araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Study of Tumor Samples in Patients Undergoing Radiation Therapy or Surgery For Primary Melanoma of the Eye

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This clinical trial is studying tumor samples in patients undergoing surgery or radiation therapy for primary melanoma of the eye.

Detailed description: OBJECTIVES:
  Primary
  -  To establish the feasibility of using fine needle aspiration (FNA) and FISH to determine tumor genotype in patients with primary uveal melanoma.
  Secondary
  -  To characterize ophthalmic complication rate of FNA for FISH analysis in patients undergoing plaque radiotherapy.
  -  To estimate disease-free survival in patients with and without tumor monosomy 3 and/or 8q amplification.
  -  To explore the relationship between tumor monosomy 3 and 8q amplification and plasma levels of tumor immune escape and invasion biomarkers (e.g., circulating granulysin, beta2-microglobulin, autotoxin, lysophosphatidic acid, matrix metalloproteinase-7, tissue inhibitor of matrix metalloproteinase, and soluble E- cadherin).
  -  To explore the psychological impact of prognostication in uveal melanoma.
  OUTLINE: Patients undergo plaque radiotherapy, enucleation, or tumor resection based upon standard of care guidelines.
  Trans-scleral fine needle aspiration (FNA) is performed at the time of plaque radiotherapy and ex vivo FNA is performed on enucleation and tumor resection specimens. Tissue samples are analyzed by fluorescence in situ hybridization (FISH). Blood samples are also collected for further analysis.
  After completion of study therapy, patients are followed up periodically.

Eligibility: Inclusion Criteria
  -  Patients must have a clinical diagnosis of melanoma of the iris, ciliary body and/or choroids
  -  Patients must have had a hepatic ultrasound and/or other suitable imaging studies to eliminate metastatic disease
  -  Patients must not have received any local or systemic therapy for uveal melanoma
  -  All patients must be informed of the investigational nature of this study and must provide written informed consent in accordance with institutional and federal guidelines. A copy of the informed consent document signed by the patient must be given to the patient
  -  Patients must have the following pretreatment laboratory findings:
  -  Bilirubin (total) </= 1.5 ml/dl
  -  AST </= 2 x normal
  -  ALT </= 2 x normal
  -  Alkaline phosphatase </= 2 x normal
  Exclusion Criteria
  -  Patients with metastasis
  -  Patients under the age of 18

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Study Of Bosutinib With Capecitabine In Solid Tumors And Locally Advanced Or Metastatic Breast Cancer

Summary: This is a research study in 2 parts assessing the following parameters of the combination of the study drug called bosutinib, and a drug called capecitabine: the safety, how well the subject's body handles the study drug, and preliminary anti-tumor activity as treatment for different types of cancers in part 1, and breast cancer only in part 2.
  In part 1, subjects will receive bosutinib and capecitabine daily at different dose levels of each drug in order to determine the highest tolerated dose of the combination study treatment. In part 2, subjects will receive bosutinib and capecitabine at this highest tolerated dose to see how well the study treatment works to treat breast cancer. In addition, genetic research testing (research analyses involving genes and gene products) will be performed on biological samples from subjects.

Detailed description: The study was prematurely discontinued following Part 1 evaluation, when the sponsor concluded that further translational biomarker analyses were needed to better define the breast tumor biomarkers that predict sensitivity to Src family kinase inhibitors. Thus the Sponsor made a determination to stop the study after Part 1 as communicated to investigators on 02Dec2010 . No subjects were enrolled into Part 2 of this study. The study was not terminated due to safety reasons.

Eligibility: Inclusion Criteria:
  Part 1:
  -  Ages eligible for study: 18 years or older.
  -  Male and female.
  -  Confirmed pathologic diagnosis of advanced breast cancer or pancreatic cancer or colorectal cancer or cholangiocarcinoma or glioblastoma not curable with available therapies, for whom bosutinib plus capecitabine is a reasonable treatment option.
  Part 2:
  -  Ages eligible for study: 18 years or older.
  -  Female.
  -  Confirmed pathologic diagnosis of locally advanced or metastatic breast cancer, or loco-regional recurrent breast cancer that is not amenable to curative treatment with surgery or radiotherapy.
  -  Documented ER+ and/or PgR+/erbB2- or ER-/PgR-/erbB2- tumor based upon recently analyzed biopsy.
  Exclusion Criteria:
  Part 1:
  -  Prior bosutinib, or any other prior Src inhibitor.
  -  Prior chemotherapy with capecitabine or 5-FU for the treatment of metastatic disease is allowed unless patient stopped therapy for toxicity.
  Part 2:
  -  Prior bosutinib, or any other prior Src inhibitor prior chemotherapy with capecitabine or 5-FU for the treatment of metastatic disease.
  -  Prior chemotherapy with capecitabine or 5-FU for adjuvant chemotherapy within the past 12 months.
  -  erbB2+ breast cancer.

