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

Clinical trial: Conjugate Pneumococcal Vaccine in Ataxia Telangiectasia (AT)

Summary: Ataxia Telangiectasia (AT) is an autosomal recessive inherited condition caused by mutations in the ATM gene1. Patients suffer from neuro-degenerative problems, usually commencing in the second year of life, and affecting predominantly the cerebellum. They also develop the characteristic superficial telangiectases. Between 60 and 80% of affected children are immunodeficient. This is associated with deficiency of immunoglobulin A (IgA ) 2, of IgG23 and of antibody responses to pneumococcal polysaccharides4. Patients suffer recurrent sino-pulmonary infections but a recent study suggests poor correlation between immune status and immunological parameters5. If uncontrolled, recurrent pulmonary infections can contribute to the development of chronic lung disease and bronchiectasis. Preventative management includes continuous prophylactic antibiotic treatment in some with the need for replacement immunoglobulin therapy in only a small proportion of cases. Antibiotics have been reasonably effective in this situation but the emergence of resistance amongst community acquired pneumococcal isolates is a cause for concern. Appropriate immunisation strategies may also have a role.
  This study is designed to look at antibody responses in a one versus two dose regimen in a cohort of AT patients recruited through the AT Society a national charitable organisation involved in providing support to families with this condition and in fostering education and research in the field.


Eligibility: Inclusion Criteria:
  -  Genetically confirmed diagnosis of AT

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

Clinical trial: Selenium in Treating Patients With Prostate Cancer

Summary: RATIONALE: Selenium may prevent or slow the growth of prostate cancer.
  PURPOSE: This randomized phase II trial is studying how well selenium works in treating patients with prostate cancer.

Detailed description: OBJECTIVES:
  -  To investigate the ability of selenium to prevent progression in patients with adenocarcinoma of the prostate.
  -  To investigate the ability of selenium to effectively modulate biomarkers of prostate cancer.
  -  To determine if selenium modifies the progression of prostate cancer based on an analysis of initial biopsy, subsequent blood biomarkers, and urological symptoms.
  -  To further establish the safety of chronic supplementation with selenium in these patients.
  OUTLINE: Patients are stratified according to Gleason score (low vs moderate). Patients are randomized to 1 of 3 treatment arms.
  -  Arm I: Patients receive oral placebo once daily for 48 months in the absence of disease progression or unacceptable toxicity.
  -  Arm II: Patients receive low-dose oral selenium once daily for 48 months in the absence of disease progression or unacceptable toxicity.
  -  Arm III: Patients receive high-dose oral selenium once daily for 48 months in the absence of disease progression or unacceptable toxicity.
  Blood and tissue samples are collected periodically for biomarker laboratory studies. Blood samples are analyzed for levels of prostate-specific antigen, chromogranin A, alkaline phosphatase, alpha tocopherol, lycopene, and other vitamins; levels of selenium by atomic absorption spectrometry; and oxidative damage to DNA. Tissue samples are analyzed for levels of Bcl-2, p53, Ki-67, thioredoxin reductase, thioredoxin, and glutathione peroxidase by immunohistochemistry and for apoptotic index by TUNEL assay.
  Patients complete urological symptom questionnaires and other questionnaires periodically.

Eligibility: DISEASE CHARACTERISTICS:
  -  Biopsy-proven adenocarcinoma of the prostate within the past 48 months
  -  Prostate-specific antigen < 50 ng/mL
  -  Gleason score < 8
  -  Currently undergoing "watchful waiting" for prostate cancer
  -  No metastatic disease
  PATIENT CHARACTERISTICS:
  -  Life expectancy ≥ 3 years
  -  AST and ALT ≤ 1.5 times upper limit of normal (ULN)
  -  Alkaline phosphatase ≤ 1.5 times ULN
  -  Bilirubin ≤ 1.5 times ULN
  -  Creatinine ≤ 1.5 times ULN
  -  No other malignancy within the past 5 years, except nonmelanoma skin cancer
  PRIOR CONCURRENT THERAPY:
  -  No prior hormone therapy, radiotherapy, chemotherapy, or surgery for prostate cancer
  -  At least 90 days since prior and no concurrent selenium (as a dietary supplement or as part of a multivitamin) exceeding 50 mcg/day

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

Clinical trial: Health-Related Quality of Life in Gay Men With Localized Prostate Cancer

Summary: RATIONALE: Gathering information about prostate cancer, treatment, and quality of life from gay men with prostate cancer may help doctors plan the best treatment.
  PURPOSE: This clinical trial is collecting information about health-related quality of life from gay men with localized prostate cancer.

