araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Study of Ticilimumab in Patients With Metastatic Colorectal Cancer Whose Disease Had Progressed After Treatment

Summary: This study is for patients with metastatic adenocarcinoma arising from the colon or rectum who have received treatment(s) for metastatic disease with subsequent disease progression. Patients who are intolerant to treatment(s) are also included. This is a study for good performance status colorectal cancer patients who have exhausted standard therapy options.


Eligibility: Inclusion Criteria:
  -  Radiographic evidence of metastatic, progressive disease following standard therapies.
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0-1.
  Exclusion Criteria:
  -  Known brain metastases or uncontrolled pleural effusions.
  -  History of chronic inflammatory or autoimmune disease.

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: The Biological Activity of Cediranib (AZD2171) in Gastro-Intestinal Stromal Tumours(GIST).

Summary: To determine the anti-tumour activity and biological effects of cediranib (AZD2171) at a dose of 45mg, primarily in Gastrointestinal Stromal Tumour (GIST) patients who are resistant to imatinib mesylate (current standard therapy) and also in patients with metastatic Soft Tissue Sarcoma (STS) resistant to standard therapy.


Eligibility: Inclusion Criteria:
  -  Histological or cytological confirmation of GIST which is resistant or intolerant to imatinib mesylate, or metastatic STS, which is refractory to standard therapies or for which no standard therapy exists
  Exclusion Criteria:
  -  Patients with type I insulin-dependent diabetes or poorly-controlled type II insulin-independent diabetes.
  -  Patients with a history of poorly controlled high blood pressure

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: A Phase I/II Study of Sunitinib Malate (SU011248) In Patients With Gastrointestinal Stromal Tumor (GIST)

Summary: Phase I;To investigate the clinically recommended dose of Sunitinib malate (SU011248) following multiple oral dosing in the first cycle (4 consecutive weeks and 2 weeks rest) by reviewing the safety and tolerability.
  Phase II;To determine the objective tumor response and the safety of Sunitinib malate (SU011248) at the clinically recommended dose.


Eligibility: Inclusion Criteria:
  -  Patients with histologically-confirmed metastatic or unresectable gastrointestinal stromal tumor (GIST).
  -  Patients previously treated with imatinib mesylate.
  Exclusion Criteria:
  -  Patients who have not recovered from the acute toxic effects of previous antineoplastic therapy or treatment with imatinib mesylate.
  -  Any tumor therapy for gastrointestinal stromal tumor (GIST) discontinued less than 4 weeks prior to starting study treatment. Imatinib mesylate discontinued less than 2 weeks prior to starting therapy.

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Evaluation of Diagnostic Value of Molecular Markers in Renal Cancer

Summary: Renal cancer is frequent and its diagnosis mainly dependant on imaging. More than 50% of renal tumors are currently diagnosed without symptoms. However, 20% of small solid tumors are benign and this percentage is much higher in atypical cystic tumors Bosniak II and III, where 76% and 59% are benign respectively. Determining the malignancy by imaging in these cases is difficult and sometimes impossible. The fine needle aspiration (FNA) cytology or biopsy is necessary. The diagnostic sensitivity and specificity with biopsy are high, but the potential tumor contamination is a major risk. The FNA cytology is simple and safe, but its sensitivity is about 50%. We are conducting a multicentric prospective study to add the molecular markers in FNA cytology as a new diagnostic method in imaging-indeterminate renal tumors.
  Four molecular markers including MN/CA9, vimentin, KIT, and S100A1 will be studied. These four markers have been reported to have a differential diagnostic value in renal tumors. MN/CA9 and vimentin are often found in conventional renal cancers. KIT is frequently expressed in renal oncocytomas and chromophobe renal cancers. S100A1 may further distinguish renal oncocytoma from chromophobe renal cancer. These markers will be analyzed by real time polymerase chain reaction (RT-PCR).
  The aim of this study is to evaluate the diagnostic performance of the association cytology-molecular markers in imaging-indeterminate renal tumors (small solid tumors and cystic tumors ≥ Bosniak III). About 156 patients will be included in five French clinical centers including Saint-Etienne, Marseille, Grenoble, Toulouse, and Nancy.
  The expected results will improve the preoperative diagnostic accuracy in renal tumors.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of kidney tumor < 4 cm
  -  Cystic kidney tumor (Bosniak > IIF)
  -  Consent signed
  Exclusion Criteria:
  -  Benign tumor confirmed
  -  Impossibility to do abdominal pelvic ultra-sound or abdominal thoracic scanner
  -  Contraindication for renal puncture

