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

Clinical trial: EGFR-TKI With Chemotherapy in NSCLC Patients With Both EGFR Mutation and BIM Deletion Polymorphism

Summary: BIM deletion polymorphism might be associated with a poor clinical response to EGFR-TKIs in patients who had NSCLC with EGFR mutations. In the study, the investigators want to use EGFR-TKI with chemotherapy as first line treatment in stage IIIB/IV NSCLC patients with both EGFR mutation and BIM deletion polymorphism.

Detailed description: BIM deletion polymorphism was a poor clinical response marker to EGFR-TKIs in NSCLC patients who had EGFR mutations. In the study, the investigators want to use EGFR-TKI with chemotherapy as 1 st treatment in stage IIIB/IV NSCLC patients with both EGFR mutation and BIM deletion polymorphism.

Eligibility: Inclusion Criteria:
  Signed informed consent Age >=18 years Histologically documented, unresectable, inoperable, locally advanced, recurrent or metastatic Stage IV Non-Small Cell Lung Cancer (NSCLC) A cytologic diagnosis is acceptable (i.e., FNA or pleural fluid cytology) Must have measurable or non-measurable disease Must be able to comply with study and follow-up procedures
  Exclusion Criteria:
  Small cell, carcinoid, or mixed small cell lung cancer Malignancies within 3 years except for adequately treated carcinoma in situ of -the cervix or basal or squamous cell skin cancer Symptomatic or untreated brain metastases Prior systemic chemotherapy for NSCLC Unstable systemic disease, including active infection, uncontrolled hypertension, unstable angina, congestive heart failure, or myocardial infarction within 6 months prior to Day 1, or serious cardiac arrhythmia requiring medication (patients with chronic atrial arrhythmia, i.e., atrial fibrillation or paroxysmal supraventricular tachycardia, are eligible) History of other diseases, metabolic dysfunction, physical examination finding, or clinical laboratory finding giving reasonable suspicion of a disease or condition that contraindicates the use of an investigational drug or that might affect the interpretation of the results of the study or render the patient at high risk from treatment complications Gastrointestinal tract disease resulting in an inability to take oral medication or a requirement for intravenous (IV) alimentation, or prior surgical procedures affecting absorption Pregnancy or lactation

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

Clinical trial: Expression of DMBT1 in Colorectal Cancer Patients

Summary: Although colorectal cancer is a preventable and curable disease if early stage tumors are removed, it is still the fourth cause of cancer worldwide and the second leading cause of death in many industrialized countries. The 5-year survival is about 55% often due to a late detection. Then, the identification of sensitive and specific molecular markers is therefore a major challenge for early diagnosis and prognosis of this disease.
  Preliminary work have reported variations in the expression of DMBT1 (deleted in malignant brain tumor 1), a glycoprotein co-secreted with mucins in the light of the glands, during several stages of colon carcinogenesis. The goal of this study is to study by mass spectrometry (MS), alterations in the repertoire of glycosylation of mucins from colorectal tumors of various stages, grades, and recurrence status.


Eligibility: Inclusion Criteria:
  -  for colon cancer: patients surgically treated for colorectal cancer at the Group of hospitals of the Catholic Institute of Lille.
  -  for adenomatous polyps : patients treated for adenomatous polyps at the Group of hospitals of the Catholic Institute of Lille.
  -  for controls: patients surgically treated for diverticular disease at the Group of hospitals of the Catholic Institute of Lille.
  Exclusion Criteria:
  -  none

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

Clinical trial: A Study of SC10914 in Patients With Advanced Solid Tumors

Summary: SC10914 is a potent selective PARP-1 and PARP-2 inhibitor. This study aims to determine the safety , tolerability , pharmacokinetic/pharmacodynamics profile of increasing doses of SC10914 when administered orally to patients with advanced solid tumors. Furthermore, the safety and efficacy of SC10914 in patients with advanced solid tumors and negative expression of ATM or BRCA1 or BRCA2 mutation will be evaluated in expanded cohorts to establish the Recommended Phase 2 Dose(RP2D).


Eligibility: Inclusion Criteria:
  -  Signed written informed consent
  -  Aged 18-70 years
  -  Dose escalation study: Subjects diagnosed with advanced solid malignancies who are refractory to standard therapies or for which no standard therapy exists/Dose Expansion study: Subjects diagnosed with advanced solid malignancies who are refractory to standard therapies or for which no standard therapy exists and negative expression of ATM or BRCA1 or BRCA2 mutation
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 to 2
  -  Have measurable lesion exists(RECIST 1.1)
  -  Life expectancy≥3 months
  -  Have adequate bone marrow, hepatic and renal functions
  Exclusion Criteria:
  -  Allergic constitution or hypersensitivity to investigational drugs or relevant drug
  -  Patients who received any previous treatment with a PARP inhibitor
  -  Patients accepted anti-cancer therapy including chemotherapy, radiotherapy, endocrinotherapy, immunotherapy, Chinese herbal treatment or other investigational drugs within 4 weeks prior to trial entry (or a longer period depending on the defined characteristics of the drugs used eg,. 6 weeks for mitomycin C or nitrosourea)
  -  With serious pre-existing medical conditions, such as significant cardiovascular disease and psychogenic disorders
  -  With family history of long QT syndrome or QTc ≥ 450 ms
  -  With persistent CTCAE ≧grade 2 toxicities (excluding alopecia) caused by prior medication
  -  With symptomatic brain metastases
  -  Pregnancy or lactation
  -  With Hepatitis B or C or human immunodeficiency virus infections

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

Clinical trial: A Study of Rucaparib in Patients With Metastatic Castration-resistant Prostate Cancer and Homologous Recombination Gene Deficiency

Summary: The purpose of this study is to determine how patients with metastatic castration-resistant prostate cancer, and evidence of a homologous recombination gene deficiency, respond to treatment with rucaparib.