Detailed description: OBJECTIVES:
  -  To enroll 200 gay men with localized prostate cancer in a cross-sectional study of prostate cancer outcomes.
  -  To complete an R01 application using pilot data collected from these patients.
  -  To complete manuscripts describing the factors that influence quality of life and treatment satisfaction in these patients.
  OUTLINE: Patients complete a web-based survey about their disease (biopsy Gleason score, PSA at diagnosis, and T-stage), treatment (treatment type, time since treatment, and use of healthcare services [e.g., oral medications for erectile dysfunction]), symptom distress, and psychosocial factors (ethnicity, health literacy, level of social support, communication with provider, relationship status, and communication with partner) that affect their health-related quality of life. The data will be used to provide the information necessary to tailor an existing prostate cancer survivorship intervention to address the specific needs of gay men with prostate cancer.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of localized prostate cancer
  -  No advanced disease
  -  Self-identified as gay
  PATIENT CHARACTERISTICS:
  -  Able to complete an online questionnaire
  -  Able to speak and understand English
  PRIOR CONCURRENT THERAPY:
  -  Not specified

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

Clinical trial: Short Arc Multifidus Study

Summary: Patients will be performing Logan short arc banding protocols to see the effect on multifidus size

Detailed description: The subjects will initially be scanned by diagnostic ultrasound by to assess the cross sectional area of their lumbar multifidi. Then they will perform 3 sets of 30 second periods of Logan Short Arc Banding on the ATM machine twice a week for 4 weeks and then they will be scanned again using diagnostic ultrasound to assess the effects of the rehabilitation exercise.

Eligibility: Inclusion Criteria:
  -  Male or Female ages 18-54
  Exclusion Criteria:
  -  Asymptomatic of: Low Back Pain, previous spinal injury, surgery or other condition affecting the spine, local infection, injury or malignancy; pregnancy or any condition affecting muscle reaction time.

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

Clinical trial: Study of Tumor Samples From Patients With Ewing Sarcoma

Summary: This laboratory study is looking at tumor samples from patients with Ewing sarcoma. 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

Detailed description: Study Subtype: Ancillary/Correlative Observational Study Model: Cohort Time Perspective: Prospective Biospecimen Retention: Samples With DNA Biospecimen Description: Tissue Study Population Description: Samples collected from AEWS0031 and patients registered on AEWS08B1 Sampling Method: Non-Probability Sample
  PRIMARY OBJECTIVES:
  I. Determine if mutation of p53, and/or deletion of the p16 locus, have prognostic value in patients with Ewing sarcoma.
  SECONDARY OBJECTIVES:
  I. Estimate the incidence of p53 mutation in Ewing sarcoma samples collected from COG studies.
  II. Estimate the incidence of p16 deletions in Ewing sarcoma samples collected from COG studies.
  III. Prepare and archive amplified genomic DNA from Ewing sarcoma samples collected from COG studies for future biologic analysis.
  OUTLINE: This is a multicenter study.
  Previously archived tumor samples are analyzed for p53 mutations and p16 deletion by immunohistochemistry, FISH, PCR, and DNA sequencing.

Eligibility: Inclusion Criteria:
  -  Diagnosis of Ewing sarcoma
  -  Banked specimens from patients enrolled on AEWS0031

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

Clinical trial: Functional Improvement of Progenitor Cells and Endothelial Function by Vildagliptin in Diabetes Mellitus (FINNjA-DM).

Summary: SDF-1, an important cytokine for neovascularisation is cleaved by (dipeptidyl peptidase IV) DPPIV.
  The aim of this study is to assess the effect of the dipeptidyl peptidase IV inhibitor vildagliptin (Galvus®) on endothelial function as well as number and functional activity of progenitor cells in patients with documented diabetes mellitus.

