araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Investigation of Protein Biomarkers of Prostate Cancer

Summary: This study is looking at biomarkers in prostate cancer.

Detailed description: 1. To establish primary culture of epithelial cells isolated from prostatectomy samples
  2. To study biomarkers in prostate cancer

Eligibility: Inclusion Criteria:
  -  Patients with prostate cancer.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Biomarkers in Patients Undergoing Transrectal Ultrasound Prostate Biopsy

Summary: RATIONALE: Collecting and storing samples of blood and urine from patients with cancer to study in the laboratory may help doctors learn more about changes that may occur in DNA and identify biomarkers related to cancer.
  PURPOSE: This laboratory study is looking at biomarkers in patients undergoing transrectal ultrasound prostate biopsy.

Detailed description: OBJECTIVES:
  Primary
  -  Identify unique proteins or peptides that are associated with prostate cancer by comparing the proteomic or metabolomic analysis of serum, plasma, and urine from patients with histological evidence of prostate cancer to those without prostate cancer (after transrectal ultrasound prostatic biopsy).
  Secondary
  -  Collect seminal fluid from a subset of patients to test the hypothesis that the fluid collected from the "target organ of injury" in prostate cancer will have a higher signal of proteins/peptides that are different from those without cancer and may help guide the identification of these differences in the serum, plasma, and urine.
  OUTLINE: This is a pilot study.
  Patients undergo collection of serum, plasma, and urine for biomarker/laboratory analysis. Samples are examined by proteomic/metabolomic analysis (by mass spectrometry) and immunoassays. Patients then undergo a transrectal ultrasonography prostatic biopsy.
  PROJECTED ACCRUAL: A total of 60 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Indication for a transrectal ultrasonography prostatic biopsy (as part of normal patient care) due to elevated prostate-specific antigen, or abnormal digital rectal examination, or surveillance for prostate cancer
  PATIENT CHARACTERISTICS:
  -  No prior or other concurrent malignancy except for curatively treated basal cell carcinoma of the skin
  -  No serious medical or psychiatric illness that would preclude informed consent
  -  No concurrent acute illness
  PRIOR CONCURRENT THERAPY:
  -  No participation in another clinical trial within the past 30 days
  -  No more than one enrollment into this study

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: A Study of Erlotinib (Tarceva) After Surgery With or Without Adjuvant Chemotherapy in Non-Small Cell Lung Carcinoma (NSCLC) Patients Who Have Epidermal Growth Factor Receptor (EGFR) Positive Tumors

Summary: This is a study to evaluate the effectiveness of erlotinib compared with a placebo sugar pill following complete surgical removal of the tumor with or without chemotherapy after surgery in Stage IB-IIIA NSCLC patients.

Detailed description: After the initiation of the study, the sponsor became aware of an error in the drug dispensing module of the interactive voice response such that most patients who were randomized prior to 07 November 2007 were dispensed the incorrect study drug at least once. Since the integrity of the data from these patients was seriously compromised, these patients were considered unevaluable for the protocol-specified analyses. These participants are referred to as the breached protocol cohort (BPC) and those still on study treatment at the time of the breach were offered the option of receiving open-label erlotinib for up to 2 years (including posttreatment and long-term follow-up assessments), not receiving open-label erlotinib but remaining in the study for posttreatment and long-term follow-up assessment, or withdrawing consent from treatment and further assessments. Participants who had discontinued study treatment prior to the breach were not offered open-label erlotinib and remained in long-term follow-up. Data from the BPC participants were analyzed separately and were not included in the assessments of primary or secondary endpoints in the randomized cohort and were not considered part of the primary analyses.The sample size for the randomized cohort was not changed due to the BPC and the data from RC and BPC were analyzed separately.