Relevance to patient case: possibly relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Study of Biomarkers in Tissue Samples From Patients With Metastatic Colon Cancer

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors identify and learn more about biomarkers related to cancer.
  PURPOSE: This research study is looking at biomarkers in tissue samples from patients with metastatic colon cancer.

Detailed description: OBJECTIVES:
  -  Determine the effect of surgical resection, in terms of physiological stress, on levels of tumor markers such as protein kinase A (PKA) expression in patients with metastatic colon cancer.
  -  Estimate variation among patients of baseline tumor markers in tumor tissue and sera.
  -  Correlate markers in tumor tissues with that in sera in these patients.
  -  Establish a tissue bank of these specimens for future studies.
  OUTLINE: Biopsy and surgical specimens are obtained before and during standard surgery (patients may have had tumor tissue obtained before study entry and stored). Serum samples and tumor tissue are analyzed by immunohistochemistry and western blot. Tumor markers (such as PKA expression) are determined and marker levels are measured in serum samples and tissues.
  PROJECTED ACCRUAL: Approximately 30 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of colon cancer
  -  Metastatic disease for which surgical resection is indicated
  -  Metastatic disease accessible for tissue biopsy OR previously biopsied tissue is available
  PATIENT CHARACTERISTICS:
  -  Platelet count ≥ 80,000/mm^3
  -  INR ≤ 1.3
  -  PTT ≤ upper limit of normal
  -  No history of bleeding disorders or abnormal clotting factors
  -  No extrahepatic biliary obstruction
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Breast Cancer With Over-expression of erbB2-BRAINSTORM

Summary: This retrospective cohort study aims to improve our understanding of the current paradigm for treatment of brain metastases in erbB2+ breast cancer patients in the Asia Pacific region. We aim to identify approximately 300 erbB2+ breast cancer patients with brain metastases diagnosed between 2006-2008 in 6 countries. Medical records will be analyzed to determine the treatment pattern for brain metastases, including anti-erbB2 therapy. Additional objectives are to understand the impact of anti-erbB2 therapy on survival after brain metastases and to investigate the relationship between anti-erbB2 therapy for brain metastases and: 1) the time interval between diagnosis of erb2+ breast cancer and brain metastasis, and 2) the occurrence of brain metastasis as the first site of disease progression.


Eligibility: Inclusion Criteria:
  1. Female patients diagnosed with erbB2+ breast cancer. ErbB2 positivity will be as determined by respective institutional standards, and will be based on medical history only.
  2. Brain metastasis diagnosis made between January 2006 - December 2008.
  Exclusion Criteria:
  1. Women who have another primary cancer diagnosed between the time of breast cancer diagnosis and brain metastasis..
  2. Patient has leptomeningeal metastases only without parenchymal brain involvement (since this pattern of the disease requires a different treatment approach.)

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Detection of Amplification of Her2 Fluorescent in Situ Hybridization (FISH) in Breast Tissue Sections

Summary: The purpose of the study is the identification of amplification level in human breast tissue. The imaging system is intended for diagnostic use as an aid to the pathologist in the detection, counting and classification of Her2 FISH stained tissue samples.