Detailed description: The peptidase CD26 (DPPIV/dipeptidyl peptidase IV) removes dipeptides from the amino terminus of proteins and thereby inactivates these cleaved proteins. It was shown, that CD26 cleaves SDF-1 into a non-mitogenic molecule. Inhibition or deletion of CD26 leads to an increased homing of hematopoietic progenitor cells to the bone marrow after transplantation by increasing the invasion capacity of these cells {Campbell et al. 2008; Christopherson et al. 2004}.
  The cytokine SDF-1 is released in response to hypoxia, is crucial for progenitor cell homing and recruitment of cells for neovascularisation. Invasion capacity is closely related to the cytokine SDF-1 and the SDF-1 receptor CXCR4 {Ceradini et al. 2004}. The in vivo neovascularisation capacity of progenitor cells is closely correlated to their functional capacity as SDF-1 induced invasion or colony-forming capacity {Heeschen et al. 2004; Britten et al. 2003; Assmus et al. 2007}.
  Therefore, the aim of this study is to assess the effect of the dipeptidyl peptidase IV inhibitor vildagliptin on endothelial function as well as number and functional activity of progenitor cells in patients with documented diabetes mellitus.

Eligibility: Inclusion Criteria:
  -  Patients with diabetes mellitus type 2 under stable medication
  -  HbA1c between 7% an 10%
  -  age between 18 and 80 years
  -  signed informed consent
  Exclusion Criteria:
  -  Atrial fibrillation (plethysmographic recordings can only obtained in sinus-rhythm)
  -  CAD with reduced left ventricular ejection fraction (LVEF <45%)
  -  Pregnancy, chronic or acute infection, fever
  -  Diabetes mellitus type 1
  -  Newly diagnosed diabetes, uncontrolled diabetes
  -  Neoplasm
  -  Known allergy to study drug
  -  Severe liver/kidney disease
  -  HIV, Hepatitis
  -  Participation at other studies within the last 30 days

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

Clinical trial: Safety Study of PLX108-01 in Patients With Solid Tumors

Summary: PLX3397 is a selective inhibitor of Fms, Kit, and oncogenic Flt3 activity. The primary objective of this study is to evaluate the safety and pharmacokinetics of orally administered PLX3397 in patients with advanced, incurable, solid tumors in which these target kinases are linked to disease pathophysiology. The secondary objective is to measure the pharmacodynamic activity of PLX3397 via blood, plasma and urine biomarkers of Fms activity.


Eligibility: Inclusion Criteria:
  -  Age 18 and older
  -  Solid tumors refractory to standard therapy
  -  For the Extension cohorts, patients must have measurable disease by RECIST criteria and meet the following disease-specific criteria:
  -  For advanced or recurrent mucoepidermal carcinoma (MEC) of the salivary gland, patients must not be candidates for curative surgery or radiotherapy.
  -  For pigmented villo-nodular synovitis (PVNS), patients must have a histologically confirmed diagnosis of inoperable progressive or relapsing PVNS, or resectable tumor requesting mutilating surgery, as well as demonstrated progressive disease in the last 12 months.
  -  For gastrointestinal stromal tumors (GIST), patients must have failed previous therapy with imatinib and sunitinib. Patients with known PDGFR mutations are excluded, but mutation testing is not required for study entry.
  -  For anaplastic thyroid cancer (ATC), patients must have histologically or cytologically diagnosed advanced ATC.
  -  For metastatic solid tumors with documented malignant pleural and/or peritoneal effusions, patients must not be receiving specific therapy for the effusion or have an indwelling drain.
  -  ECOG performance status 0 or 1
  -  Life expectancy >= 3 months
  -  Adequate hepatic, renal, and bone marrow function
  Exclusion Criteria:
  -  Specific anti-cancer therapy within 3 weeks of study start
  -  Uncontrolled intercurrent illness
  -  Refractory nausea or vomiting, or malabsorption
  -  Mean QTc >= 450 msec (for males) or QTc >= 470 msec (for females)

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

Clinical trial: Efficacy Study of Olaparib With Paclitaxel Versus Paclitaxel in Gastric Cancer Patients

Summary: To assess the efficacy of olaparib when given in combination with paclitaxel compared with paclitaxel alone as defined by progression-free survival (PFS), in all patients with recurrent and metastatic gastric cancer who progress following first-line therapy


