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

Clinical trial: Biomarkers in Tissue Samples From Patients With Breast Cancer Treated With Bevacizumab

Summary: RATIONALE: DNA analysis of tumor tissue may help doctors predict how well patients will respond to treatment.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with breast cancer treated with bevacizumab.

Detailed description: OBJECTIVES:
  Primary
  -  To demonstrate that vascular endothelial growth factor-A (VEGFA) haplotypes that are associated with an increased VEGFA expression will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab in ECOG-E2100 (but not for the control arm).
  -  To demonstrate that candidate single nucleotide polymorphisms (SNPs) will further improve the predictive capacity of outcome (efficacy and toxicity) in patients enrolled in ECOG-E2100.
  -  To demonstrate that tumor VEGFA amplification or borderline amplification (estimated 14% frequency) will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab on ECOG-E2100 whereas those with VEGFA deletion (estimated 11% frequency) will predict inferior outcome.
  -  To demonstrate that VEGFA amplification/deletion will not predict outcome in the control arm of ECOG-E2100.
  Secondary
  -  To demonstrate that tumor VEGFA amplification will predict increased protein expression as ascertained by IHC.
  -  To demonstrate that a combined algorithm calculated from tumor-specific variability (VEGFA amplification/deletion) and host-specific variability (SNPs) will optimally predict outcome (efficacy) with bevacizumab in patients enrolled on ECOG-E2100.
  OUTLINE: This is a multicenter study.
  Previously collected tumor-derived DNA is analyzed for VEGFA amplification/deletion and haplotype as biomarkers for outcome after bevacizumab treatment. Gene expression, polymorphism, protein expression analysis, and IHC are performed on the samples.

Eligibility: DISEASE CHARACTERISTICS:
  -  Enrolled on ECOG-E2100
  PATIENT CHARACTERISTICS:
  -  Not specified
  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: Analysis of Tumors From Patients With Inherited Cancers Having Had Two Surgeries (Primary + Recurrent, or 2 Separate Types of Cancer)

Summary: This study will analyze tumor tissue from patients with known genetic mutations (BRCA1, BRCA2, CHK2, etc) who have tumor tissue available from two surgeries, either primary/recurrent, or two different anatomical sites.

Detailed description: This study will recruit individuals with known BRCA1 and BRCA2 mutations or mutations in similar cancer causing genes such as CHK2 or PALB2 who have had a cancer removed by surgery or biopsied two or more times with available pathological blocks. We wish to enroll individuals who have had more than one surgery or biopsy for cancer allowing us to obtain tumor blocks from more than one time point. Such patients would include those with one cancer which has recurred or more than one separate cancer. We will conduct a brief interview with the subject to obtain personal information about medical and treatment history. In addition, we will collect clinical information from their treating physician(s) to correlate molecular findings with clinical responses to treatment and survival and recurrence data. We will collect background clinical information and family history information and a copy of the genetic test results documenting their cancer causing mutation. We will recruit only patients with known BRCA1 or BRCA2 mutations or known mutations in other cancer causing genes such as CHK2 or PALB2 and will not perform genetic testing on non-tumor tissue for any new information on genetic susceptibility in patient samples. Enrolled subjects will donate a blood sample that will be obtained locally and shipped to the research laboratory, and this cost will be entirely covered by the research group.

Eligibility: Inclusion Criteria:
  -  Male or female
  -  Age 18 or older
  -  documented mutation in BRCA1, BRCA2 or other known cancer causing gene
  -  one or more cancer with available stored tissue blocks or slides
  -  willing to donate 16cc of blood
  -  able to understand English and provide informed consent
  Exclusion Criteria:
  -  unable or unwilling to provide informed consent
  -  patient does not have tissue blocks available
  -  minor, under age 18

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

Clinical trial: Prostate Cancer Antigen 3 (PCA-3) Gene Project

Summary: Nowadays, prostate cancer screening is largely widespread although it is not recommended yet. This screening includes primarily digital rectal examination and PSA.
  Recently, a new specific genetic marker of prostate cancer has been discovered. It is PCA-3 gene.
  The main objective is to evaluate prospectively this new marker in patients treated for prostatic pathology (benign or malign) in the department.

