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

Clinical trial: Mechanisms and Predictors of Unusual Radiation or Chemotherapy Toxicity

Summary: In general, the toxicity of radiation therapy and chemotherapy exhibits a strong dose-response relationship. However, patients receiving similar doses still exhibit a range of toxicity responses due to a variety of factors, including comorbid conditions, disease (cancer) specific factors, and inter-individual genetic variation. A very small percentage of patients experience side effects that are either extremely severe or extremely mild compared to the majority of patients for the dose of radiation or chemotherapy given. Currently, the reasons for this are not entirely clear, but likely relate to patient specific factors such as immune response, cell/tissue repair capacity and other factors that fundamentally rely on rare genetic variations at loci involved in these responses. For example, patients with homozygous deletions in DNA damage response genes such as ATM are uniquely sensitive to DNA damaging agents. Many patients with severe, homozygous mutations in such genes have other sequela that lead to medical recognition of the syndrome prior to therapy. The investigators hypothesize that patients with unusually severe toxicity from therapy that do not exhibit classical signs of homozygous mutation syndromes are heterozygous for nonfunctional or hypofunctional alleles at these loci, such that the defect is only uncovered under the relatively acute, severe stress on that pathway by radiation or chemotherapy. Conversely, patients with very mild reactions could exhibit rare variants/combinations of variants that make them uniquely resistant to chemotherapy or radiotherapy toxicity.
  The purpose of the study is to better understand these mechanisms with the eventual goal of developing predictive markers that will allow us to help individually tailor cancer therapy is in future patients. Will accomplish these goals by studying a variety of factors from a single vial of blood. These will include circulating proteins and hormones, circulating cells and the levels and sequences of white blood cell DNA or RNA using a variety of techniques including but not limited to determination of cytokine/hormone levels, proteomic analysis, immunocytochemical assays, whole exome sequencing and qPCR.


Eligibility: Inclusion Criteria:
  -  Subjects will be age 18 or greater Subjects will have undergone chemotherapy and/or radiotherapy and experienced unusually mild or severe toxicity.
  Exclusion Criteria:
  -  Subjects for who, after initial review of medical records by study team personnel are not judged by the PI and/or sub-investigators to have sufficiently unusual toxicity from therapy.

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

Clinical trial: The Link Between BRCA Mutation and Endothelial Function

Summary: This study evaluates the effect of BRCA1&2 mutations on cardiovascular diseases by to comparing the endothelial function of male BRCA mutation carriers with that of age matched non-BRCA mutation carriers.


Eligibility: Inclusion Criteria:
  -  Known carrier or non-carrier, confirmed by genetic testing of BRCA 1/2 mutation
  -  Able and willing to sign an informed consent
  Exclusion Criteria:
  -  History of, or current, malignancy
  -  History of:
  -  Myocardial infarction
  -  Ischemic or Hemorrhagic cerebrovascular conditions
  -  Arterial embolic and thrombotic events
  -  Ischemic heart disease
  -  Prior coronary artery or ilio-femoral artery revascularization (percutaneous or surgical procedures)
  -  Peripheral vascular disease (e.g. claudication, prior vascular surgery/intervention)

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

Clinical trial: Non-Invasive Chromosomal Evaluation of 22q11.2

Summary: This study is being conducted to develop and evaluate a cell-free fetal DNA test (Ariosa Test) for non-invasive prenatal detection of 22q11.2 chromosomal deletion or duplication. Investigators will be evaluating subjects with abnormal U/S.