Eligibility: Inclusion Criteria:
  -  Recurrent or metastatic gastric cancer that has progressed following first line-therapy
  -  Confirmed ATM protein status by IHC archival tumour sample
  -  At least one lesion (measurable and/or non-measurable) that can be accurately assessed by imaging (CT/MRI) at baseline and follow up visits
  Exclusion Criteria:
  -  More than one prior chemotherapy regimen for the treatment of gastric cancer in the metastatic or recurrent setting
  -  Any previous treatment with a PARP inhibitor, including olaparib
  -  Patients with second primary cancer, except; adequately treated non melanoma skin cancer, curatively treated in situ cancer of the cervix, or other solid tumours curatively treated with no evidence of disease for >5 years

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

Clinical trial: The Effectiveness of 18F-fluorocholine Positron Emission Tomography (PET) in Detecting, Staging and Following-up Prostate Cancer

Summary: Choline is one of the components of phosphatidylcholine, an essential element of phospholipids in the cell membrane. Some malignant cells show their ability to actively incorporate choline to produce phosphocholine and phosphatidylcholine to facilitate tumor cell duplication. The efficacy of 18F-fluorocholine (18F-FCH) for localizing primary or metastatic prostate cancer has been recently reported in limited studies. This study will be conducted to delineate the effectiveness of 18F-FCH PET in (1) differentiating benign prostate hypertrophy (BPH) from prostate cancer, (2) staging prostate cancer, (3) following-up patients with prostate cancer after initial curative therapy.

Detailed description: Background:
  Prostate cancer is a leading cause of cancer death for male in Taiwan. Although 18F-FDG PET has been shown to be an effective tool in diagnosing many malignancies, previous studies have shown that 18F-FDG is not a suitable PET tracer for detecting prostate cancer. Choline is one of the components of phosphatidylcholine, an essential element of phospholipids in the cell membrane. Some malignant cells show their ability to actively incorporate choline to produce phosphocholine and phosphatidylcholine to facilitate tumor cell duplication. The efficacy of 18F-fluorocholine (18F-FCH) for localizing primary or metastatic prostate cancer has been recently reported in limited studies.
  Purpose:
  This study will be conducted to delineate the effectiveness of 18F-FCH PET in (1) differentiating benign prostate hypertrophy (BPH) from prostate cancer, (2) staging prostate cancer, (3) following-up patients with prostate cancer after initial curative therapy.
  Patients and Methods:
  This study will include
  1. Group 1: 50 patients with BPH
  2. Group 2: 50 patients with newly diagnosed prostate cancer and
  3. Group 3: 50 patients who have received curative treatment for prostate cancer and are suspicious of recurrence/metastases because of a persistent increase in their serum PSA.
  18F-FCH whole-body PET will be performed for each patient
  Expected Results:
  To evaluate the effectiveness of 18F-FCH in the diagnosis, staging and follow-up of prostate cancer.

Eligibility: Inclusion Criteria:
  Group 1: 50 patients with BPH
  1. Age above 35 years old
  2. Histologically confirmed BPH
  3. Informed consent signed
  Group 2: 50 patients with newly diagnosed prostate cancer and
  1. Age above 35 years old
  2. Histologically confirmed prostate cancer
  3. Informed consent signed
  Group 3: 50 patients who have
  1. Age above 35 years old
  2. Histologically confirmed prostate cancer and had received curative treatment for prostate cancer
  3. suspicious of recurrence/metastases because of a persistent increase in their serum PSA
  4. Informed consent signed
  Exclusion Criteria:
  -  Patients with other known malignancies will be excluded.

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

Clinical trial: Pancreatic Cancer Genetics

Summary: The aim of this study is to determine the frequency of the three most common BRCA1 and BRCA2 genetic mutations that are commonly found in Ashkenazi Jewish patients with pancreatic cancer. Testing for BRCA1 and BRCA2 mutations in relatives of hereditary pancreatic cancer patients may have a significant impact; allowing for early screening, treatment, and resection of pre-malignant tissue or malignant lesions.