Detailed description: Nowadays, prostate cancer screening is largely widespread although it is not recommended yet. This screening includes primarily digital rectal examination and PSA.
  The main drawback is the poor PSA specificity. Prostate cancer diagnosis is only histologic diagnosis (mainly by prostate biopsies). However, prostate needle biopsies have a poor rentability and are negative in 60 to 80%. Recently, a new specific genetic marker of prostate cancer has been discovered. It is PCA-3 gene. This gene encodes for RNAm noncoding. So, RNA expression must be assayed by RT-PCR. The main objective is to evaluate prospectively this new marker in patients treated for prostatic pathology (benign or malign) in the department.
  PCA-3 assay will be made from urine specimens collected by vesical catheterism just before surgery. Moreover, the investigators will analyse expression of several prostatic markers (genes coding for androgen receptor and steroid alpha-reductase type 1 and 2). The main objective is to improve the prostate cancer diagnosis specificity. Gene expression will be assayed by RT-PCR.
  Prostatic cells in urine specimens will be confirmed by assay of PSA gene expression. Normalization of data will be performed using 3 housekeeping genes expression (ß-actin, K-a-1 tubulin and Glyceraldehyde-3-phosphate).
  The originality of this clinical study compared to previous reports, consists to two elements. Firstly, all patients included in our study will be operated for a prostate cancer or a BPH. So, the risk to ignore a prostate cancer will be low unlike prostate biopsies made for a prostate cancer screening. Secondly, PCA-3 assay will be coupled with others prostatic specific markers.

Eligibility: Inclusion Criteria:
  -  Patients operated for a prostate cancer or a benign prostatic hypertrophy
  -  Patients not in state of emergency
  Exclusion Criteria:
  -  Patients with an urinary infection proved bacteriologically
  -  Patients with a vesical malign disease
  -  Patients in state of emergency

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

Clinical trial: Clinical Study to Evaluate the Maximum Tolerated Dose of BAY1000394 Given in a 3 Days on / 4 Days Off Schedule in Subjects With Advanced Malignancies

Summary: Clinical study to determine safety, tolerability, to measure how the drug is metabolized by the body and to determine the maximum tolerated dose of BAY1000394 given in an intermittent 3 days on / 4 days off schedule to patients with advanced malignancies


Eligibility: Inclusion Criteria:
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 - 1
  -  Life expectancy of at least 12 weeks
  -  Subjects with advanced, histologically or cytologically confirmed solid tumors, refractory to any standard therapy, have no standard therapy available, or subjects must have actively refused any treatment which would be regarded standard, and / or if in the judgment of the investigator, experimental treatment is clinically and ethically acceptable
  -  At least 1 tumor lesion measurable by computer tomography (CT) scan or magnetic resonance imaging (MRI) according to RECIST 1.1
  -  Adequate bone marrow, liver, and renal functions as assessed by the following laboratory requirements to be conducted within 14 days prior to the first dose of study drug
  Exclusion Criteria:
  -  History of cardiac disease: congestive heart failure > NYHA Class II, unstable angina (anginal symptoms at rest), any episodes of angina or history of myocardial infarction, cardiac arrhythmias requiring anti-arrhythmic therapy (beta blockers or digoxin are permitted), previous venous or arterial thrombotic events, pulmonary embolism
  -  Moderate or severe hepatic impairment, i.e. Child-Pugh class B or C(3)
  -  History of human immunodeficiency virus (HIV) infection or chronic hepatitis B or C
  -  Active clinically serious infections of CTCAE > Grade 2 (CTCAE v4.02)
  -  Symptomatic metastatic brain or meningeal tumors unless the subject is > 3 months from definitive therapy, has no evidence of tumor growth on an imaging study within 4 weeks prior to study entry, and is clinically stable with respect to the tumor at the time of study entry. Subjects must not be on acute steroid therapy or taper off steroid therapy (chronic steroid therapy is acceptable provided that the dose is stable for 4 weeks prior to study entry and following screening CT / MRI scan). Subjects with neurological symptoms should undergo a CT / MRI scan of the brain to exclude new or progressive brain metastases. Spinal cord metastasis is acceptable
  -  Seizure disorder requiring therapy (such as steroids or anti-epileptics)
  -  History of organ allograft
  -  Evidence or history of bleeding disorder, i.e. any hemorrhage / bleeding event of CTCAE > Grade 2 within 4 weeks prior to prior to the first dose of study drug

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

Clinical trial: A Study of MK-4827 for the Treatment of Mantle Cell Lymphoma (MK-4827-002)

Summary: This study will investigate the efficacy and safety of MK-4827 in participants with relapsed mantle cell lymphoma (MCL) and in a subset of participants with inactivation of the Ataxia-Telangiectasia Mutated (ATM) gene.


