy of the Medication Diary will be given to patients whose dose is reduced due to adverse events. Patients should log in their daily dose onto the diary, including missed, skipped, or vomited doses. If the patient vomits after taking the tablets, the dose is replaced only if the tablets can actually be seen and counted. If a patient misses a dose, he or she should be instructed to resume dosing with the next scheduled dose.  
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5.7.1 CTEP agents 5.7.1.1 Erlotinib  
1) Erlotinib will be administered at a dose of 150 mg once daily every three weeks.  
2) Tablets should be taken once daily preferably in the morning with up to 200 mL of water 1 hour before or 2 hours after food.  
3) Patients should wear sunscreen protection, hat, and long sleeves to avoid sun as it can exacerbate skin rash.  
4) Patients should be instructed to store Erlotinib at room temperature. 5) Patients should be advised to drink plenty of water or take rehydration fluids to avoid dehydration if diarrhea occurs.
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5.7.1.2 AZD6244 Hydrogen Sulfate 1) AZD6244 hydrogen sulfate will be administered at a dose of 75 mg twice  
  
  
daily (BID), approximately 12 hours apart, every three weeks.  
2) Advise the patient to take AZD6244 doses on an empty stomach (no food or  
  
drink other than water for 1 hour before or 2 hours after dosing).  
3) Patients should be instructed to store AZD6244 at room temperature. 4) Patients should be advised to drink plenty of water or take rehydration fluids to avoid dehydration if diarrhea occurs.  
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5) Patients should avoid excessive sun exposure and use adequate sunscreen protection if sun exposure is anticipated.
5.7.1.3 MK-2206  
1) MK-2206 will be administered orally at a dose of 200 mg weekly every four weeks.  
2) Patients should take MK-2206 - 2 hours before or after a meal. 3) Patients should be instructed to store MK-2206 at room temperature.  
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4) Patients should be advised to drink plenty of water or take rehydration fluids to avoid dehydration if diarrhea occurs.
5.7.1.4 Lapatinib  
1) Lapatinib will be administered orally at a dose of 1500 mg daily every three weeks.  
2) Patients should take Lapatinib - 1 hour before or after a meal. 3) Patients should be instructed to store Lapatinib at room temperature. 4) Patients should be advised to drink plenty of water or take rehydration fluids to avoid dehydration if diarrhea occurs.
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5) Routine monitoring for cardiac function (ECHO/MUGA) should be performed at baseline and every other cycle of treatment.
5.7.2 Other agents 5.7.2.1 Sunitinib  
1) Sunitinib will be administered orally at a dose of 50 mg daily for 4 consecutive weeks followed by 2 weeks of rest (drug holiday) with no sunitinib every 6 weeks.  
2) Patients will take sunitinib once daily in the morning, with or without food, as desired. 3) Patients should be instructed to store Sunitinib at room temperature. 4) Patients should be advised to drink plenty of water or take rehydration fluids to avoid dehydration if diarrhea occurs.  
5) Because hypertension is a known and potentially serious but rare adverse event associated with sunitinib malate treatment, patients will have their blood pressure monitored and recorded weekly during the first cycle of therapy, either at the doctor's office or using any calibrated electronic device (such as those found at a local drug store or pharmacy). (See Section 6 for hypertension management and dose reduction guidelines.)
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6) Routine monitoring for cardiac function (ECHO/MUGA) should be performed at baseline and then every other cycle of treatment in the following groups of patients: (1) those entering the trial with NYHA Class II cardiac dysfunction (see Appendix D), (2) those with a history of Class II heart failure who are asymptomatic on treatment, and (3) in those previously exposed to anthracyclines or thoracic irradiation if the heart was included in the radiotherapy port. Routine cardiac monitoring is not required in patients with no known cardiac dysfunction at entry or in the absence of clinically observed adverse cardiac events.  
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7) Although adrenal gland insufficiency is rarely seen with sunitinib treatment, patients should be clinically followed for the signs and symptoms of this complication, especially
(1) patients with comorbidities associated with adrenal dysfunction, (2) patients with preexisting adrenal insufficiency (primary or secondary), and (3) patients with concomitant stress (e.g., fever, infection, bleeding, serious accident, surgery) that may precipitate overt adrenal insufficiency in the presence of subclinical sunitinib-induced adrenal toxicity. If clinically indicated, objective testing for adrenal gland function should be conducted.  
8) Patients with bulky solid tumors should be monitored closely for pneumothorax, intestinal fistulae, or intestinal perforation in the event of rapid tumor destruction.  
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9) Patients should be alerted to the possibility that sunitinib capsules can cause a yellow discoloration of the skin on direct contact. If this happens, the patient should wash immediately with soap and water.
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5.8 general concomitant medication and