Eligibility: Inclusion Criteria:
  1. Patient is ≥18 years of age and able to provide consent or, if under the age of 18, the patient has parental consent and child assent provided as required by the governing ethics committee.
  2. If pregnant, patients must have a singleton pregnancy and be at least 10 weeks gestation at the time of the study blood draw.
  3. Patients must meet at least one of the following conditions at the time of enrollment:
  1. are pregnant with abnormal fetal cardiac findings on ultrasound and is undergoing evaluation with prenatal genetic testing or planned post-natal genetic testing in the immediate newborn period;
  2. are pregnant with fetal ultrasound findings consistent with a 22q11.2 deletion/duplication phenotype and is undergoing evaluation with prenatal genetic testing or planned post-natal genetic testing in the immediate newborn period;
  3. are pregnant with a fetus known to have a 22q11.2 deletion/duplication confirmed by genetic testing with documentation is available;
  4. are biologically related parent of an enrolled child has chromosomal deletion/duplication in the region of 22q11.2;
  4. If the site is selected to enroll control patients, they must be pregnant women undergoing prenatal genetic evaluation for 22q11.2 deletion/duplication.
  Exclusion Criteria
  Patients meeting any of the following criteria will be excluded from the study:
  1. Patient has history of malignancy treated with chemotherapy and/or major surgery, or bone marrow transplant.

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

Clinical trial: Written Genetic Counseling and Mutation Analysis of BRCA1 and BRCA2 to Patients With Breast Cancer

Summary: The overall purpose of the study is to evaluate a method for offering mutation analysis of BRCA1 and BRCA2 to all patients with newly diagnosed breast cancer, regardless of age at diagnosis and family history. Information about the study as well as pre-test genetic counseling will primarily be given in a written way. In addition to that, if a study participant wishes to, she can also receive pre-test telephone genetic counseling.

Detailed description: Study population:
  All patients with newly diagnosed breast cancer in southern Sweden are offered inclusion in the SCAN-B study at the time of diagnosis pre-surgery. If they consent to that, a part of the tumor is sent to a lab in Lund, Sweden, for research purposes (RNA sequencing etc.). Patients that are included in the SCAN-B study are eligible for inclusion in BRCAsearch, see inclusion and exclusion criteria.
  Study procedure (summary):
  1. An envelope with written information is given to the patient at the visit to the surgeon the week after surgery. This envelope contains a written genetic counseling, information about the study, an informed consent form, psychosocial questionnaires and our contact information (telephone, e-mail). The patient can contact a genetic counselor for pre-test telephone genetic counseling if she wishes to.
  2. BRCA1 and BRCA2 are analyzed by full sequencing.
  3. Non-carriers are informed about the test result with a letter. Mutation carriers and VUS (variants of uncertain significance) are telephoned and given a time for an appointment at the Department of Clinical Genetics within a week.
  4. Psychosocial self-reported questionnaires (HAD scale, EORTC QLQ-C30, EORTC QLQ-BR23) are delivered at 3 times: At invitation to the study, one month after information about test result, and one year after information about test result.

Eligibility: Inclusion Criteria:
  1. The patient is included in the SCAN-B study.
  2. The patient is recently diagnosed with an invasive breast cancer or a ductal cancer in situ.
  3. The patient has signed an informed consent form.
  Exclusion Criteria:
  1. The patient is unable to understand the written information in Swedish.
  2. The patient's psychological state, due to chronic och temporary reasons, is such that one could suspect that information about the study or genetic testing could be substantially detrimental to the psychological well-beeing.

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

Clinical trial: A Study of Ibandronate (Bondronat) in Participants With Malignant Bone Disease

Summary: This study will assess the efficacy and safety of ibandronate (Bondronat), administered intravenously (IV) or orally (PO), in participants with malignant bone disease and moderate to severe pain. Participants will be randomized to receive ibandronate either as a 6-mg IV infusion every 3 to 4 weeks or a 50-mg tablet PO daily. Pain response and Karnofsky Performance Index (KPI) will be measured at intervals throughout the study. The anticipated time on study treatment is 4 months and the target sample size is 150 individuals.


Eligibility: Inclusion Criteria:
  -  Adults at least 18 years of age
  -  Malignant bone disease due to multiple myeloma or cancer of the lung, prostate, gastrointestinal (GI) tract, ovary, or bladder
  -  Bone pain defined as a Brief Pain Inventory (BPI) most acute pain score greater than or equal to 4
  -  Radiologically confirmed bone disease disease
  Exclusion Criteria:
  -  Previous treatment with ibandronate (Bondronat) within previous 2 months
  -  Severely impaired renal function
  -  Known brain metastases

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

Clinical trial: The Predictive Value of Coexisting TMPRSS2-ERG Gene Fusion and PTEN Deletion in Prostate Cancer Patients With Biochemical Failure Status Post Salvage or Radical Radiation Therapy

Summary: The objective of the study is to evaluate the predictive value of TMPRSS2-ERG gene fusion and PTEN in patients with high risk prostate cancer treated with first line LHRH agonist after biochemical failure.