Eligibility: Inclusion Criteria :
  -  Participant must have a diagnosis of MCL that has relapsed after at least one prior chemotherapy regimen or for which the participant has refused standard therapy
  -  Participant has measureable disease defined by lymphadenopathy, organomegaly, bone marrow involvement and/or circulating lymphoma cells. At least one lesion must be > 2 cm in the longest diameter and measurable in 2 perpendicular dimensions
  -  Participant has a performance status of 0, 1, or 2 on the Eastern Cooperative Oncology Group (ECOG) Performance Scale
  -  Female participants of child-bearing potential agree to use two approved contraceptive methods or remain abstinent throughout the study
  -  Male participants agree to use an adequate method of contraception throughout the study
  -  Participant has no history of prior cancer except certain cervical, skin, or prostate cancers, or has undergone potentially curative therapy with no recurrence for five years, or is deemed at low risk for recurrence
  -  Participant has not had any platelet or red blood cell transfusions or colony stimulating factor support during the month prior to treatment
  -  Participant has a pre-study diagnostic formalin fixed paraffin-embedded tumor tissue sample available
  Exclusion Criteria :
  -  Participant has had chemotherapy, radiotherapy, or biological therapy within 4 weeks of screening
  -  Participant has a history of central nervous system (CNS) lymphoma
  -  Participant requires the use of corticosteroids
  -  Participant is pregnant, breastfeeding, or expecting to conceive or father children during the study
  -  Participant is known to be human immunodeficiency virus (HIV)-positive
  -  Participant has a history of Hepatitis B or C

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

Clinical trial: Assessing DNA Changes in High Risk Prostate Cancer to Determine Prognosis

Summary: One of the biggest problems facing prostate cancer patients and their treating physicians is who needs to be treated and when. Common clinical and pathological parameters are useful (PSA, Gleason score, etc.) but do not clearly predict who will benefit from treatment and who will fail. Genetic markers for tumor aggressivity would be of greater value. The finding that the TMPRSS2-ERG gene fusion is associated with an increase risk of cancer progression is important. TMPRSS2 is controlled by androgen (testosterone) and ERG is part of a family of proteins which have a role in controlling cell growth, cell specialization and producing tumors. As a consequence of this gene fusion, production of the ERG protein increases in the presence of testosterone and could be key to the development of prostate cancer, resistance to treatment and poor outcome. The PTEN gene is known to have a role as a tumor suppressor. Its deletion is a contributing factor in the development of prostate cancers and poor outcome. The coexistence of the two markers could be associated with a higher risk of recurrence.
  To date there have been no studies regarding the presence of either of these two markers or their coexistence in high risk prostate cancer patients who, despite radiation therapy and androgen suppression, develop biochemical failure (their PSA levels rise once again). Patients participating in the PCS IV study (high risk prostate cancer treated with radiation therapy plus either 18 or 36 months of hormonal suppression) who have had biochemical failure or 3 years of follow-up post hormonal therapy will be approached.
  Tumor blocks from consenting patients will be collected and analyzed for the presence of the TMPRSS2-ERG gene fusion and the PTEN deletion at the Pathology Department of the Jewish General Hospital. Statistical analysis will be carried out to see whether either or both markers are present, whether they are associated with certain clinical and pathological high risk factors, and whether they can be used to predict which patients will fail treatment.


Eligibility: Inclusion Criteria:
  -  patients with prostate cancer post radical radiation therapy and LHRH agonist treated in PCSIV clinical trial
  -  biochemical failure (PSA nadir + 2) or minimum follow-up of 3 years post completion of hormonal therapy
  -  high risk group
  1. gleason score 8-10
  2. PSA ≥ 20 ng/ml
  3. T3 or T4

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

Clinical trial: Real Life Evaluation of Lupron in the Management of Prostate Cancer: A Canadian Post Marketing Observational Study

Summary: The purpose of this study is to evaluate the Canadian Real Life Evaluation of the Effectiveness of Lupron in the Management of Prostate Cancer.

Detailed description: This is a Canadian Post Marketing Observational Study utilizing a prospective cohort design. Patients with Prostate Cancer who are prescribed Lupron will be entered into the study cohort and will be followed for a maximum of 36 months with recommended assessments at 3, 6, 12, 18, 24, 30 and 36 months after baseline. Treatment of the patients and follow up will be according to the physician's judgment, regional regulations and the product monograph.

Eligibility: Inclusion Criteria:
  -  Has provided written informed consent allowing the use of their data for the study and providing permission for contact by the study personnel
  -  Diagnosed with Prostate Cancer
  -  Prescribed Lupron as part of his treatment by his treating physician
  Exclusion Criteria:
  -  Currently participating in another prospective study including controlled clinical trials and observational studies.
  -  Patient cannot or will not sign informed consent
  -  Survival expectancy less than 2-3 years as per the treating physician's judgment
  -  Presence of other condition that, in the opinion of the treating physician, prohibits the patient from participating in the study or obscures the assessment of the treatment of Prostate Cancer
  -  History of alcohol or drug abuse
  -  No longer than 6 months of therapy if currently on luteinizing hormone-releasing hormone (LHRH) treatment