5.8.1 General Guidelines: Concomitant Medications D
A concomitant medication is any medication a patient entering the trial is using and is expected to continue using for some portion of the trial as well as any medication the patient uses during the course of the trial. Study drugs are not considered concomitant medication. All concomitant medications recorded at trial entry must have a related, ongoing concomitant illness listed under the medical history at the time of patient entry into the trial unless the medication is used for prophylaxis. Patients may continue to use any ongoing medications not prohibited by the protocol. All prescription and over-the-counter medications at trial entry as well as any new medications started during the trial must be documented. The documentation should continue until 30 days from the end of the last study drug treatment. No other anti-cancer therapy including chemotherapy, radiation therapy, hormonal cancer therapy and immunotherapy, or experimental medications are permitted while the patients are receiving treatment under one of the targeted therapy arms of this trial. Any disease progression that requires other specific anti-tumor therapy will be cause for discontinuation from study medication. Patients who are receiving steroids for complications of their primary malignancy may enroll on the study and continue receiving steroids as long as needed. Because there is a potential for interaction of all of the medications used in the experimental arms, with other concomitantly administered drugs through the cytochrome P450 system, the case report form (CRF) must capture the concurrent use of all other drugs, over-the-counter medications, or alternative therapies. The Principal Investigator should be alerted if the patient is taking any agent known to affect or with the potential to affect selected CYP450 isoenzymes. A
comprehensive list of CYP3A4 inhibitors, inducers, and substrates is provided (see Appendix F). In addition, patients and their caregivers should be provided the patient information sheet
(see **Appendix G**) describing potential interactions of the study agents with other drugs, remedies, and medications.  
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Additionally, the patient's smoking history should be documented in the CRF, including the number of packs smoked/day (if a current smoker).
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5.8.1.1 diarrhea

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Diarrhea should be treated with the following regimen: loperamide (4 mg PO) at onset of symptoms, followed by 2 mg loperamide every 2 hours while awake (or 4 mg PO every 4 hours while sleeping) up to a maximum of 16 mg loperamide per day.  
5.8.1.2 Nausea and vomiting The nausea and vomiting that may occur with investigational agents should be managed through the use of appropriate simple supportive measures (e.g., prochlorperazine or metoclopramide).
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5.8.1.3 hand-foot syndrome

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This may be treated with topical emollients (such as Aquaphor), topical or systemic steroids, and/or antihistamine agents. Vitamin B6 (pyridoxine; 50-150 mg orally each day) may also be used. Avoid exposure to heat, hot water, pressure, or friction. Use of soft, well-fitting shoes may help, as may use of acetaminophen if needed for analgesia.
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5.8.1.4 rash

