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

Clinical trial: MSCs For Treatment of Azoospermic Patients

Summary: In this study, we performed autologous BMDMSC transplantation to the testis of Azoospermic patients in a trial to enhance and activate the spermatogonial stem cells of the testis and aiming to produce motile sperm.

Detailed description: Bone marrow aspirated and stem cells were isolated, cultured and characterized using flow cytometer. Stem cells prepared according to GMP regulations then injected into rete testis using special syringe. Patients follow up will carried out for a year , three month interval. FSH, testosterone, testicular size as well as sexual potency will assessed every three months.

Eligibility: Inclusion Criteria:
  -  All Non obstructive Azoospermic Patients.
  -  Azoospermic Patients due to Administration of Chemo/Radiotherapy.
  Exclusion Criteria:
  -  Patients with Testicular Cancer.
  -  Patients with Complete Deletion of Chromosome Y AZF (a,b,c) Regions.

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

Clinical trial: Radical Retropubic Prostatectomy Versus Conventional External Beam Radiotherapy for Clinically Localized Prostate Cancer

Summary: The purpose of this study is to evaluate the effectiveness of the two most established primary treatments for patients with clinically localized prostate cancer: radical retropubic prostatectomy, and external-beam radiotherapy. The primary aim is assessing biochemical disease-free survival, overall survival, and prostate cancer-specific survival. As secondary objectives quality of Life impact of treatments' side effects will be also assessed.

Detailed description: Eligible patients had clinically localized (clinical TNM classification T1 or T2), biopsy-proven adenocarcinoma of the prostate and were randomly treated with RRP or EBRT. Exclusion criteria included prior treatment for prostate cancer, the presence of metastatic disease on imaging studies, the receipt of neoadjuvant androgen ablation before registration, and an inability to read or understand Italian language. The institutional review boards of every participating centre approved the study design. Every patient enrolled signed an informed-consent form approved by the institutional review boards. Clinical information collected from the medical record included pre-treatment serum prostate-specific antigen (PSA) level, clinical T classification, and biopsy Gleason score. Follow-up assessments were completed before treatment and every 3 months after treatment. Subjects who sought primary treatment elsewhere or did not return follow-up questionnaires beyond the initial assessment were excluded from this analysis.

Eligibility: Inclusion Criteria:
  -  Age 75 years or younger
  -  Diagnosis of prostate cancer, as verified by cytologic or histologic examination the tumor is well differentiated to moderately well differentiated
  -  Untreated, clinically localized prostate cancer, with a tumor stage of T1, or T2
  -  Prostate specific antigen (PSA) level of ≤10 ng/ml
  -  Bone scan with no abnormalities
  -  Health status that would permit radical prostatectomy
  -  Life expectancy of more than 10 years.
  Exclusion Criteria:
  -  PSA >10 ng/ml
  -  Bone scan consistent with metastatic disease
  -  Other evidence that cancer of the prostate is not clinically localized
  -  Life expectancy less than 10 years
  -  Serum creatinine greater than 3 mg/dl
  -  Myocardial infarction within last 6 months
  -  Unstable angina Class III or IV
  -  Severe pulmonary disease
  -  Liver failure
  -  Severe dementia
  -  Debilitating illness Malignancies, except for nonmelanomatous skin cancer, in the last 5 years.

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

Clinical trial: Prostate Cancer Screening in Men With Germline BRCA2 Mutations

Summary: The purpose of this study is to determine the incidence of prostate cancer in men with the BRCa2 gene mutation as an independent indicator for prostate cancer screening.

Detailed description: This is a cohort screening study to prospectively identify the incidence of prostate cancer in a population of BRCA2 carriers. All men identified to have a BRCA2 mutation as part of the Yale Cancer Genetic Counseling Program will be approached and offered participation in the study via our program newsletter, BRCA listserv, Facebook page and a targeted mailing.
  Standard of care screening at the Yale Cancer Center for men with a normal prostate cancer risk consists of a PSA test and prostate physical examination beginning at age 50 years and if either is abnormal an MRI of the prostate followed by Fusion-targeted biopsy of the prostate is performed.

