araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: DNA Analysis of Tumor Tissue Samples From Patients With Human Papilloma Virus-Associated Cancer of the Oropharynx

Summary: RATIONALE: Studying samples of tumor tissue in the laboratory from patients with cancer may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This laboratory study is looking at the DNA in tumor tissue samples from patients with human papilloma virus-associated cancer of the oropharynx.

Detailed description: OBJECTIVES:
  -  Analyze PIK3CA expression and mutation and p110α amplification and expression in tumor tissue samples from patients with human papilloma virus positive (HPV+) and human papilloma virus negative (HPV-) squamous cell carcinoma (SCC) of the oropharynx.
  -  Determine proliferation and survival after PI3K inhibition in HPV(+) and HPV(-) oropharyngeal SCC cell lines and in HPV E6 and E7 expressing cells.
  -  Determine proliferation and survival after PI3K inhibition in short-term cultures of tumor tissue samples from patients with HPV(+) and HPV(-) primary SCC of the oropharynx.
  OUTLINE: Previously collected tumor tissue samples are analyzed for HPV DNA by PCR amplification and direct sequencing of PCR products; expression of E6 protein and relative expression of PIK3CA by qRT-PCR; amplification of PIK3CA by Southern blotting; mutation of PIK3CA; expression of p110α, phospho-AKT, total AKT, and FOXO1 by polyacrylamide gel electrophoresis (PAGE) and immunoblotting; and the effect of PI3K inhibition on cell cycle and apoptosis by flow cytometry. Pharmacological studies are performed on oropharyngeal squamous cell carcinoma cell lines and short-term cultures and HPV E6 and E7 expressing cells using LY 294002 in vitro to analyze response to PI3K inhibition. Results of response to PI3K inhibition will be correlated with HPV status, PIK3CA expression, amplification, and mutation, and p110α expression.
  PROJECTED ACCRUAL: A total of 20 HPV(+) and 20 HPV(-) tumor tissue specimens from patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Undergoing operative procedures for biopsy and/or resection of squamous cell carcinoma (SCC) of the oropharynx
  -  Tumor tissue sample available from the Head and Neck Tissue Repository and Clinical Database of Vanderbilt University
  -  No tumors with human papilloma virus (HPV) DNA sequences but no expression of E6
  PATIENT CHARACTERISTICS:
  -  See Disease Characteristics
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Identifying Prognostic Factors in Patients Receiving Tegafur-Uracil for Stage II Colon Cancer That Was Completely Removed By Surgery

Summary: RATIONALE: Studying samples of tumor tissue in the laboratory from patients with cancer may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors predict which patients will respond to treatment.
  PURPOSE: This laboratory study is looking at prognostic factors in patients receiving tegafur-uracil for stage II colon cancer that was completely removed by surgery.

Detailed description: OBJECTIVES:
  -  Identify the prognostic factors in patients with curatively resected stage II colon cancer receiving adjuvant chemotherapy with tegafur-uracil.
  -  Identify predictive factors of chemosensitivity to this regimen in these patients.
  OUTLINE: Available tumor tissue samples are analyzed by real-time reverse transcriptase-PCR for TS, DPD, TP, OPRT, VEGF, cyclooxygenase-2, and FPGS; by PCR for microsatellite instability and genomic deletions on chromosome arm 18q; and pathologically for tumor budding, Crohn's-like lymphoid reaction, category of extent of poor differentiation, and fibrotic cancer stroma. The candidate prognostic and predictive markers are analyzed for correlation with disease-free survival, relapse-free survival, and overall survival of patients.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed adenocarcinoma of the colon or rectosigmoid
  -  Stage II disease
  -  Must be registered on clinical trial TMDU-BRI-CC-05-01
  -  Must have resected tumor tissue available
  -  No hereditary colorectal cancer
  PATIENT CHARACTERISTICS:
  -  ECOG performance status 0-1
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Biomarkers in Samples From Patients With Chronic Lymphocytic Leukemia Treated on Clinical Trial ECOG-2997

Summary: RATIONALE: Studying samples of cells in the laboratory from patients with cancer may help identify biomarkers related to cancer. It may also help doctors learn how patients respond to treatment.
  PURPOSE: This laboratory study is analyzing samples of cells from patients with chronic lymphocytic leukemia who were treated on clinical trial ECOG-2997.