Rash should be treated with standard acne therapies, including topical and oral antibiotics used to treat acne such as the following: minocycline, topical tetracycline, topical clindamycin, topical silver sulfadiazine, diphenhydramine, or oral prednisone (short course).  
5.8.1.5 Other protective / preventative measures  
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Patients on Erlotinib should wear sunscreen protection, hat, and long sleeves to avoid sun as it can exacerbate skin rash.  
5.8.1.5.1 Myelossupression related complications Patients with neutropenic fever or infection should be evaluated promptly and treated with IV antibiotic therapy or therapeutic colony-stimulating factors as appropriate following the ASCO guidelines [J Clin Oncol 18(20):3558-85, 2000]. Packed red blood cell and platelet transfusion should be administered as clinically indicated. Erythropoietic agents may be used at the discretion of the treating physician.  
5.8.1.5.2 Additional recommendations for patients in Sunitinib arm
- Use of agents with proarrhythmic potential (terfenadine, quinidine, procainamide, disopyramide, sotalol, probucol, bepridil, haloperidol, risperidone, indapamide, and flecainide) is not permitted during treatment with this drug. A comprehensive list of agents with proarrhythmic potential can be found at http://torsade.org .
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- Sunitinib is primarily metabolized by liver enzymes, particularly CYP3A4. Coadministration of potent inhibitors or inducers of this enzyme can result in significant changes in exposure to sunitinib (e.g., a mean 1.8-fold increased exposure with ketoconazole and a mean 4-fold decrease with rifampin). For this reason, use of the following agents is not permitted before or during enrollment in this arm of the study:  
| azole antifungals (ketoconazole,                                                                                                                                                                                                                      | Verapamil                                                                            |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------|
| itraconazole)                                                                                                                                                                                                                                         | O                                                                                    |
| clarithromycin                                                                                                                                                                                                                                        | HIV protease inhibitors (indinavir,  saquinavir, ritonavir, atazanavir,  nelfinavir) |
| erythromycin                                                                                                                                                                                                                                          | Delavirdine                                                                          |
| diltiazem Inducers - prohibited 12 days before dosing and during study. I rifampin Phenytoin rifabutin St. John's wort carbamazepine Efavirenz phenobarbital Tipranavir - Steroid use is not recommended during sunitinib treatment unless absolutely |                                                                                      |  
- Steroid use is not recommended during sunitinib treatment unless absolutely necessary (e.g., for treatment of adverse events or protocol-required premedication) because many steroids (e.g., prednisone, prednisolone, dexamethasone, etc.) effectively lower sunitinib exposure through CYP3A4 interactions.  
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- The use of coumarin-derivative anticoagulants such as warfarin (Coumadin®) is not recommended, although doses of up to 2 mg daily are permitted for prophylaxis of thrombosis.  
5.8.1.5.3 Additional recommendations for patients in AZD6244 arm
- Ophthalmologic exam (including slit-lamp) - to be performed in patients experiencing visual disturbances while in the trial.  
- Echocardiogram or MUGA scan (measurement of LVEF) - to be performed in patients with symptoms (AEs) suggestive of cardiac impairment (congestive heart failure, oedema, dyspnea).  
- Decreases in LVEF from baseline (if known) may be investigated according to the algorithm (note- this appears as a word doc in the in AZD6244 ISS study guide)
- All new dyspnea AEs or worsening of pre-existing dyspnea AEs should be followed according to the dyspnea algorithm (note this appears in the AZD6244 ISS study guide)
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5.9 **Protocol Evaluation**  
5.9.1 Prior to each treatment cycle (please refer to Section 5.3 for definition of a cycle):
5.9.1.1 SOAP progress note.  
5.9.1.2 Laboratory examination:
5.9.1.2.1 Hematological Profile: CBC with differential and platelet count.  
5.9.1.2.2 Biochemical Profile: Sodium, potassium, chloride, CO2, BUN, creatinine, glucose, AST, ALT, alkaline phosphatase, bilirubin, albumin, total protein, LDH, calcium, phosphorous and magnesium.  
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5.9.1.3 Vital signs including weight. 5.9.2 Restaging and Imaging:
Restaging will be performed at the end of every two cycles, +/- 1 week, as defined for each treatment arm. Therefore, restaging will be performed every 6 weeks +/- 1 week for the Erlotinib, AZD6244, and Lapatinib arms; every 8 weeks +/- 1 week for the MK-2206 arm, and every 12 weeks +/- 1 week for the Sunitinib arm. Imaging modalities will consist of CT or MRI, as appropriate for disease evaluation. The use of FDG-PET will be allowed but it would be considered exploratory and its results will not be used for treatment decisions.  
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5.10 duration of therapy /

In the absence of treatment delays due to adverse events, treatment under any of the investigational arms (Erlotinib, AZD6244, MK2206, Lapatinib and Sunitinib) may continue until one of the following criteria applies:
- Disease progression as defined by Section 13.  
- Intercurrent illness that prevents further administration of treatment. - Delay of treatment due to toxicity of ≥3 weeks. - Unacceptable adverse event(s)*.  
- Non-compliance to therapy regimen.  
- Pregnancy  
  