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: An Open-Label, 18FDG-PET Pharmacodynamic Assessment of the Effect of BIIB021 in Subjects With Gastrointestinal Stromal Tumors (GIST)

Summary: This study will examine the effect of BIIB021 on GIST growth and metabolism.


Eligibility: Inclusion Criteria:
  -  Ability to understand the purpose and risks of the study and provide signed and dated informed consent and authorization to use protected health information (PHI) in accordance with national and local subject privacy regulations.
  -  Age greater than or equal to 18 years at the time of informed consent.
  -  Pathologically confirmed GIST refractory to, intolerant of, or not a candidate for imatinib and sunitinib therapy.
  -  FDG PET standard uptake value (SUVmax; averaged over a maximum of 5 lesions) greater than or equal to 2 at screening.
  -  ECOG performance status of less than or equal to 2.
  -  Lab values consistent with adequate renal hepatic and bone marrow function.
  -  Must utilize effective contraception.
  Exclusion Criteria:
  -  Prior treatment with imatinib, sunitinib, or sorafenib with in 14 days of day 1.
  -  Prior treatment with Hsp90 inhibitors at any time.
  -  Prior antitumor therapies including prior experimental agents, approved antitumor small molecules (excluding imatinib, sunitinib, or sorafenib) and biologics, or radiotherapy with in 28 days or <3 half lives (whichever is longer) before start of BIIB021treatment.
  -  Diabetes treated with insulin and/ or concurrent severe or uncontrolled other medical disease (i.e, systemic infection, hypertension, coronary artery disease, congestive heart failure).
  -  History of/ or predisposition to seizures.

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Kinase Genotyping of Gastro Intestinal Stomach Tumors (GISTs) From Patients Enrolled in Pfizer A6181112 Phase IIIb Trial

Summary: The purpose of this study is to determine the genetic makeup of gastro intestinal stomach tumors (GISTs) from patients enrolled in the A6181112 phase IIIb trial. Tumor samples will be screened for mutations and this information will be used to determine whether the progression-free survival of patients being treated with the cancer medication sunitinib is related to the underlying genotype of their GIST.

Detailed description: In this companion study, we will analyze the genomic DNA from the GIST tumor specimens of patients enrolled in the in the A6181112 phase IIIb trial at participating U.S. and ex-U.S. medical centers. Specifically, GIST samples will be screened for mutations in KIT gene exons 9, 11, 13 and 17, and PDGFRA gene exons 12, 14 and 18, to determine the primary kinase genotype. Subset analyses will be performed and compared with the overall PFS rates observed in patients with primary and secondary imatinib resistance. Based on data from a previous phase I/II trial, our hypothesis is that patients with either primary or secondary imatinib resistance having a KIT exon 9-mutant or WT GIST will have a longer PFS when treated with sunitinib than patients with exon 11-mutant GIST. We further hypothesize that this difference will be observed among patients treated with high-dose imatinib.

Eligibility: Inclusion Criteria:
  -  Patients enrolled in Pfizer A6181112
  Exclusion Criteria:
  -  Patients who do not consent for analysis of their tumor in this companion study

Relevance to patient case: possibly relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Efficacy and Safety of AMN107 in Patients With GastroIntestinal Stromal Tumors (GIST) Who Have Failed Both Imatinib and Sunitinib

Summary: This study will evaluate the efficacy and safety of nilotinib in gastrointestinal stromal tumors patients who failed imatinib and sunitinib therapy.