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

Clinical trial: Individualized Chemotherapy Based on BRCA1 and RRM1 mRNA for Advanced Non-small Cell Lung Cancer (NSCLC)

Summary: Gemcitabine, docetaxel, CPT-11 and cisplatin are effective in 1st line treatment of advanced non-small cell lung cancer (NSCLC). Platinum-based doublets including gemcitabine, docetaxel or CPT-11 are standard 1st regimens. BRCA1 and RRM1 expression levels are reported to be associated with sensitivity of the tumor cells to cytotoxic agents. Some Phase II or III trials did prove feasibility of customized chemotherapy based upon expression levels of one or two biomarkers in the NSCLC patients. The investigators think customized chemotherapy may further improve efficacy of chemotherapy in advanced NSCLC. But there is no randomised trial to compare efficacy of standard chemotherapy with individualized chemotherapy in this setting. So, the investigators plan to initiate this phase II trial to compare efficacy between standard chemotherapy of gemcitabine/cisplatin versus customized chemotherapy in chemonaive NSCLC patients.

Detailed description: Primary end point:ORR Secondary end point:PFS,OS,safety,QOL,etc.

Eligibility: Inclusion Criteria:
  1. Written informed consent,
  2. Histologically confirmed stage M1a or M1b NSCLC,
  3. Aged over 18 years old,
  4. Measurable disease,
  5. Life expectancy of at least 12 weeks,
  6. No prior chemotherapy or target therapy,
  7. No brain metastases or spinal cord compression,
  8. Less than 10% body weight loss,
  9. ECOG performance status 0-2,
  10. Adequate vital organ function (haematological, renal, hepatic, etc).
  11. Enough tissue for detection of BRCA1 and RRM1 expression.
  Exclusion Criteria:
  1. Prior systemic cytotoxic chemotherapy or EGFR TKI therapy,
  2. Positive pregnancy test,
  3. Another active malignancy, other than superficial basal cell and squamous cell or carcinoma in situ of the cervix, within the last 5 years,
  4. Patients with brain metastases or spinal cord compression,
  5. Allergy to gemcitabine, cisplatin, docetaxel, CPT-11,
  6. Any unstable systemic disease including active infection,
  7. No enough tissue for detection of BRCA1 and RRM1

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

Clinical trial: Test of Chamber Pressure to Divers and Chamber Attendants

Summary: SCUBA divers and chamber inside attendants will undergo a brief hyperbaric chamber excursion and will be asked to what chamber pressure they were compressed and what gas they breathed.

Detailed description: In clinical trials evaluating hyperbaric oxygen, blinding can be challenging. Options for participant blinding include offering regular air at a lower pressure than the hyperbaric oxygen intervention, or compressing all participants to the same pressure but providing different gas mixes to the active and sham arms.
  In some trials of hyperbaric oxygen for brain injury, investigators offer a sham chamber session (regular air at 1.2 atmospheres absolute [atm abs]) compared to the active intervention, hyperbaric oxygen (100% oxygen at 1.5 atm abs). It is unknown whether individuals familiar with pressure changes, such as divers and hyperbaric chamber inside attendants, could discern the difference between these pressures and thereby become unblinded to study allocation.
  In this study, 80 experienced divers and chamber inside attendants will be enrolled and randomly assigned to one of four possible chamber pressures and one of two breathing gases. After a brief hyperbaric chamber excursion, they will be asked to what chamber pressure they were compressed and what gas they breathed. If participants can accurately report chamber pressure or breathing gas, pressure-familiar individuals should be excluded from blinded clinical trials of hyperbaric oxygen.

Eligibility: Inclusion Criteria:
  -  Adult, age 18 - 65 years
  -  Completion of medical history questionnaire without concerns identified for exposure to increased pressure
  -  Familiarity with atmospheric pressure change:
  -  Experienced and active hyperbaric chamber inside attendant: more than 50 hyperbaric compressions, with more than 4 have been in the last 4 months; or
  -  Experienced and active SCUBA diver: more than 20 lifetime compressed gas open water (not swimming pool) dives, with more than 10 in the last 12 months
  -  Able to equalize middle ear pressure easily
  Exclusion Criteria:
  -  Pregnancy
  -  Known risk for barotrauma, as identified on the medical history questionnaire, such as:
  -  Recent (within 12 months) inner ear or sinus surgery
  -  Spontaneous pneumothorax
  -  Pulmonary cysts
  -  Emphysema
  -  Bullous lung disease
  -  Chronic obstructive pulmonary disease needing chronic active therapy
  -  Inability to tolerate chamber confinement or pressure
  -  Presence of heart failure
  -  Presence of any implanted electrical device, except hyperbaric-approved pacemakers
  -  Presence of middle-ear tympanostomy tubes

Relevance to patient case: not relevant