Detailed description: Pancreatic cancer is the fourth leading cause of death from malignancy in the United States. Up to 15% of pancreatic cancers have a hereditary component. Several gene mutations and cancer syndromes have been identified that are frequently found in greater frequency in individuals with pancreatic cancer, including the breast ovary cancer syndrome (BRCA1/BRCA2 mutations). No studies adequately describe the epidemiology of inherited pancreatic cancer and genetic risk factors that may modify the penetrance of BRCA1/BRCA2 mutations. The primary aim of this study is to determine the frequency of BRCA1 (185delAG,5382insC) and BRCA2 (6174delT) mutations in Ashkenazi Jewish pancreatic cancer patients. Secondary endpoints will include determining the individual frequency of these mutations and other disease-modifying mutations, death from any cause, disease-free survival, and stage of disease at time of presentation, differences in tissue pathology, risk factors, treatment decisions and development of metachronous malignancies.
  The investigator plan to study about 100 patients, which will enable the true frequency of the mutation to be estimated. Although the impact of BRCA1/BRCA2 mutations will be initially studied in the Ashkenazi population, these data will be widely applicable to other pancreatic cancer patients carrying BRCA1/BRCA2 mutations. Testing for BRCA1 and BRCA2 mutations in relatives of hereditary pancreatic cancer patients may allow early screening, treatment, and resection of pre-malignant tissue or malignant lesions.

Eligibility: Inclusion Criteria:
  -  Patients diagnosed with pancreatic cancer.
  -  Patients are of Ashkenazi Jewish descent.
  -  Patients have been Columbia Pancreatic Cancer Prevention Program Registry and Tissue Bank for High-Risk Individuals (IRB-AAAA6154).
  Exclusion Criteria:
  -  Inability to provide informed consent.
  -  Under the age of 18 years old.

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

Clinical trial: Genetic Predictive Model Based on Single Nucleotide Polymorphisms in the DNA Repair Pathway and Drug Metabolis/Transport Pharmacogenetics in the Prediction of Response and Treatment Outcomes in Acute Myeloid Leukemia

Summary: The main component in the treatment of acute myeloid leukemia (AML) is consist of anthracycline (such as daunorubicin or idarubicin) and cytarabine. Inter-individual variability of transport/metabolism of the chemotherapeutic agent and several genetic pathways involved in the drug action might be associated with different response following the treatment for AML usually consisted of chemotherapy and/or transplantation. One of potential pathways involved in the drug action is DNA repair pathway, accordingly single nucleotide polymorphisms (SNPs) in the DNA repair machinery pathway might be a predictive marker for therapy outcomes in AML.
  Several genes were involved in the DNA repair machinery which are 1) Nonhomologous end joining (NHEJ) pathway involved in the G1/S phase, 2) Homologous recombinational repair (HRR) pathway involved in the S/G2 phase. XRCC4, LIG4, MRN and ATM are well known genes involved in the NHEJ pathway, while MRE11, RAD50, NBS1 (MRN), RAD51, XRCC2, XRCC3, RAD51B, RAD51C, RAD 51D, RAD52 or RAD54 are known to be associated with HRR pathway.
  A study suggested that the SNPs in the DNA repair pathway was involved in the susceptibility of secondary AML developing after chemotherapy or autologous hematopoietic stem cell transplantation, thus these SNP markers could become a predictive marker for secondary AML. However, it has never been investigated for multiple candidate pathways simultaneously with relateively larger number of patients. Accordingly, the current study attempts to investigate the potential role of the genotype markers in multiple candidate pathways, esp. focused on the DNA repair machinery, with respect to response following chemotherapy or survival of AML patients.
  Total of over 500 archived samples from the patients diagnosed as acute myeloid leukemia at the Samsung Medical Center, Seoul, Korea will be included, and genomic DNAs will be extracted and will be examined for their genotypes of the candidate SNPs involved in the DNA repair pathways. Then statistical analysis will be pursued for single marker analysis, haplotype analysis and for the construction of genetic risk model based on the multivariate analysis.


Eligibility: Inclusion Criteria:
  -  patients with acute myeloid leukemia
  -  15 years or older
  -  patients treated with induction/consolidation chemotherapy
  -  patients with available bone marrow sample
  Exclusion Criteria:
  -  acute biphenotypic leukemia

Relevance to patient case: not relevant