Eligibility: Inclusion Criteria:
  -  Documented disease progression during imatinib and sunitinib therapy OR intolerance to imatinib and/or sunitinib
  -  At least one measurable site of disease on CT/MRI scan
  -  PS≤2
  -  Normal organ, electrolyte, and bone marrow function
  Exclusion Criteria:
  -  Previous treatment with nilotinib or any other drug in this class or other targeted therapy
  -  Treatment with any cytotoxic and/or investigational drug ≤ 4 weeks prior to study entry
  -  Impaired cardiac function
  -  Use of coumarin derivatives (i.e. warfarin)
  -  Women who are pregnant or lactating
  Other protocol-defined inclusion/exclusion criteria may apply.

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Imatinib Mesylate in Treating Patients With Liver Metastasis From a Gastrointestinal Stromal Tumor

Summary: RATIONALE: Imatinib mesylate may stop the growth of tumor cells by blocking some of the enzymes needed for cell growth.
  PURPOSE: This phase II trial is studying the side effects of imatinib mesylate and to see how well it works in treating patients with liver metastasis from a gastrointestinal stromal tumor.

Detailed description: OBJECTIVES:
  -  To evaluate the safety and efficacy of imatinib mesylate in patients with resectable hepatic metastasis secondary to gastrointestinal stromal tumor.
  OUTLINE: This is a multicenter study.
  Patients receive oral imatinib mesylate daily. Treatment continues in the absence of disease progression or unacceptable toxicity.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of gastrointestinal stromal tumor (GIST)
  -  Hepatic metastasis meeting the following criteria:
  -  No more than 3 hepatic metastases
  -  Clinically diagnosed as surgically resectable with no macroscopic residual tumor
  -  Synchronous hepatic metastasis allowed provided primary tumor is also resectable
  -  No metastatic tumor that requires radiofrequency ablation and/or microwave coagulation therapy to control the disease
  -  No extrahepatic metastasis
  -  No history of GIST recurrence
  PATIENT CHARACTERISTICS:
  -  ECOG performance status 0-1
  -  Leukocyte count ≥ 3,000/μL
  -  Neutrophil count ≥ 1,500/μL
  -  Hemoglobin ≥ 8.0 g/dL
  -  Platelet count ≥ 75,000/μL
  -  Total bilirubin ≤ 2.0 mg/dL
  -  ALT and AST < 120 IU/L
  -  GTP < 210 IU/L
  -  Not pregnant
  -  No poorly controlled diabetes mellitus
  -  No NYHA class III-IV cardiac function
  -  No hepatitis B or hepatitis B carriers
  -  No other malignancy requiring treatment
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics
  -  No prior imatinib mesylate
  -  No prior interventional radiology for metastatic disease
  -  No other concurrent treatment, including surgery or radiotherapy, for metastatic lesions

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Surgery in Treating Patients With Liver Metastasis From a Gastrointestinal Stromal Tumor

Summary: RATIONALE: Surgery may be an effective treatment for liver metastasis from a gastrointestinal stromal tumor.
  PURPOSE: This phase II trial is studying how well surgery works in treating patients with liver metastasis from a gastrointestinal stromal tumor.

Detailed description: OBJECTIVES:
  -  To evaluate the safety and efficacy of surgery in patients with resectable hepatic metastasis secondary to gastrointestinal stromal tumor.
  OUTLINE: This is a multicenter study.
  Patients undergo surgical resection of hepatic metastasis.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of gastrointestinal stromal tumor (GIST)
  -  Hepatic metastasis meeting the following criteria:
  -  Clinically diagnosed as surgically resectable with no macroscopic residual tumor
  -  No more than 3 hepatic metastases
  -  Synchronous hepatic metastasis allowed provided primary tumor is also resectable
  -  Does not require radiofrequency ablation and/or microwave coagulation therapy to control the disease
  -  No extrahepatic metastasis
  -  No history of GIST recurrence
  PATIENT CHARACTERISTICS:
  -  ECOG performance status 0-1
  -  Leukocyte count ≥ 3,000/μL
  -  Neutrophil count ≥ 1,500/μL
  -  Hemoglobin ≥ 8.0 g/dL
  -  Platelet count ≥ 75,000/μL
  -  Total bilirubin ≤ 2.0 mg/dL
  -  ALT and AST < 120 IU/L
  -  GTP < 210 IU/L
  -  Not pregnant
  -  No poorly controlled diabetes mellitus
  -  No NYHA class III-IV cardiac function
  -  No hepatitis B or hepatitis B carriers
  -  No other malignancy requiring treatment
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics
  -  No prior interventional radiology for metastatic disease
  -  No prior or concurrent imatinib mesylate
  -  No other concurrent treatment