Eligibility: Inclusion Criteria:
  -  Primary tissue from patient's surgery must be epidermal growth factor receptor (EGFR)-positive by certain tests
  -  Patients may have up to 4 cycles of chemotherapy after surgery
  -  Complete removal of the tumor by surgery
  -  Able to start drug under the following timelines:
  -  6 months from the day of surgery for patients who get chemotherapy
  -  3 months from the day of surgery for those who do not get chemotherapy
  -  Confirmed diagnosis of Stage IB-IIIA NSCLC
  -  Patients must be accessible for follow-up visits
  Exclusion Criteria:
  -  History of prior radiotherapy for NSCLC either before or after surgery
  -  History of heart disease or uncontrolled heart arrhythmias within the previous year
  -  History of poorly controlled gastrointestinal (GI) disorders that could affect the absorption of study drug
  -  History of other cancer except certain skin or cervical cancers, patients who have had other cancer are eligible if they have remained disease free for at least 5 years
  -  Patients who have received chemotherapy for NSCLC before surgery
  -  Tumors with mixed histology of NSCLC and Small Cell Lung Cancer (SCLC). Patients with carcinoid tumors are not eligible.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Genetic Counseling in Women at Risk for BRCA1 or BRCA2 Mutations

Summary: RATIONALE: Genetic counseling and using an interactive computer program may help women at risk for breast cancer make medical decisions about treatment.
  PURPOSE: This randomized clinical trial is studying standard genetic counseling to see how well it works when given together with or without a medical decision-making computer program in women at risk for BRCA1 or BRCA2 mutations.

Detailed description: OBJECTIVES:
  -  Evaluate the impact of BRCA1/BRCA2 testing among members of hereditary breast-ovarian cancer families.
  -  Evaluate the long-term impact of genetic counseling and testing on psychosocial and behavioral outcomes.
  -  Evaluate the relative impact of standard genetic counseling (SGC) versus SGC plus the interactive decision-aid (IDA) on medical decision-making.
  -  Evaluate the relative impact of SGC vs SGC + IDA on psychological well-being.
  -  Explore the mechanisms by which the SGC + IDA intervention impacts on psychosocial and behavioral outcomes.
  OUTLINE: This is a multicenter study.
  Eligible women are asked to participate in a baseline telephone interview over 30 minutes and then invited to a genetic counseling session over 1.5-2 hours that includes information about BRCA1/2 testing. Patients are then offered BRCA1/2 testing, and the test results (i.e., mutation carrier vs noncarrier) are presented at a subsequent in-person individual genetic counseling session over 1.5-2 hours. Patients who tested positive for BRCA1 or 2 mutation are randomized to 1 of 2 counseling arms. All other patients proceed to follow up.
  -  Arm I (standard genetic counseling): No further counselor-initiated contact is scheduled.
  -  Arm II (individualized decision aid): Patients are asked to view an interactive computer program that is designed to help the patients make medical decisions based on their breast cancer risk.
  Outcome assessments, including quality of life assessment, are conducted at 2, 6, and 12 months.
  PROJECTED ACCRUAL: A total of 950 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Members of hereditary breast/ovarian cancer families (in which there is at least a 10-20% prior probability of a BRCA1/2 mutation) OR who have a first-degree relative with a known BRCA1 or BRCA2 mutation
  -  Prior diagnosis of breast cancer allowed
  -  Must not be undergoing active treatment
  -  Patients with prior bilateral mastectomy are eligible for study but not eligible for randomization
  PATIENT CHARACTERISTICS:
  -  Female only
  -  No psychiatric or cognitive disorder that would preclude giving informed consent
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Randomized Customized Adjuvant Chemotherapy (GECP-SCAT)

Summary: Randomized Study of Customized Adjuvant Chemotherapy based on BRCA1 mRNA Levels in Completely Resected stages II-IIIA Non-Small-Cell Lung Cancer Patients.

Detailed description: Randomized, phase III, predictive pharmacogenomic, open, prospective, international, multicenter study in patients with non-small-cell lung carcinoma (NSCLC) after complete resection and with N1 or N2 involvement