Detailed description: OBJECTIVES:
  -  To analyze the expression of a variety of informative molecules using a unique high-resolution flow cytometric immunophenotyping technology in samples from patients with chronic lymphocytic leukemia enrolled in clinical trial ECOG-2997.
  OUTLINE: Cell samples are analyzed for the following prognostic biomarkers: ZAP-70, phospho-Syk, phospho-GSK-3β, phospho-Akt, phospho-ZAP-70, cyclin D1, cyclin D2, p21cip1, phospho-ReIA, IkappaBα, Bax, Mcl-1, PTEN, phospho-Erk1/2, and phospho-MEK1/2. Biomarker signals are amplified using enzymatic amplification staining to obtain high resolution detection of cell-surface markers on leukemic cells. Biomarker expression levels are measured using fluorescence activated cell sorting analysis. Relationships between clinical outcomes, standard flow cytometric analysis, cytogenetic studies, and high resolution immunophenotyping will also be assessed.

Eligibility: DISEASE CHARACTERISTICS:
  -  Stored frozen viable cells from patients with chronic lymphocytic leukemia treated on clinical trial ECOG-2997
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Study of PF-05212384 (Also Known as PKI-587)Administered Intravenously To Subjects With Solid Tumors

Summary: This is a two-part study of a compound called PF-05212384 (also known as PKI-587). The purpose of part 1 is to identify the Maximum Tolerated Dose (MTD) of PF-05212384 using a Continual Reassessment Method (CRM). Part 1 will include subjects with any solid tumor. In Part 2 two cohorts will be enrolled. One cohort will assess safety, tolerability and preliminary efficacy in 20 subjects at the MTD and will include subjects with breast cancer, ovarian cancer, endometrial cancer, colorectal cancer renal cancer or glioblastoma (a type of brain tumor). The other cohort will include 5 to 15 subjects with any type of tumor who consent to provide tumor biopsies while participating in the study.


Eligibility: Inclusion Criteria:
  -  Pathologic diagnosis of any solid tumor
  -  Incurable cancer, with disease progression following at least 1 therapy with no further standard treatment available in the opinion of the investigator.
  -  At least 1 evaluable lesion per RECIST criteria
  Exclusion Criteria:
  -  Clinically unstable primary or metastatic CNS tumors
  -  Subjects with known diabetes
  -  QTc interval greater than 470 ms.

Relevance to patient case: possibly relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: A Study of the Safety and Pharmacology of GDC-0941 in Combination With Erlotinib in Patients With Advanced Solid Tumors

Summary: This is an open-label, multicenter, Phase Ib dose-escalation study to assess the safety, tolerability, and pharmacokinetics (PK) of oral (PO) GDC-0941 administered in combination with PO erlotinib in patients with advanced solid tumors and patients with locally advanced or metastatic non-small cell lung cancer (NSCLC) who have failed at least one prior chemotherapy regimen.