Eligibility: Inclusion Criteria:
  -  Well stained breast tissue slides with bright Her2 signals
  Exclusion Criteria:
  -  Very old slides that were already bleached

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Safety and Efficacy Study of BMS-908662 Alone or in Combination With Cetuximab in Subjects With K-RAS or B-RAF Mutation Positive Advanced or Metastatic Colorectal Cancer

Summary: The purpose of the study is to identify a safe and tolerable dose of BMS-908662 in combination with cetuximab; and then to evaluate the tumor response to BMS-908662 when administered alone or in combination with cetuximab

Detailed description: Phase 1: Single Arm Study
  Phase 2: Randomized Controlled, Parallel

Eligibility: Inclusion Criteria:
  -  Subjects with K-RAS (codon 12 or 13) or B -RAF (V600E) mutation positive advanced or metastatic colorectal cancer who have relapsed or are refractory to 2 or more standard systemic anticancer regimes for metastatic disease, or are intolerant to existing therapies.
  -  Histologic or cytologic confirmation of the diagnosis.
  -  Eastern Cooperative Oncology Group (ECOG) ≤ 1
  -  Adequate organ & marrow function.
  Exclusion Criteria:
  -  Uncontrolled or significant cardiovascular disease.
  -  Phase 2: Prior therapy with a RAF inhibitor.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

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: ERBB2 amplification

Clinical trial: FNA Tumor Sampling for CD137 Modulation: A Pilot Study

Summary: The purpose of this study is to better understand the biology of the body's immune response to monoclonal antibody therapy for cancer. Your health information will be used to identify your tissues. The tissue we obtain may be useful for research or education, resulting in new drugs, therapies or diagnostic procedures.


Eligibility: ALL Patients:
  1. Patient must have a lymphoma, squamous cell carcinoma of the head and neck, HER2+ breast adenocarcinoma, colorectal adenocarcinoma, or other solid tumor.
  2. Patients must not have received any immunosuppressive or anti cancer agent within 2 weeks prior to the first planned FNA biopsy.
  3. The patient's therapeutic plan must include a standard therapeutic monoclonal antibody (such as rituximab, cetuximab/panitumumab or trastuzumab) or an investigational monoclonal antibody) to be administered on a schedule such that a FNA biopsy can be done within one week prior, and/or peripheral blood drawn immediately prior to the first dose of the therapeutic mAb and immediately to 24-336 hours post dose. Patients not receiving any other anti- cancer or immunosuppressive (steroids) modality within that time frame are preferred, though use of such agents does not exclude them from the study.
  4. Patients not receiving any immunosuppressive or anti-cancer agent within 2 weeks prior to the first planned FNA biopsy are preferred.
  5. Informed consent must occur and be documented per institutional rules prior to the first planned FNA biopsy and blood draw.
  Patients Providing an FNA in addition to Blood Samples: Criteria applicable to FNA, and not required for patients providing PBMCs without FNA. Patients without tumors amenable to FNA will be candidates for blood sampling only.
  If patients do not meet inclusion criteria, then they will be excluded from participating in this study.
  1. Patients must have a normal WBC and platelet count, must have no evidence of coagulopathy and must not have received irreversible platelet inhibitors (aspirin) for 2 weeks and reversible platelet inhibitors (other NSAIDS) for one week prior to the initial FNA biopsy.
  2. Patients may not be taking therapeutic anticoagulation (target INR of >=2) (warfarin or heparin).
  3. Patients must have tumor masses amenable to minimally invasive fine needle aspiration by direct visualization and/ or palpation of the tumor. Generally this will be a biopsy of the primary tumor site or superficial regional lymph nodes.

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: A Study of Capecitabine [Xeloda] in Combination With Trastuzumab [Herceptin] and Oxaliplatine in Patients With Resectable Gastric Cancer

Summary: This study will evaluate the disease free survival rate of a combination of capecitabine [Xeloda] and oxaliplatin (XELOX) with trastuzumab [Herceptin] in patients with resectable gastric cancer. The combination of Xeloda (orally, 1000 mg/m2 on day 1-14 of every cycle) and Herceptin (intravenously, 8 mg/kg loading dose, then 6 mg/kg on days 1-14 of every cycle) will be administered for three cycles prior to surgery to resect the tumor. If complete resection, R0 or microscopic residual tumor R1 is achieved, patients will continue with three cycles of XELOX and Herceptin and then for completion of 12 months treatment with Herceptin alone. Oxaliplatin will be administered intravenously at a dose of 130 mg/m2 on day 1 in every cycle. The anticipated time on study drug will be 12 months.