Eligibility: Inclusion Criteria:
  -  Patients with histological confirmation of non-small-cell lung carcinoma.
  -  Complete surgical resection of the disease.
  -  Tumoral tissue available for molecular analysis.
  -  N1 (stage II) or N2 (stage IIIA) lymph node involvement in the study of the operative piece.
  -  Men or women age 18 years or older.
  -  Patients with a performance status of 2 or less according to the ECOG classification.
  -  Patients with the following laboratory results: ANC < 1500/L, Hb < 10 g/dL, platelets <100,000/L, bilirubin < 1.0 mg/dL, AST and ALT < 1.5 upper limit of normality, creatinine clearance < 60 mL/min.
  -  Complete recovery from surgery within 6 weeks.
  -  Patients who have given written informed consent before initiating any specific study screening procedure.
  Exclusion Criteria:
  -  Patients who have received previously chemotherapy or radiotherapy for the study disease.
  -  Impossibility of complying with chemotherapy treatment due to cultural or geographic circumstances.
  -  Patients with active infection, heart disease, or any other serious disease, in the judgment of the investigator.
  -  Women who are pregnant or in the period of lactation.
  -  Patients with a previous diagnosis of malignant disease in the last five years except for carcinoma in situ of the uterine cervix or skin cancer other than melanoma.
  -  Patients under treatment with investigational agents.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: The Effect of Radiation on Semen Quality and Fertility in Men With Prostate Cancer

Summary: Many younger men are diagnosed with prostate cancer. These patients are often choosing radiation therapy as their primary treatment. The effect of this therapy on fertility will have a direct impact on their decision about therapeutic options and fertility preservation. The researchers hypothesize that when patients are treated with radiation for localized prostate cancer, infertility can occur due to direct damage to seminiferous tubules affecting sperm quality.

Detailed description: Prostate cancer is the most common malignant disease among men. Many young men are diagnosed with localized prostate cancer. Some of these men are choosing to manage their prostate cancer with radiation therapy. The radiation therapy delivers minimal dose exposure to adjacent organs. We hypothesize that when patients are treated with radiation therapy for localized prostate cancer, decreased fertility can occur due to damage of seminiferous tubules, which may affect sperm quality. This study will assess the impact of radiation therapy on semen and seminal fluid.

Eligibility: Inclusion Criteria:
  -  Subjects with histologically confirmed low risk to moderate stage prostate cancer (Gleason 6 - 7) treated with brachytherapy or external beam radiation
  -  > 12 months ago
  Exclusion Criteria:
  -  Subjects with a prior history of infertility
  -  Subjects who have undergone vasectomy
  -  Subjects who have received LHRH therapy for prostate cancer < 6 months ago
  -  Subjects who have received anti-androgens < 3 months ago
  -  Subjects using alpha blockers within 7 days of specimen provision
  -  Subjects who have taken finasteride or dutasteride within the previous 4 months.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Chemotherapy for Patients With Osteosarcoma

Summary: The primary purpose of your participation in this study is to help answer the following research questions, and not to provide you treatment for your condition.
  -  To assess how well treatment with pemetrexed works for patients with your type of cancer
  -  To assess for any side effects that might be associated with pemetrexed.
  -  To look at the characteristics and levels of certain of your genes and proteins to learn more about osteosarcoma and how pemetrexed works in your body.


Eligibility: Inclusion Criteria:
  -  Histological diagnosis of high grade locally advanced or metastatic osteosarcoma
  -  Must have one prior chemotherapy regimen for advanced disease
  -  At least 1 unidimensional measurable lesion by computed tomography (CT) scan
  -  Have a good performance status
  -  Adequate organ function
  Exclusion Criteria:
  -  Have a serious concomitant systemic disorder (for example active Human Immunodeficiency Virus infection)
  -  Have brain metastases not adequately treated
  -  Significant weight loss (that is more than 20%) over the previous 6 weeks before study entry
  -  Inability or unwillingness to take folic acid or vitamin B12 supplementation and corticosteroids
  -  Pregnant or breast-feeding

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Broccoli, Peas and PIN

Summary: This is a parallel human intervention trial to determine to what extent a dietary intervention of broccoli or peas can change the expression (switching on or off) of genes in prostate tissue in men diagnosed with high-grade Prostate Intraepithelial Neoplasia (PIN).