Eligibility: Inclusion Criteria:
  -  All men ≥30 years of age with at least a ten-year life expectancy
  -  A known BRCA2 mutation
  -  Ability to have an MRI
  -  Able to give informed consent will be approached to participate in the study
  Exclusion Criteria:
  -  If a man has received or is currently receiving treatment for prostate cancer

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

Clinical trial: Detection of Oncogenic Tumor Mutations in the Urine and Blood of Lung and Colorectal Cancer Patients

Summary: The purpose of this study is to see whether gene mutations can be found in the urine or blood of lung cancer patients and urine of colorectal cancer patients. Gene mutations are when DNA in a gene is damaged in a way that changes the genetic message carried by that gene. Gene mutations can sometimes cause lung cancers. These gene mutations are only found in lung and colorectal cancer cells, not the normal cells in your body. All lung cancer tumors and colorectal cancer tumors are now tested for different gene mutations as their presence affects lung cancer treatment. Tumor samples obtained from a biopsy or surgery are typically tested for these gene mutations.


Eligibility: Inclusion Criteria:
  Lung cancer:
  For patients participating in Part A (initial testing) and Part B (serial testing):
  -  Patients must have a diagnosis of stage IV lung adenocarcinoma undergoing systemic therapy.
  -  Patients must have had or intend to have EGFR mutation testing (specifically including exon 19 deletions and L858R) performed on their tumor with results available from a CLIA certified laboratory.
  -  ≥ 18 years of age
  Specific to patients participating in Part B (serial testing):
  -  Patients must be planning to receive cancer care at Memorial-Sloan Kettering.
  -  Patients must have a confirmed EGFR mutant lung cancer (exon 19 deletions and L858R) with molecular testing results available from a CLIA certified laboratory.
  -  Must be within 3 months of their diagnosis of metastatic lung cancer.
  -  Treatment plan should include an EGFR tyrosine kinase inhibitor, but may concurrently be on a therapeutic protocol.
  Colorectal Cancer:
  For patients participating in Part A (initial testing) and Part B (serial testing):
  -  Patients must have a diagnosis of stage IV colorectal adenocarcinoma undergoing systemic therapy or have recently progressed on therapy including anti-EGFR based therapy.
  -  Patients must have had or intend to have RAS/RAF mutation testing on their tumor with results available from a CLIA certified laboratory. For the patients who recently progressed on anti-EGFR must have tumor tissue molecular analyses preformed (prior to enrolling or a plan to test it at the time of enrollment).
  -  >18 years of age
  Specific to patients participating in Part B (serial testing):
  -  Patients must be planning to receive cancer care at Memorial-Sloan Kettering.
  -  Patients must have a confirmed RAS/RAF mutant colorectal cancer with molecular testing results available from a CLIA certified laboratory.
  -  Must be within 3 months of their diagnosis of metastatic colorectal cancer.
  Exclusion Criteria:
  lung cancer and colorectal cancer
  -  Comorbidities that would prohibit or make serial urine collection difficult or impossible

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

Clinical trial: Prospective Evaluation of Stereotactic Body Radiotherapy for Metastatic Prostate Cancer

Summary: The investigators aim to test the safety and feasibility of prostate gland stereotactic body radiotherapy (SBRT) plus best systemic therapy in newly diagnosed metastatic prostate cancer.

Detailed description: The investigators and other investigators have previously documented the safety and efficacy of definitive intent stereotactic body radiotherapy (SBRT) in the treatment of localized prostate cancer.
  In the metastatic setting for multiple malignancies, improved survival rates and disease outcomes have been shown with definitive treatment of the primary disease site. This concept of "cytoreductive" surgery or decreasing the primary tumor burden is now considered the standard of care for metastatic colon, ovarian, renal cell, and some breast carcinomas (plus post-surgery irradiation).
  With new guidelines and declining rates of PSA screening, the incidence of newly diagnosed metastatic prostate cancer is expected to increase. A recent population-based study has concluded significant improvements in the definitive treatment of the local prostate cancer in the stage IV setting with either radical prostatectomy or conventional prostate radiation treatments/brachytherapy. To our knowledge, one prospective phase II trial is currently accruing patients to best systemic therapy or best systemic therapy (BST) plus definitive treatment with either radical prostatectomy or conventionally fractionated radiation therapy
  The investigators hypothesize that the addition of primary disease SBRT to best systemic therapy for newly diagnosed metastatic prostate cancer would be associated with an acceptable safety profile, quality of life, disease progression, and overall survival. The addition of SBRT to best systemic therapy is also expected to be better-received for stage IV patients (with relatively limited prognosis), vs. fully fractionated radiation therapy, brachytherapy, or radical prostatectomy. The above endpoints would initially be tested in a prospective phase II multi-institutional trial and in comparison with historical controls.