Detailed description: The objective of the study is to evaluate the predictive value of TMPRSS2-ERG gene fusion and PTEN in patients with high risk prostate cancer treated with first line LHRH agonist after biochemical failure.
  Patients in this study will be treated with standard hormonal treatment. Patients will remain on treatment regardless of rising PSA. PSA, other systemic therapy maybe added and the patients with oligometastasis could be treated with radiation therapy; this would be at the discretion of the treating oncologist.
  The primary endpoint of this study is to determine the predictive value of TMPRSS2-ERG gene fusion and PTEN in hormonal refractory free survival and clinical progression rate in three years. The secondary endpoints are to evaluate the relation between Gleason score and TMPRSS2-ERG gene fusion and PTEN independently and together, the relation between T stage and TMPRSS2-ERG gene fusion and PTEN independently and together, and to determine the association of these markers with overall survival.

Eligibility: Inclusion Criteria:
  -  T3a +
  -  PSA > 20
  -  Gleason 8 or higher
  -  Karnofsky performance status ≥ 70.
  -  Signed study-specific informed consent
  Exclusion Criteria:
  -

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

Clinical trial: Whey Protein Supplement in Combination With Physical Exercise and Nutrition Program

Summary: This study evaluates physical performance in cancer outpatients during a multimodal therapy. Half of the patients will receive physical exercise und nutrition program in combination with a specially formulated whey protein supplement, while the other half will receive standard care.

Detailed description: The time period of Intervention will last 3 month, measurements will be conducted at baseline and 3 month. After 6 month there will be an additional follow-up test point to assess the sustainability of the intervention. The 3-month intervention study consists of a physical exercise program and nutrition counseling in combination with a specially formulated whey protein supplement high in leucine. The standardized training program will be performed twice a week in the physical department of the Kantonsspital Winterthur (KSW) and once a week in a home based setting. Additionally, participants of the intervention group will be aks to consume 15 g of the nutrient supplement powder with approximately 150 ml water. On workout days the supplement should be taken twice a day and on the remaining days once a day. During the three month intervention study participants will take part in a nutrition counseling for at least three times.

Eligibility: Inclusion Criteria:
  -  Advanced cancer patients not eligible for curative treatment: lung cancer, gastrointestinal cancer, breast cancer, prostate cancer, ovarian cancer, pleural mesothelioma, urothelium carcinoma, renal cell carcinoma
  -  WHO performance status ≥ 2
  -  Able to walk independently at least 100 meters
  -  Estimated life expectancy of ≥ 6 month
  Exclusion Criteria:
  -  Patients currently using nutritional supplements with branched chain amino acids
  -  Enteral or parenteral nutrition within 1 month
  -  History of ileus within 1 month
  -  Psychiatric disorder precluding understanding of information on trials related topics and giving informed consent
  -  Milk protein allergy

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

Clinical trial: A Study to Evaluate the Efficacy of Venetoclax in Relapsed/Refractory Participants With Chronic Lymphocytic Leukemia (CLL) Including Those With 17p Deletion or TP53 Mutation or Those Who Have Received a Prior B-cell Receptor Inhibitor.

Summary: The purpose of this open-label, single-arm study is to evaluate the efficacy of venetoclax monotherapy in approximately 250 participants with relapsed/refractory CLL including those with the 17p deletion or TP53 mutation (assessed by local lab) OR those who have received prior treatment with a B-cell receptor inhibitor. The starting dose of venetoclax is 20 mg once daily. The dose must be gradually increased over a period of 5 weeks up to the daily dose of 400 mg. Participants may continue receiving venetoclax for up to 2 years. After the treatment period, participants may continue on into a 2-year follow-up period.