Detailed description: Cancer is one of the main causes of death among humans in the world. Prostate cancer affects 20,000 men in the UK alone each year. Diet is known to be a major factor that influences risk of cancer. Therefore, changes to the diet may alter cancer risk. Cruciferous vegetables, particularly broccoli, provide the diet with a substantial source of plant chemicals called glucosinolates. Previous research has indicated that glucosinolates break down to form isothiocyanates (ITCs) that can be absorbed in the body. Further research has indicated that ITCs may protect the body against the development of prostate cancer. However, the mechanisms behind this effect are not fully understood.
  ITCs are thought to be powerful anti cancer agents as they can modulate the expression (switching on or off) of specific genes involved in the removal of toxic substances such as carcinogens from the body. In this study we wish to evaluate the effect of consumption of a conventionally bred cultivar of broccoli containing high levels of ITCs on gene expression in prostate tissue to gain a better understanding of its mechanism of action. Several studies suggest a further protection against cancer amongst individuals who have a deletion of certain genes.
  This pilot study comprises a 12-month intervention of either 400g ITC-enriched broccoli per week of 400g garden peas in men at high risk of developing prostate cancer. Changes in gene expression of prostate biopsy tissue will be compared before and after 6 and 12 months of intervention in both dietary groups.

Eligibility: Inclusion Criteria:
  -  Men with a previous diagnosis of high-grade Prostatic Intraepithelial Neoplasia
  -  BMI >18.5 or <35
  -  Aged between 30-70 years
  Exclusion Criteria:
  -  Undergoing chemopreventive therapy
  -  Receiving testosterone replacement medicines
  -  Active infection requiring treatment
  -  BMI <18.5 or >35
  -  Diagnosed with diabetes
  -  Unable to give informed consent

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Germline Alterations of Tumor Susceptibility Genes in New York Cancer Patients

Summary: The basic premise of this research proposal is to determine whether there is any significant association between germline polymorphisms and cancers of colon, bladder, breast, testicular, prostate, ovaries, kidney, lung, lymphoid organs, and head and neck. This is an exploratory study designed to generate hypotheses for further research.

Detailed description: To establish significant correlations between genetic polymorphisms and cancer, a largescale, systematic comparison of genetic alterations utilizing a case-control methodology is proposed. To date, such studies have been limited due to the large number of samples necessary for obtaining statistical significance, and the lack of rapid and accurate methods to screen for genetic polymorphisms. We propose to utilize an anonymized design to obtain DNA from residual material from routine diagnostic blood tests, to link these samples to a limited set of clinical variables, and to test for the frequency of candidate low-penetrance cancer susceptibility alleles. These data will be combined with similar data from a control group of age- and ethnically-matched volunteers for a related cohort study to be conducted separately. Polymorphisms to be screened for include those involving the genes PTEN, APC, TGF βR-I, BLM, CHK2, a p85 phosphoprotein, ATM, ER, PR, MCP-1, MPIF, CCR2/5, CCR3, and SULT1A1. Cancers to be included are breast, bladder, kidney,colon, testicular, lung, prostate, ovarian, lymphoid neoplasms, and head and neck carcinomas. Genes with SNPs known to be relevant for either the development or treatment of lymphoid malignancies will also be targeted. Specifically, candidate genes will be selected from 1) cytokine signaling, 2) DNA repair, and 3) apoptosis regulatory pathways.

Eligibility: Inclusion Criteria:
  -  Patients with a histologic diagnosis of cancer of the colon, breast, bladder, kidney, testicles, lungs, prostate, head and neck, or lymphoid organs, who have donated a diagnostic blood sample as either an inpatient or outpatient at MSKCC.
  -  All patients who have two or more histologic diagnoses of the same primary tumor type involving the above sites.
  -  Patients of Ashkenazi Jewish ancestry with a histologic diagnosis of cancer of any type.
  -  Samples ascertained as part of protocol 98-024A(1) are also eligible for ascertainment in this study.
  Exclusion Criteria:
  -  MSKCC patients without a histologic diagnosis of cancer of the breast, bladder, kidney, colon, testicles, lungs, prostate, or lymphoid malignancy (including all types of lymphoma) will not be eligible for the AMDeC sponsored component of the study.