Eligibility: Inclusion Criteria:
  -  Histologically-confirmed, adenocarcinoma of the prostate
  -  Clinical Stage T1b - T4, NX-0-1, M1
  -  Any Gleason score
  -  PSA<1000
  -  ECOG Performance Status 0-2
  -  No prior prostate radiation or other definitive therapy
  Exclusion Criteria:
  -  Prior prostatectomy or cryotherapy of the prostate
  -  Prior radiotherapy to the prostate or lower pelvis
  -  Implanted hardware or other material that would prohibit appropriate treatment planning or treatment delivery, in the investigator's opinion
  -  Chemotherapy for a malignancy in the last 5 years
  -  History of an invasive malignancy (other than this prostate cancer, or basal or squamous skin cancers) in the last 5 years

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

Clinical trial: Cancer Prevention in Women With a BRCA Mutation

Summary: This study aims to develop a follow-up telephone-based genetic counselling (FTGC) intervention for women with a BRCA1 or BRCA2 mutation who have received genetic counseling in the past. Typically, when women undergo genetic testing, they receive standard genetic counselling prior to testing in order to fully understand the procedure and associated implications. If a woman's genetic test results are positive for a mutation, cancer prevention options are then discussed with a counsellor. However, in Canada, there is currently no formal follow-up counselling for women with a BRCA mutation to provide ongoing guidance and support about latest risk reduction strategies. Standard care relies on women making contact for any follow-up questions or concerns they may have. As a result, these women might not have the most current information regarding genetic risk assessment and prevention options. Therefore, individuals are being asked to participate in this study to aid research about the efficacy of FTGC in women with a BRCA mutation.


Eligibility: Inclusion Criteria:
  -  Confirmed BRCA mutation
  -  Age 35 to 70 years
  -  No previous bilateral salpingo-oophorectomy
  -  No previous or current ovarian cancer
  -  At least 12 months since genetic testing or most recent contact by Narod follow-up study
  -  Can speak and understand English
  Exclusion Criteria:
  -  Currently receiving treatment for another cancer diagnosis
  -  Pregnant
  -  Given birth in the last 6 months
  -  Booked surgical date for BSO

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

Clinical trial: Pancreatic Cancer Screening of High-Risk Individuals in Arkansas

Summary: 100 subjects who have a family history of pancreatic cancer (PC), or known genetic syndromes associated with increased risk of pancreatic cancer, will be followed for five years. This data will be used to determine the pancreatic cancer and precancerous lesion detection rate in High Risk Individuals (HRIs). Subjects may agree to annual imaging and annual biomarkers or to biomarkers only.


Eligibility: Inclusion Criteria:
  -  Have a family history of PC as listed below or who have one of the following syndromes: Peutz-Jeghers syndrome - STK11; BRCA 1 and 2; PALB2; ATM; FAMMM / P16; HNPCC (Lynch) / MMR genes; Hereditary pancreatitis - PRSS1
  -  Individuals with three or more affected blood relatives (1st, 2nd or 3rd degree)
  -  Individuals with two or more affected blood relatives with PC, with at least one affected FDR, should be considered for screening.
  -  Patients with a history of Peutz-Jeghers syndrome should be screened, regardless of family history of PC.
  -  Patients with a known p16 (FAMMM syndrome) with one affected 1st or 2nd degree relative will be considered for screening.
  -  Patients with a known BRCA1 or BRCA2 mutation with one affected 1st or 2nd degree relative should be considered for screening.
  -  Patients with a known PALB2 mutation with one affected family member should be considered for screening.
  -  Patients with a known Mismatch-repair gene-mutation carriers (Lynch syndrome) with one affected family member should be considered for screening.
  Exclusion Criteria:
  -  Not candidates for surgery