Eligibility: Inclusion Criteria:
  -  Participant has Eastern Cooperative Oncology Group (ECOG) performance score of less than or equal to 2
  -  Participant has relapsed/refractory disease (received at least 1 prior therapy)
  -  Participant has diagnosis of CLL that meets published 2008 Modified IWCLL NCI-WG Guidelines and:
  -  has an indication for treatment according to the 2008 Modified IWCLL NCI-WG criteria
  -  has clinically measurable disease (lymphocytosis greater than 5 × 109/L and/or palpable and measurable nodes by physical exam and/or organomegaly assessed by physical exam)
  -  In addition, participants:
  -  with or without 17p deletion or TP53 mutation, assessed by a local laboratory in bone marrow or peripheral blood AND/OR
  -  may have been previously treated with a prior B-cell receptor inhibitor
  -  Participant must have adequate bone marrow function, coagulation profile, renal, and hepatic function, per laboratory reference range at Screening
  Exclusion Criteria:
  -  Participant has developed Richter's transformation or Prolymphocytic leukemia
  -  Participant has previously received venetoclax
  -  History of active malignancies other than CLL within the past 2 years prior to first dose of venetoclax, with the exception of:
  -  adequately treated in situ carcinoma of the cervix uteri
  -  adequately treated basal cell carcinoma or localized squamous cell carcinoma of the skin
  -  previous malignancy confined and surgically resected (or treated with other modalities) with curative intent
  -  Participant has active and uncontrolled autoimmune cytopenias (for 2 weeks prior to Screening), including autoimmune hemolytic anemia and idiopathic thrombocytopenic purpura despite low dose corticosteroids
  -  Participant has undergone an allogeneic stem cell transplant grade 2:
  -  Any anti-cancer therapy including chemotherapy, or radiotherapy;
  -  Investigational therapy, including targeted small molecule agents
  -  Participant is human immunodeficiency virus (HIV) positive
  -  Participant has known allergy to both xanthine oxidase inhibitors and rasburicase

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) in Participants With Non-Small Cell Lung Cancer (NSCLC)

Summary: This study will assess potentially predictive markers of efficacy in participants with NSCLC receiving oral erlotinib (Tarceva) therapy. The anticipated time on study treatment is until disease progression, unacceptable toxicity or death.


Eligibility: Inclusion Criteria:
  -  Advanced NSCLC
  -  Tumor accessible for biopsy by bronchoscopy
  -  Disease progression following course of standard chemotherapy, or participants unwilling/unable to undergo chemotherapy
  Exclusion Criteria:
  -  Unstable systemic disease
  -  Any other malignancies in the last 5 years
  -  Brain metastases
  -  Previous treatment with therapy acting on the epidermal growth factor receptor (EGFR) axis

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

Clinical trial: Identification of Hematological Malignancies and Therapy Predication Using microRNAs as a Diagnostic Tool

Summary: MiRNAs are small (~19-25 nucleotides) non-coding RNA molecules that bind to mRNA in a sequence-specific manner. MiRNAs regulate gene expression at the post-transcriptional level. MiRNAs regulate critical cell processes such as metabolism, apoptosis, development, cell cycle, hematopoietic differentiation and have been implicated in the development and progression of several types of cancers, including hematological malignancies. Over-expression, amplification and/or deletion of miRNAs and miRNA-mediated modification of epigenetic silencing can all lead to oncogenic pathways.
  Hematologic cancers, which are caused by the malignant transformation of bone marrow cells and the lymphatic system, are usually divided into three major clusters: leukemia, lymphoma, and multiple myeloma. To date, some of the hematological malignancies are very aggressive that early diagnosis is essential for improving prognosis and increasing survival rates. However, current diagnostic methods have various limitations, such as insufficient sensitivity, specificity, it is also time-consuming, costly, and requires a high level of expertise, which limits its application in clinical contexts. Thus, development of new biomarkers for the early detection and relapse of hematological malignancies is desirable.
  Some of the innate properties of miRNAs make them highly attractive as potential biomarkers. MiRNAs can be readily detected in small volume samples using specific and sensitive quantitative real-time PCR; they have been isolated from most body fluids, including serum, plasma, urine, saliva, tears and semen and are known to circulate in a highly stable, cell-free form. They are highly conserved between species, allowing the use of animal models of disease for pre-clinical studies. Furthermore, tumor cells have been shown to release miRNAs into the circulation and profiles of miRNAs are altered in the plasma and/or serum of patients with cancer. A growing number of publications confirm that miRNAs can be a useful biomarker for hematological malignancies diagnosis and progression.