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Treatment Patterns in Gastrointestinal Stromal Tumors in the Community Oncology Setting

Summary: This is a retrospective medical record abstraction to evaluate the patterns of care for Gastrointestinal stromal tumors (GIST) in the community setting. Patient demographics and characteristics along with the treatments received will be described. Investigators will establish the percentage of patients who undergo surgery, the percentage of patients who are treated with kinase inhibitors as well as in what setting (adjuvant or metastatic) as well as the duration of therapy. Physician information will also be collected to assess for differences in treatment based on physician or geographical differences.


Eligibility: Inclusion Criteria:
  -  Patients diagnosed with GIST based on ICD-9 code from January 2005 to present will be eligible. This will include current active patients as well as patients who have expired and have medical chart available.

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: An Investigational Drug, PF-02341066, Is Being Studied In Patients With Advanced Non-Small Cell Lung Cancer With A Specific Gene Profile Involving The Anaplastic Lymphoma Kinase (ALK) Gene

Summary: This is a Phase 2 trial that will evaluate the safety and efficacy of PF-02341066 in patients with advanced non-small cell lung cancer with a specific gene profile involving the ALK gene. This trial will also allow patients from a Phase 3 trial who received standard of care chemotherapy (Study A8081007) to receive PF-02341066.


Eligibility: Inclusion Criteria:
  -  histologically or cytologically proven diagnosis of non-small cell lung cancer
  -  positive for the ALK fusion gene (test provided by either a central laboratory. Local laboratory may be used for certain cases)
  -  may have received pemetrexed or docetaxel from previous Phase 3 trial (A8081007) and discontinued treatment due to Response Evaluation Criterion in Solid Tumors (RECIST)-defined progression. or, once the primary endpoint of Study A8081007 has been analyzed and the results made available, at any time without RECIST-defined progression.
  -  Tumors can be measurable or non measurable
  Exclusion Criteria:
  -  prior treatment with PF-02341066
  -  received no prior systemic treatment, chemotherapy or EGFR tyrosine kinase inhibitor, for advanced non-small cell lung cancer
  -  current enrollment in another therapeutic clinical trial

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: An Investigational Drug, PF-02341066 Is Being Studied Versus Standard Of Care In Patients With Advanced Non-Small Cell Lung Cancer With A Specific Gene Profile Involving The Anaplastic Lymphoma Kinase (ALK) Gene

Summary: This is a Phase 3 trial comparing the safety and anti-tumor activity of PF-02341066 versus pemetrexed or docetaxel in patients with advanced non-small cell lung cancer with specific gene profile involving the ALK gene after failure of one previous chemotherapy regimen that included one platinum drug.


Eligibility: Inclusion Criteria:
  -  histologically or cytologically proven diagnosis of non-small cell lung cancer
  -  positive for the ALK fusion gene (test provided by a central laboratory)
  -  must have had disease progression after only one prior chemotherapy and that regimen but must have included one platinum drug
  -  tumors must be measurable
  Exclusion Criteria:
  -  prior treatment with PF-02341066
  -  current treatment in another clinical trial

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Study of Tumor Samples in Patients Undergoing Treatment for Gastrointestinal Stromal Tumors on Clinical Trial ACOSOG-Z9001

Summary: RATIONALE: Studying the genes expressed in samples of tumor tissue from patients with cancer may help doctors identify biomarkers related to cancer.
  PURPOSE: This research study is looking at tumor samples in patients undergoing treatment for gastrointestinal stromal tumors on clinical trial ACOSOG-Z9001.