- Patient decides to withdraw from the study arm or stop therapy. - Deterioration of the patient's condition that render further treatment unacceptable in the judgment of the investigator.
* Patients removed from study arm due to unacceptable adverse events, will continue to be followed in clinic, at least every 4 weeks until all adverse events have resolve to grade I or less.
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5.11 duration of follow up

All patients that are not receiving active investigational treatment (Erlotinib, AZD6244, MK2206, Lapatinib and Sunitinib), including those on the NOS arm and those deemed as "Screen Failures," will continue to be followed until death or the patient decides to withdraw from the study. These patients will be followed either with clinic visits or phone interviews every 4 months (+/- 2 months). If patient is receiving treatment at an outside facility, pertinent medical records should be sent to the PI at the participating institution for data collection. The following information will be collected:
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- Date of follow up
- Is patient dead or alive?  
- If dead, document exact date of death.  
o Drug name(s)  
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- Further chemotherapy / biotherapy treatment(s)
o Date(s) of administration (month/year)
o Response to treatment
- Document date of disease progression
- Document ECOG PS
* No toxicity information will be collected for patients being followed in the NOS arm.
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5.12 off study criteria

Patients will be removed from study for:
- Screening failure  
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- Death - Patient decides to withdraw from the study - At the investigator's discretion - Lost to follow-up The reason for study removal and the date the patient was removed will be documented in the Case Report Form.  
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5.13 off-study procedure

Authorized staff must notify Central Registration Office (CRO) when a subject is taken offstudy. A Participant Status Updates Form from the web site
(http://home.ccr.cancer.gov/intra/eligibility/welcome.htm) main page must be completed and  
sent via encrypted email to: NCI Central Registration Office (HOIS) ncicentralregistrationl@mail.nih.gov.
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6 dosing delays/dose modifications

Patients enrolled in one of the experimental study arms may continue to receive additional cycles of therapy provided that the patient meets the following criteria on Day 1 of each cycle:
- ANC > 1,000/mcL  
- Platelets > 100,000/mcL
- Non-hematologic toxicity recovered to < grade 2 (or tolerable grade 2 or baseline)  
- No evidence of progressive disease
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In the event of an adverse event at least possibly related to the agent, the doses of such agent should be adjusted according to the guidelines shown in the Dose Delays / Dose Modifications tables shown below (Sections 6.1 and 6.2). If an adverse event is not covered in such tables, doses may be reduced or held at the discretion of the investigator for the subject's safety. Subjects with adverse events that are manageable with supportive therapy may not require dose reductions (e.g., nausea/vomiting may be treated with antiemetics, diarrhea may be treated with loperamide, and electrolyte abnormalities may be corrected with supplements rather than by dose reduction).  
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Subjects will be withdrawn from the study arm if they fail to recover to CTC Grade 0-1 or tolerable grade 2 (or within 1 grade of starting values for pre-existing laboratory abnormalities) from a treatment-related adverse event within 21 days OR they experience agent related adverse events requiring dose modification despite two previous dose reductions (i.e. would require a 3rd dose reduction) unless the investigator and CTEP monitor agree that the subject should remain in the study arm because of evidence that the patient is/may continue deriving benefit from continuing study treatment (i.e. patient has PR, CR, SD > 3 months). The appropriate reduced dose will be determined after discussion between the principal investigator and CTEP monitor.  
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6.1 ctep agents 6.1.1 erlotinib