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: A Study Of Oral PF-02341066, A C-Met/Hepatocyte Growth Factor Tyrosine Kinase Inhibitor, In Patients With Advanced Cancer

Summary: PF-02341066 may work in cancer by blocking the cell growth, migration and invasion of tumor cells. PF-02341066 is a new class of drugs called c-Met/Hepatocyte growth factor receptor tyrosine kinase inhibitors. This compound is also an inhibitor of the anaplastic lymphoma kinase (called ALK) tyrosine kinase and ROS receptor tyrosine kinases. This research study is the first time PF-02341066 will be given to people. PF-02341066 is taken by mouth daily.


Eligibility: Inclusion Criteria:
  -  Advanced malignancies (except leukemias), histologically proven at diagnosis; Histologically confirmed advanced malignancies that are known to be sensitive to PF-03241066 inhibition, e.g. ALK, c-MET and ROS
  -  Solid tumors must have measurable disease (Recommended Phase 2 Dose Cohort patients with non-measurable disease may enter on a case-by-case basis); not required for DDI sub-studies.
  -  Adequate blood cell counts, kidney function, liver function and Eastern Cooperative Oncology Group (ECOG) score of 0 or 1 (for the Recommended Phase 2 Cohort, a ECOG score of 2 may be allowed on a case-by-case basis)
  Exclusion Criteria:
  -  Major surgery, radiation therapy or anti-cancer therapy within 2 to 4 weeks of starting study treatment, depending on the patient cohort
  -  Prior stem cell transplant except of patients with neuroblastoma, lymphoma or myeloma
  -  Active or unstable cardiac disease or heart attack within 3 months of starting study treatment

Relevance to patient case: not relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: [18F]-Fluoro-2-Deoxy-D-Glucose and -[18F] Dihydro-Testosterone Pet Imaging in Patients With Progressive Prostate Cancer

Summary: This study will use PET scans, which is a type of x-ray test that uses a radiotracer, to see whether these scans may be better able to find places in the body where your prostate cancer may have spread.

Detailed description: Our preliminary studies have shown that whole body FDG-PET imaging identifies areas of abnormal metabolism in a majority of tumor sites in patients with progressive disease and that changes in FDG accumulation parallel changes in PSA after treatment. This suggests that changes in FDG metabolism may provide an early assessment of treatment outcomes. In previous work we established a methodology to examine a radiotracer in patients with progressive disease and abnormal imaging studies, which we have applied to the clinical states of non-castrate and castrate metastatic disease. This design is characterized by:
  1) Evaluation of uptake on a site-by-site basis in relation to conventional studies 2) Standardization of uptake values in tumor relative to a normal organ 3) Controlling for progression using standard measures of progression including a rising PSA, new or enlarging lesions on bone or transaxial imaging, and new symptoms of disease. In the present study we are evaluating fluorinated dihydrotestosterone (FDHT) in addition to FDG. FDHT is targeted to the AR and has been shown in preliminary studies to visualize prostate cancers in man. This study will apply our established methods to investigate FDHT imaging in patients with progressive prostate cancer. In the selected cases where tumor is available, we will study associations between FDHT accumulation and AR expression.

Eligibility: Inclusion Criteria:
  -  Patients with histologically confirmed prostate cancer.
  -  Progressive disease manifest by either:
  -  Imaging modalities:
  -  Bone Imaging: New osseous lesions on bone imaging (bone scintigraphy or NaF PET scan) and/or MRI or CT: An increase in measurable soft tissue disease, or the appearance of new sites of disease. Or
  -  Biochemical progression: A minimum of three rising PSA values from a baseline that are obtained 1 week or more apart, or 2 measurements 2 or more weeks apart.
  -  Visible lesions by either CT, bone imaging, or MRI consistent with disease.
  -  Informed consent.
  Exclusion Criteria:
  -  Previous anaphylactic reaction to either FDHT or FDG
  -  Hepatic: Bilirubin > 1.5 x upper limit of normal (ULN), AST/ALT >2.5 x ULN, albumin < 2 g/dl, and GGT > 2.5 x ULN IF Alkaline phosphatase > 2.5 x ULN
  -  Renal: Creatinine >1.5 x ULN or creatinine clearance < 60 mL/min

Relevance to patient case: not relevant