Eligibility: Inclusion Criteria:
  -  Documented locally advanced or metastatic solid tumors for which standard therapy either does not exist or has proven ineffective or intolerable (dose-escalation stage only)
  -  Documented locally advanced or metastatic NSCLC in patients who have failed at least one prior chemotherapy-based regimen for incurable disease (cohort-expansion stage only)
  -  Adequate organ function as assessed by laboratory tests
  -  Evaluable disease or disease measurable per Response Evaluation Criteria in Solid Tumors (RECIST)
  -  Agreement to use an effective form of contraception for the duration of the study
  Exclusion Criteria:
  -  Any anti-cancer therapy (e.g., chemotherapy, biologic therapy, or hormonal therapy) within a specified timeframe prior to first study treatment
  -  Prior treatment with PI3K pathway-inhibiting agents (cohort-expansion stage only)
  -  History of Grade >= 3 fasting hyperglycemia or diabetes requiring regular medication
  -  Current clinically significant and uncontrolled systemic disease (e.g., cardiovascular, pulmonary, or metabolic)
  -  History of clinically significant cardiac or pulmonary dysfunction
  -  History of malabsorption syndrome or other condition that would interfere with enteral absorption
  -  Clinically significant history of liver disease
  -  Any condition requiring full-dose anticoagulants, such as warfarin, heparin, or thrombolytic agents
  -  Active autoimmune disease and/or need for corticosteroid therapy
  -  Known brain metastases that are untreated, symptomatic, or require therapy
  -  Pregnancy, lactation, or breastfeeding

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Safety of BKM120 Monotherapy in Advanced Solid Tumor Patients

Summary: This is a first-in-man, phase I clinical research study with BKM120, a potent and highly specific oral pan-class I phosphatidylinositol-3-kinase (PI3K) inhibitor. The study consists of a dose escalation part followed by a MTD expansion part.
  Once the MTD has been defined, the MTD expansion part will be opened for enrollment.


Eligibility: Inclusion Criteria:
  All patients:
  -  Histologically-confirmed advanced solid tumors
  -  Progressive, recurrent unresectable disease
  -  World Health Organization (WHO) Performance status ≤ 2
  -  No history of primary brain tumor or brain metastases
  MTD Expansion part:
  -  Histologically-confirmed advanced solid tumors
  -  Progressive, recurrent unresectable disease
  -  World Health Organization (WHO) Performance status ≤ 2
  -  No history of primary brain tumor; no brain metastases unless asymptomatic and clinically stable for ≥ 3 months
  -  Patients with genetic or molecular alteration of the PI3K pathway
  Exclusion Criteria:
  -  Prior treatment with a PI3K inhibitor
  -  History of or active major depressive episode, bipolar disorder, schizophrenia, or history of suicidal attempt or ideation
  -  No clinically manifest diabetes mellitus (treated and/or with clinical signs)
  -  No acute or chronic renal disease
  -  No acute or chronic liver disease
  -  No acute or chronic pancreatitis
  -  No unresolved diarrhea
  -  No impaired cardiac function or clinically significant cardiac diseases such as ventricular arrhythmia, congestive heart failure, uncontrolled hypertension
  -  No acute myocardial infarction or unstable angina pectoris within the past 3 months
  -  Not pregnant or nursing and fertile patients must use barrier contraceptives
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: definitely relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Initiation of Colon Cancer Screening in Veterans or "Start Screening Now"

Summary: Initiation of colon cancer screening in veterans is a theory-based stepped intervention to increase first time colorectal cancer screening (CRCS) among male and female veterans age 50 and over.

Detailed description: Colorectal cancer (CRC) is the 2nd leading cause of cancer deaths in the US and risk increases with age. Colorectal cancer screening (CRCS) offers the possibility of both early detection and prevention. For those at average risk, CRCS beginning at age 50 is recommended. However, awareness and use of CRCS tests are low. We propose to conduct a randomized controlled trial to develop and test stepped interventions to increase initial uptake of CRCS in a nationally-representative, ethnically-diverse sample of male and female veterans. Our specific aims are to: (1) develop and pre-test stepped intervention components that are theory and evidence-informed; (2) implement and evaluate the process, efficacy, and cost-effectiveness of stepped interventions to increase an initial CRCS among male and female veterans aged 50-64 years; and (3) analyze the association between predictor variables and CRCS initiation and the mediating and moderating effects of the interventions, after each step. In Step 1, we will evaluate a theory-based minimal cue delivered by a letter, telephone call, or automated telephone call compared with a survey-only control group to determine whether the 3 different delivery channels are equally efficacious and cost-effective. Minimal cues are a cost-effective method that prompts to action those more willing to change and are easy to disseminate in real-world settings. Persons who do not complete CRCS in Step 1 will be randomized in Step 2 to more intensive interventions that address resistance. In Step 2 we will determine whether a theory-based, tailored telephone intervention, using principles of Motivation Interviewing, is effective when delivered as part of a sequential intervention process in which early adopters have been removed from the population. Step 2 also will determine whether an automated approach, telephone-linked communication (TLC), is as effective as a telephone counselor in promoting initiation of CRCS. Steps 1 and 2 together will address the important issue of the "dose" needed to encourage completion of CRCS. After each step, we will examine the mediating and moderating effects of the intervention to identify determinants of completion. For cancer screening intervention research to have the broadest public health impact, interventions must have the potential for dissemination. We designed our trial to move us toward the goal of disseminable interventions with evidence of external validity.