Table 6. Erlotinib Monotherapy Dose Level Reductions  
| Dose Level            | Erlotinib Dose   |
|-----------------------|------------------|
| Starting Dose         | 150 mg/day       |
| First Dose Reduction  | 100 mg/day       |
| Second Dose Reduction | 75 mg/day        |  
  
| Table 7. Dosage Modification Criteria for Erlotinib–related Toxicities Erlotinib dosage  Guideline for management   |                                                                                                                                                                                                                                   |                                                                                                                                                            |                 |
|---------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------|
| Toxicity                                                                                                            | Grade                                                                                                                                                                                                                             | modification*                                                                                                                                              |                 |
| Keratitis                                                                                                           | 1                                                                                                                                                                                                                                 | None                                                                                                                                                       | No intervention |
| 2 (if < 14                                                                                                          | None                                                                                                                                                                                                                              | Preservative-free artificial tears,                                                                                                                        |                 |
| days)                                                                                                               | ointments, and/or other therapies  as clinically indicated, with a                                                                                                                                                                |                                                                                                                                                            |                 |
| 2 (if >14                                                                                                           | Hold until recovery to ≤ grade 1                                                                                                                                                                                                  | follow-up examination within                                                                                                                               |                 |
| days)                                                                                                               | And then                                                                                                                                                                                                                          | 2 weeks                                                                                                                                                    |                 |
| Reduce 1 dose level                                                                                                 |                                                                                                                                                                                                                                   |                                                                                                                                                            |                 |
| V ≥3                                                                                                                | Hold until recovery to ≤ grade 1 And then  Reduce 1 dose level*                                                                                                                                                                   |                                                                                                                                                            |                 |
| Diarrhea                                                                                                            | 1                                                                                                                                                                                                                                 | None                                                                                                                                                       | No intervention |
| O                                                                                                                   |                                                                                                                                                                                                                                   |                                                                                                                                                            |                 |
| 2                                                                                                                   | None if tolerable  If not tolerable, hold until  resolution to grade ≤ 1, then  resume at the same dose.  If intolerable grade 2 recurs  after resumption, hold until  resolution to grade ≤ 1 and  resume with 1 dose reduction. | Loperamide (4 mg at first onset,  followed by 2 mg every 2–4 hrs  until diarrhea free for 12 hrs)                                                          |                 |
| ≥ 3  (despite  optimal  loperamide  use)                                                                            | Hold until recovery to ≤ grade 1  And then  Reduce 1 dose level* I                                                                                                                                                                |                                                                                                                                                            |                 |
| Rash                                                                                                                | 1                                                                                                                                                                                                                                 | None                                                                                                                                                       | No intervention |
| 2                                                                                                                   | None if tolerable  If not tolerable, hold until  resolution to grade ≤ 1, then  resume at the same dose.  If intolerable grade 2 recurs  after resumption, hold until  resolution to grade ≤ 1 and  resume with 1 dose reduction. | Any of the following:  minocycline, topical tetracycline  or clindamycin, topical silver  sulfadiazine, diphenhydramine,  oral prednisone (short course) D |                 |
| ≥ 3                                                                                                                 | Hold until recovery to ≤ grade 1 And then  Reduce 1 dose level                                                                                                                                                                    |                                                                                                                                                            |                 |  
| Bilirubin                                                                                                                                                                                                             | ≥3 x ULN                                                                                          | Hold until grade ≤2  And then  Reduce 1 dose level                                                 |                          |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------|--------------------------|
| Liver  transamin ase                                                                                                                                                                                                  | > 5 x ULN                                                                                         | Hold until grade ≤2  And then  Reduce 1 dose level                                                 |                          |
| V                                                                                                                                                                                                                     |                                                                                                   |                                                                                                    |                          |
| Signs and symptoms of                                                                                                                                                                                                 | Hold pending diagnosis                                                                            |                                                                                                    |                          |
| interstitial pneumonitis                                                                                                                                                                                              | Permanently discontinue if  diagnosis is confirmed and  considered possibly related to  erlotinib | Patient should be thoroughly  evaluated, closely monitored, and  supported as clinically indicated |                          |
| Other                                                                                                                                                                                                                 | ≥ 2 prolonged  clinically                                                                         |                                                                                                    |                          |
| toxicity                                                                                                                                                                                                              | significant  toxicity                                                                             | Hold until recovery to ≤ grade 1 And then  Reduce 1 dose level*                                    | Treatment as appropriate |
| *if dose has been previously held for grade 2 rash or diarrhea, and grade 2 symptoms recur, OR if  the patient finds the symptoms unacceptable, hold dose until recovery to ≤ grade 1 and then reduce  dose one level |                                                                                                   |                                                                                                    |                          |  
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