Eligibility: Inclusion Criteria:
  -  Adult patients over 18 years of age
  -  Locally advanced resectable HER2-positive gastric or esophagogastric junction adenocarcinoma (Sievert types I, II, III)
  -  Measurable (RECIST criteria) or assessable disease
  -  ECOG performance 0-2
  -  Life expectancy of 12 weeks or more
  Exclusion Criteria:
  -  Immeasurable lesion as the only evidence of disease
  -  Previous chemotherapy or radiotherapy for gastric neoplasm or some kind of previous surgical resection of the tumor (except diagnostic laparoscopy)
  -  Concomitant heart disease

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Comparison of the Diagnostic Accuracy of 3D Volume Acquisition MRI With CT in Staging Colonic Cancer

Summary: The purpose of this study is to determine whether MRI is more accurate than CT in determining the T stage, N stage, depth of tumour invasion and extra mural venous invasion (EMVI) preoperatively in colon cancer.

Detailed description: The patient will proceed with their usual colon cancer assessment and treatment, including colonoscopy with biopsy and histology and preoperative CT chest abdomen and pelvis. In addition, patients who enroll in the study will have 2 preoperative MRIs of their abdomen and pelvis performed. One of these will be performed on a 1.5T and the other will be performed on a 3.0T MRI scanner. We will use 20mg of IM buscopan to reduce bowel mobility for each scan. A coronal scout scan will be taken to identify the tumour and select the target volume. IV gadolinium (a contrast agent routinely used in MRI scans to help identify different tissues) will be administered, and a 3D VIBE scan (T1 weighted) will be performed of the target volume. The liver will also be imaged at this time to look for liver metastases. A T2 weighted 3D volume acquisition will then be obtained of the target volume containing the tumour (and its lymphatic drainage).
  The MRI will be independently reported by an expert without knowledge of the results of any other investigations. The results of the MRI scan will then be made available to the clinical team. The patient will then proceed as normal with any other investigation which the clinical team feel is necessary, and be treated as normal for their colon cancer. The patient will proceed with their surgery as normal, and the specimen removed at the time of the operation will be examined in the pathology laboratory to determine the exact stage of the cancer.
  The accuracy of CT and MRI in staging colon cancer will then be determined against the reference standard provided by the histology examination.

Eligibility: Inclusion Criteria:
  -  patients undergoing treatment for colon cancer
  -  patients undergoing primary surgery for colon cancer and who do not require neo-adjuvant therapy on the basis of their pre-operative CT
  Exclusion Criteria:
  -  age <18
  -  unable to consent
  -  consent withheld or withdrawn
  -  Unable to have an MRI (e.g pacemaker, metal implant)
  -  Allergy or contraindications to busocopam, gadolinium, small bowel contrast agent

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: ERBB2 amplification

Clinical trial: Erlotinib Re-Challenge for Recurrent EGFR-mutant Lung Cancer in Patients Who Previously Received Adjuvant Erlotinib or Gefitinib

Summary: The purpose of this study is to measure the ability of erlotinib to effectively treat recurrent lung cancer which carries an EGFR mutation lung cancer after prior treatment with erlotinib or gefitinib received in the post-surgical or post-radiation setting.


Eligibility: Inclusion Criteria:
  -  A history of stage I-IIIB NSCLC
  -  Previously underdone definitive surgery or radiation
  -  Received prior adjuvant treatment or neoadjuvant with erlotinib or gefitinib for a total of at least 3 months at any time
  -  Stopped adjuvant erlotinib or neoadjuvant at least 2 months prior to date of first imaging demonstrating recurrence
  -  Pathologic evidence of recurrent lung cancer, confirmed at MSKCC EGFR sensitizing mutation (point mutation in exons 18 or 21, or deletion in exon 19) must be documented in the primary or recurrent tumor
  -  Tissue from their recurrent tumor must be submitted for EGFR mutation testing, and to evaluate for the presence of the T790M mutation (results do not need to have been reported to be eligible)
  -  Measurable disease by RECIST; if received prior irradiation, then must have a target lesion outside the irradiated field
  -  Signed informed consent
  -  Age > or = to 21 years old
  -  Persons of reproductive potential must agree to use an adequate method of contraception throughout treatment and for at least 4 weeks after study drug is stopped
  Exclusion Criteria:
  -  Prior progressive disease while receiving erlotinib or gefitinib therapy
  -  Patients with known pre-existing interstitial lung disease
  -  Total bilirubin greater than 1.8 mg/dl, excepting patients known to have Gilbert's syndrome
  -  AST or ALT greater than five times the upper limit of normal
  -  Pregnant or lactating women
  -  Medically unfit for erlotinib therapy as determined by treating oncologist

Relevance to patient case: not relevant