Eligibility: Inclusion Criteria:
  -  Male or Female Veteran age 50 to 64
  Exclusion Criteria:
  -  Prior CRCS
  -  History of colon or bowel cancer, Crohn's disease, ulcerative colitis
  -  History of colon polyps
  -  Currently active duty military
  -  Outside of age range

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Low-Literacy Physician-Patient Intervention Promoting Colorectal Cancer Screening

Summary: The purpose of this study is to evaluate the effectiveness of a low literacy, physician and patient-directed intervention to promote colorectal cancer (CRC) screening among the medically underserved.

Detailed description: This study will test the separate and combined effect of two of these interventions: 1) a provider communication skills training using a continuous quality improvement (CQI) framework, and 2) a brief, multimedia Patient Education Program (PEP) that incorporates plain language, graphic design, and audio voice-over to overcome literacy limitations. Our provider intervention has demonstrated efficacy to significantly improve CRC screening recommendation rates. Our multimedia program has also been field tested among patients with limited literacy and was able to improve patient knowledge and intention to receive screening.
  We will implement both provider-only and combined provider-patient strategies within a federally qualified health center network to determine the most effective and efficient approach to promote CRC screening in these settings. Results from the study, supplemented by cost analyses and the process evaluation will directly inform translational strategies for cancer prevention within difficult community-based healthcare settings.

Eligibility: Inclusion Criteria:
  -  Patients aged 50-75 years of age (in month 1 of the study)
  -  Patients have had two or more visits to the clinic during the past two years
  -  ACCESS Community Health Network patients
  -  University of Illinois Hospital & Health Sciences System patients
  -  Patients ages 50 - 75 as of the start of the intervention study
  -  English or Spanish-Speaking
  Exclusion Criteria:
  -  Patients <50 or > 75 years of age
  -  Patients who have had fewer than two or more visits to the clinic during the past two years
  -  Personal history of CRC or colorectal polyps, or of inflammatory bowel disease and a family history with a first-degree relative with CRC or colorectal polyps.
  -  Unable to speak English or Spanish
  -  Compliant with CRC screening (FOBT or FIT within the past year; flexible sigmoidoscopy within past 5 years; colonoscopy within past 10 years)

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Neoadjuvant Treatment of Colon Cancer

Summary: This study will investigate
  -  the effect of preoperative combination chemotherapy in patients with locally advanced colon cancer with mutation in the KRAS, BRAF or PIK3CA gene
  -  the effect of preoperative combination chemotherapy in combination with biological treatment in patients without mutation in the KRAS, BRAF or PIK3CA gene.