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

Clinical trial: Anticancer Activity of Nicotinamide on Lung Cancer

Summary: Nicotinamide is an inhibitor of human sirtuins (HDAC III), and is found to re-activate epigenetically silenced tumor suppressors, RUNX3 (runt-related gene 3) and others, in cancer cells. Nicotinamide was found to be effective in several animal cancer models including lung, bladder, liver, etc. The purpose of this study is to determine whether nicotinamide is also effective in the treatment of human lung cancer.

Detailed description: The standard therapy to the EGFR (epidermal growth factor receptor) mutation positive non-small-cell lung cancer patients who are not eligible to operation is to administer EGFR-TKIs (tyrosine kinase inhibitors, gefitinib or erlotinib). To determine the effectiveness of nicotinamide on lung cancer, nicotinamide or placebo tablet will be co-administered with gefitinib or erlotinib for two years until the event or censoring occurs. The stratified block randomization was designed with 3 covariates (EGFR mutation status, kind of EGFR-TKI, ECOG (Eastern Cooperative Oncology Group) performance status score variation). The size of lesions will be checked every other months by radiology. PD (progressive disease) will be assessed according to RECIST(Response Evaluation Criteria in Solid Tumors)1.1. After observing 36 events, an interim analysis of hazard ratio by Cox proportional hazard regression will be performed. The final analysis will be done by the same protocol after observation of 72 events. The significance level of the interim and final analysis were set to 0.0075 and 0.0209 respectively. Response rate, quality of life (measured by 10 questions at every visit), and overall survival will be analysed together. All other adverse reactions will be analysed and reported, if there.

Eligibility: Inclusion Criteria:
  -  Operation-impossible stage 4 non-small-cell lung carcinoma (NSCLC), or recurred terminal stage NSCLC after previous operation or radiation therapy
  -  EGFR mutated (exon 19 deletion or L858R mutation)
  -  Life expectation more than 3 months
  -  More than 1 measurable lesions by RECIST 1.1 which were not exposed to radiation previously
  -  ECOG (Eastern Cooperative Oncology Group ) performance status grade 0~2
  -  Who signed the informed consent form
  Exclusion Criteria:
  -  Who had received chemotherapy or EGFR tyrosin kinase inhibitors previously, except whom had received operation at least 6 months ago and received supplementary chemotherapy
  -  Who has metastasized brain lesion that needs operation or radiation therapy
  -  Above grade 2, CTCAE (Common Toxicity Criteria for Adverse Effects) 4.0 criteria for blood, liver and kidney
  -  Who does Not agree to contraception
  -  Who has allergy to nicotinamide

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

Clinical trial: Evaluation of PSMA-based PET as an Imaging Biomarker in Prostate Cancer

Summary: This research is being done to see if an investigational radioactive imaging agent (radiotracer) called 18F-DCFPyL can help us find prostate cancer at its original site in the prostate gland and in distant sites (bone, lymph nodes) in men diagnosed with prostate cancer before surgery.

Detailed description: The investigators propose to evaluate the feasibility of using a novel small molecule PET radiotracer, DCFPyL to target prostate cancer prostate-specific membrane antigen (PSMA). PSMA is a well studied cell surface marker of prostate cancer with increased expression associated with higher tumor grade and advanced metastatic tumors. More specifically it is associated with a higher Gleason score and there is evidence it can serve as a potential marker for prostate tumor carcinogenesis, progression and as a AR signaling surrogate marker of ADT response. This small molecule PET radiotracer specifically targeting an important prostate specific marker of AR signaling dynamics following ADT, tumor progression and metastatic potential warrants validation as an in-vivo non-invasive imaging biomarker for PSMA expression and prostate cancer detection.