Detailed description: OBJECTIVES:
  Primary
  -  To examine polymorphisms in selected genes involved in the detoxifying/metabolizing and DNA repair pathways in relation to specific mutations and types of mutation in the c-kit gene in tumor tissue from patients with gastrointestinal tumors (GIST) undergoing treatment on clinical trial ACOSOG-Z9001.
  Secondary
  -  To examine approximately 758 polymorphisms among candidate genes involved in detoxification/metabolism, cell cycle control, and DNA damage/repair in relation to specific mutations and types of mutation in the c-kit gene in tumor tissue from GIST patients for hypothesis generation. (exploratory)
  -  To conduct an exploratory analysis of the polymorphism distribution in these patients. (exploratory)
  -  To examine the association between the above polymorphisms and major toxicity (Grade 3/4) of adjuvant imatinib mesylate. (exploratory)
  OUTLINE: Tumor samples are used for polymorphism and mutation analysis.

Eligibility: DISEASE CHARACTERISTICS:
  -  Tumor samples from patients with gastrointestinal stromal tumors enrolled on clinical trial ACOSOG-Z9001

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Phase III Trial to Evaluate the Elortinib vs Gefitinib in Advanced NSCLC With EGFR Exon 19 or 21 Mutations

Summary: This is a randomized controlled trial to compare efficacy and safety between erlotinib and gefitinib in advanced NSCLC harboring EGFR exon 19 or 21 mutations.Eligible patients were randomized to receive erlotinib or gefitinib in any line settings.The primary endpoint was progression-free survival (PFS).

Detailed description: Patients with stage IV NSCLC who have EGFR exon 19 or 21 mutations will randomized to received oral erlotinib 150mg or gefitinib 250mg once daily until disease progression or unacceptable toxicity. Method of direct DNA sequencing of tumor tissue is used to analysis EGFR mutation status of exons 18-21. The response will be evaluated by RECIST criteria first month,second month and then repeat every 3 months after the beginning of the treatment weeks.

Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed stage IIIB (wet) or IV NSCLC.
  -  Patients with positive EGFR exon19 or exon21 mutation as confirmed by direct sequencing histologically.
  -  Signing the informed consent form.
  -  The vital organ functions are tolerant to therapy.
  -  Have recovered to CTCAE2 grade below from toxicity of previous chemotherapy and radiotherapy
  -  PS 0-2 scores.
  -  Functional reserve of bone marrow is adequate, e.g. white blood cell count ≥3.0×109/L, planet count ≥90×109/L, and HB≥80×109/L.
  -  Serum bilirubin is 2 times less than the upper limit of normal (ULN), ALT and AST are 3 times less than ULN; for liver metastases, ALT and AST need to be 5 times less than ULN; creatinine should be 2 times less than ULN.
  Exclusion Criteria:
  -  Informed consent is not provided.
  -  Women of pregnancy or breastfeeding.
  -  Have difficulty in swallowing.

Relevance to patient case: not relevant
Patient case: 56-year-old female with gastrointestinal stromal tumor; genetic feature: PDGFRA (D842V)

Clinical trial: Collection of Biospecimen & Clinical Information in Patients w/ Gastrointestinal Cancers

Summary: We have an active research program in gastrointestinal cancers including clinical trials, epidemiologic, and translational studies. We would like to establish a biospecimen bank linked to useful clinical information in order to learn more about diagnostic, predictive and prognostic markers for gastrointestinal cancers.
  PRIMARY OBJECTIVES:
  1. To collect and store tumor and normal tissue (previously collected paraffin embedded or frozen specimen) and blood in patients with gastrointestinal (GI) cancers.
  SECONDARY OBJECTIVES:
  1. Collect detailed clinical information via a patient questionnaire that includes demographic, socioeconomic, lifestyle, family, past medical, medication and cancer histories
  2. Collect details about the tumor specimen extracted from patient charts.


Eligibility: Inclusion Criteria:1. Patients are eligible if they have a histologically proven gastrointestinal cancer (esophageal, gastroesophageal junction, gastric, small intestine, appendix, colon, rectum, anus, liver, gallbladder, bile ducts, pancreas, neuroendocrine, and GI stromal tumor).
  2. 18 years of age or older
  3. Ability to understand and the willingness to sign a written informed consent document.
  Exclusion Criteria:None

Relevance to patient case: not relevant