Eligibility: Inclusion Criteria:
  -  Histologically verified locally advanced T3 or T4 colon cancer assessed by CT scan
  -  Analysis of KRAS, BRAF, PIK3CA
  -  Age ≥18 år
  -  Performance status ≤ 2
  -  Hematology
  -  ANC ≥ 1.5x10^9/l. Thrombocytes ≥ 100x10^9/l.
  -  Biochemistry
  -  Bilirubinaemia ≤ 3 x UNL. ALAT ≤ 5 x UNL
  -  Consent to translational research
  -  Fertile women must present a negative pregnancy test and use secure birth control during and 3 months after treatment.
  -  Written and orally informed consent.
  Exclusion Criteria:
  -  Clinically significant cardiovascular disease (including myocardial infarction, unstable angina, symptomatic congestive heart failure, serious uncontrolled cardiac arrhythmia) ≤ 1 year before enrollment, active severe infections or other concurrent disease.
  -  Peripheral neuropathy NCI grade >1
  -  Other malignant disease within 5 years prior to enrollment, except basal cell squamous carcinoma of the skin and cervical carcinoma-in-situ
  -  Other investigational treatment within 30 days prior to treatment start
  -  History of interstitial lung disease e.g. pneumonitis or pulmonary fibrosis or evidence of interstitial lung disease on baseline chest CT scan.
  -  Bleeding tumors
  -  Hypersensitivity to one or more of the substances

Relevance to patient case: definitely relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: Pemetrexed and Gemcitabine for Treatment Resistant Patients With Metastatic Colorectal Cancer and KRAS Mutations

Summary: This study aims to investigate the efficacy and safety of the combination of pemetrexed and gemcitabine in heavily pre-treated, chemotherapy resistant colorectal cancer patients with KRAS mutations.


Eligibility: Inclusion Criteria:
  -  Histologically verified adenocarcinoma in colon or rectum
  -  Age >18
  -  Metastatic colorectal cancer progressed after chemotherapy regimens containing fluoropyrimidines, oxaliplatin and irinotecan.
  -  KRAS mutation in primary tumour or metastasis.
  -  Measurable disease according to RECIST
  -  ECOG performance status 0, 1 or 2
  -  Adequate function of liver, kidneys and bone marrow measured by biochemistry (max. 2 weeks before enrolment)
  -  EDTA clearance: Uncorrected GFR > 45 ml/min.
  -  Neutrophilocytes ≥1.5 x 10^9/l, leukocytes ≥3.0 x 10^9/l, thrombocytes ≥100x10^9/l
  -  ALAT ≤ 3 x upper normal value (ULN), bilirubin ≤ 3 x upper normal value, Aptt and INR normal (or 2-3 at AC treatment). (ALAT and basic phosphatase ≤ 5 x upper normal value in case of liver metastases).
  -  Blood samples and paraffin embedded tissue from primary tumour and/or metastases for translational research.
  -  Fertile men and women (women <2 year after last menstruation) must use efficient birth control.
  -  Signed informed consent.
  Exclusion Criteria:
  -  Clinically significant other concurrent disease making the patient unfit for participation in the study according to the investigator.
  -  Other malignant disease within 5 years prior to study enrolment, except from planocellular and basal cell carcinomas in the skin or carcinoma-in-situ cervix.
  -  Other experimental treatment within 30 days prior to treatment start.
  -  Pregnant or breastfeeding women.
  -  Clinical or radiological signs of CNS metastases.
  -  Planned radiation of target lesions.
  -  Concurrent vaccination against yellow fever.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: A Study Of Combined C- MET Inhibitor And PAN-HER Inhibitor (PF-02341066 And PF-00299804) In Patients With Non- Small Cell Lung Cancer

Summary: Lung cancer tumors become resistant to the first generation epidermal growth factor receptor (EGFR) inhibitors erlotinib or gefitinib by changing and increasing the activity of two cell signaling pathways: the cMET pathway and the EGFR pathway. Both resistance mechanisms can occur at the same time, in the same patient and even in the same tumor. This study combines a second generation EGFR inhibitor and a cMET inhibitor to block both these pathways in order to overcome resistance and treat this disease.


Eligibility: Inclusion Criteria:
  -  advanced non small cell lung cancer (dose escalation phase)
  -  acquired resistance to erlotinib or gefitinib (expansion phase)
  -  mandatory entrance biopsy (expansion phase)
  Exclusion Criteria:
  -  interstitial lung disease
  -  unstable brain metastases
  -  leptomeningeal disease

Relevance to patient case: not relevant