Eligibility: Inclusion Criteria:
  -  Men 18 years of age or greater with recently diagnosed prostate cancer with planned radiation and ADT.
  -  Key inclusion criteria (the entire list of inclusion and exclusion criteria will appear later in section 4 of the protocol)
  -  Newly diagnosed prostate cancer pathologically proven by prostate biopsy
  -  Prostate biopsy histology grade ≥ Gleason 8-10
  -  Patients considered as candidates for and medically fit to undergo radiation and ADT
  -  At least 10 days after most recent prostate biopsy
  Exclusion Criteria:
  -  Prior pelvic external beam radiation therapy or brachytherapy
  -  Chemotherapy for prostate cancer
  -  Hormone deprivation therapy
  -  Investigational therapy for prostate cancer
  -  Hemorrhagic cystitis or active prostatitis

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

Clinical trial: Shear Wave Elastography of Prostate Cancer

Summary: Evaluation of significant Shear Wave Elastography Parameters for Prostate Biopsy and Prostate Cancer detection.

Detailed description: This Study will evaluate the Shear Wave Elastography (SWE) Parameters for Prostate Biopsy and Prostate Cancer detection.

Eligibility: Inclusion Criteria:
  -  Suspicious for prostate cancer with no pretreatment and Prostata specific Antigen (PSA) >4ng/ml or PSA velocity > 0.75 ng/ml per year or suspicious transrectal digital examination
  -  Status after external beam radiotherapy of the prostate in localized prostate cancer and suspicious for local prostate cancer recurrence
  Exclusion Criteria:
  -  None.

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

Clinical trial: Human Prostate Tissue Model to Maintain and Study Prostate Cancer Stem Cells

Summary: This pilot research trial studies the use of a human prostate tissue model to maintain and study prostate cancer stem cells. A human prostate tissue model uses leftover tissue that was removed during surgery from patients with non-cancerous enlargement of the prostate (benign prostatic hyperplasia) and may create an environment similar to the natural environment of the human body. Prostate cancer stem cells are cells that cause cancer to grow. Using real tissue to create an environment to study stem cells may help doctors learn more about how they work and how they respond to treatments.

Detailed description: PRIMARY OBJECTIVES:
  I. To optimize a decellularized prostate tissue model for the maintenance of prostate cancer stem cells.
  SECONDARY OBJECTIVES:
  I. To investigate the self-renewal and differentiation ability of human prostate cancer stem cells (CSCs) (tumor-associated calcium signal transducer 2 [TROP2]+ cells) in the above mentioned decellularized prostate tissue model.
  II. To compare the number of CSCs according to key patient characteristics, including race, age, Gleason, metastasis status, and previous cancer treatment(s).
  OUTLINE:
  Tissue samples are collected from patients with benign prostatic hyperplasia for decellularization and preparation as human extracellular matrix for growing human prostate CSCs. Tissue samples are also collected from patients with prostate cancer for the analysis of TROP2+ cells by flow cytometry.

Eligibility: Inclusion Criteria:
  -  Male patients scheduled for a prostatectomy
  -  Ability to understand and the willingness to sign an Institutional Review Board (IRB)-approved informed consent document
  Exclusion Criteria:
  -  Patients with prostate involvement secondary and as a result of metastasis or spread of cancerous cells from other organs

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

Clinical trial: Characterization of 3q29 Deletion Syndrome and 3q29 Duplication Syndrome

Summary: The 3q29 deletion syndrome is caused by a deletion of a small part of human chromosome 3, and the duplication syndrome is caused by a duplication of this same small region. The purpose of this study is to understand the medical and behavioral consequences of these syndromes.

Detailed description: People with 3q29 deletion syndrome are missing a small part of a region on human chromosome 3, and people with 3q29 duplication syndrome have an extra part of their chromosome 3. Sometimes babies are born with a deletion or duplication of part of human chromosome 3, even though their parents have an intact chromosome 3. This is called de novo (or new) abnormalities.

Eligibility: Inclusion Criteria:
  -  Diagnosis of 3q29 deletion or 3q29 duplication
  -  Consent from parents or guardians or an adult with 3q29 deletion or 3q29 duplication that does not require a legal guardian or an adult who is the healthy sibling of an individual with 3q29 deletion or 3q29 duplication or a healthy age-matched control
  Exclusion Criteria:
  -  Clinically significant medical disease that would prohibit participation in the study procedures

Relevance to patient case: not relevant