Eligibility: Inclusion Criteria:
  -  Newly diagnose patients with: Diffused large B cell lymphoma, Follicular lymphoma, Multiple myeloma and Hodgkin lymphoma.
  -  Patients after chemotherapy (5-30 days).
  -  Above age 18.
  Exclusion Criteria:
  -  Non-HIV/HCV/HBV Below age 18.

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

Clinical trial: Visually Enhanced Education About Prostate Cancer

Summary: This randomized clinical trial studies how well visually enhanced education works in improving prostate cancer and treatment knowledge in patients with prostate cancer that has not spread to other places in the body. Visually enhanced education includes pictures, drawings, and photos, may help doctors better convey information about radiation and prostate cancer to patients.

Detailed description: PRIMARY OBJECTIVES:
  I. Our goal is to conduct a randomized controlled trial to determine the impact of a visual presentation in the context of a radiation oncologist's discussion with patient during consultation on patient satisfaction at end of consultation visit and at end of treatment, on anxiety at start of treatment, on decision regret following treatment, and on perception of side effects following treatment. Of note, the attending radiation oncologist will be responsible for reviewing the Powerpoint presentation with the patient, taking time to answer any questions that the patient has
  OUTLINE: Patients are randomized into 1 of 2 arms.
  ARM A (STANDARD EDUCATION): Patients receive a standard prostate cancer radiation oncology consultation.
  ARM B (VISUAL ENHANCED EDUCATION): Patients receive a visually enhanced prostate cancer educational Powerpoint presentation including prostate anatomy, pathologic results, surgical options, radiation therapy, and prognosis with pictographs during radiation oncology consultation.

Eligibility: Inclusion Criteria:
  -  Patient must have non-metastatic, biopsy proven prostate cancer
  -  Must be referred to radiation oncology clinic
  Exclusion Criteria:
  -  Prior surgery or radiation therapy for prostate cancer
  -  Patients who are blind are excluded

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

Clinical trial: Genetic Factors of Idiopathic Polypoidal Vasculopathies in the ATM Gene (Ataxia Telangiectasia Mutated)

Summary: Polypoidal choriodal vasculopathy (PCV) is an ophthalmologic disease, characterized by vascular abnormalities of the walls of small choroidal vessels, reproducing the specific aspect of polyps (cluster aspect). PCV is one of the "boundary-forms" of age related macular degeneration.
  These vasculopathies can be idiopathic. Following the radiotherapy treatments of active and occult-typed neovessels in Age-Related Macular Degeneration (ARMD), 10% of the patients would present typical polypoidal vasculopathic lesions. These polypoidal secondary lesions have been induced by radiotherapy treatment and may show an increased sensibility to radiation in these patients.
  Such an increase of radiosensibility is noticed in ataxia telangiectasia syndrome, in relation to the ATM gene mutations. The secondary or idiopathic polypoidal vasculopathic lesions are to be brought closer to telangiectasias in Ataxia Telangiectasia. Considering the iatrogenic component of radiotherapy in the secondary forms of ataxia telangiectasia, it seems legitimate to search for predisposing variants to polypoidal vasculopathies in the ATM gene.
  Considering the frequency of PCV worldwide, it seems important to identify the predisposing genetic factors of the ATM gene. These biomarkers to the pathology might enable us to offer prevention (reinforced protection against radiations, including light) and to develop therapeutics (recruitment of other kinases, ATM's partners, in the stability and cellular control of DNA).


Eligibility: Inclusion Criteria:
  -  Adult caucasian patient
  -  Polypoidal choriodal vasculopathy
  -  Informed written consent
  Exclusion Criteria:
  -  History of cephalic radiotherapy
  -  Absence of affiliation to social security or universal health coverage (CMU)

Relevance to patient case: not relevant