Eligibility: Inclusion Criteria:
  -  Be 18 years old at the time the informed consent form is signed
  -  Have a histologically or cytologically confirmed adenocarcinoma or poorly differentiated carcinoma of the prostate
  -  Be surgically or medically castrated, with serum testosterone levels of ≤ 50 ng/dL (1.73 nM)
  -  Experienced disease progression after having received at least 1 but no more than 2 prior next-generation androgen receptor-targeted therapies, and 1 prior taxane-based chemotherapy, for castration-resistant disease
  -  Have a deleterious mutation in BRCA1/2 or ATM, or molecular evidence of other homologous recombination deficiency
  Exclusion Criteria:
  -  Active second malignancy, with the exception of curatively treated non-melanoma skin cancer, carcinoma in situ, or superficial bladder cancer
  -  Prior treatment with any PARP inhibitor, mitoxantrone, cyclophosphamide or any platinum-based chemotherapy
  -  Symptomatic and/or untreated central nervous system metastases
  -  Pre-existing duodenal stent and/or any gastrointestinal disorder or defect that would, in the opinion of the investigator, interfere with absorption of rucaparib

Relevance to patient case: definitely relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: A Study of Venetoclax in Subjects With Relapsed or Refractory Chronic Lymphocytic Leukemia in the Presence of 17p Deletion

Summary: This is a Phase 2, open-label, single-arm, multicenter study, evaluating the efficacy of venetoclax in participants with relapsed or refractory Chronic Lymphocytic Leukemia (CLL) in the presence of 17p deletion.


Eligibility: Inclusion Criteria:
  -  Participant must have a diagnosis of relapsed or refractory chronic lymphocytic leukemia (CLL) that meets 2008 Modified International Workshop for Chronic Lymphocytic Leukemia (IWCLL) NCI-WG Guidelines and the following:
  -  Participant must have an indication for treatment according to the 2008 Modified IWCLL National Cancer Institute-Working Group (NCI-WG) Guidelines;
  -  Participant must have measurable disease (B-lymphocytosis greater than 5 × 10^9/L or an enlarged lymph node(s) (LDi > 1.5 cm at baseline) or hepatomegaly or splenomegaly due to CLL);
  -  Participant must have relapsed or refractory CLL after receiving at least one prior line of therapy
  -  Relapsed - must have completed at least 2 cycles of one prior line of therapy;
  -  Refractory - must have progressed after at least 1 cycle of one prior line of therapy;
  -  Participant must have 17p deletion, assessed by a central laboratory
  -  Participant must have an Eastern Cooperative Oncology Group (ECOG) performance score of less than or equal to 2.
  -  Participant must have adequate bone marrow function, coagulation profile, renal, and hepatic function, per laboratory reference range at Screening
  Exclusion Criteria:
  -  Participant has undergone an allogeneic stem cell transplant.
  -  Participant has developed Richter's transformation confirmed by biopsy.
  -  Participant has prolymphocytic leukemia.
  -  Participant has active and uncontrolled autoimmune cytopenias (for 2 weeks prior to screening), including autoimmune hemolytic anemia (AIHA) and idiopathic thrombocytopenic purpura (ITP).
  -  Participant has previously received venetoclax.
  -  Participant is known to be positive for Human Immunodeficiency Virus (HIV).
  -  Participant has received a biologic agent for anti-neoplastic intent within 30 days prior to the first dose of study drug.
  -  Participant has received any of the following within 14 days or 5 half-lives (whichever is shorter) prior to the first dose of study drug, or has not recovered to less than Common Toxicity Criteria (CTC) grade 2 clinically significant adverse effect(s)/toxicity(s) of the previous therapy:
  -  Any anti-cancer therapy including chemotherapy, or radiotherapy;
  -  Investigational therapy, including targeted small molecule agents.
  -  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: EGFRdelEx19 and KRAS Exon 2 Mutation Detection in EBUS-TBNA

Summary: First-line treatment with afatinib prolongs overall survival in patients with metastatic non-small-cell lung cancer (NSCLC) harboring EGFR exon 19 deletion mutations. Conversely, somatic KRAS mutations are negative predictors for benefit from EGFR-targeting agents. In this study we want to compare a new highly sensitive method for the detection of EGFRdelEx19 and KRAS Exon 2 with targeted-resequencing multiplex-PCR (NGS).

Detailed description: First-line treatment with afatinib prolongs overall survival in patients with metastatic non-small-cell lung cancer (NSCLC) harboring EGFR exon 19 deletion mutations. Conversely, somatic KRAS mutations are negative predictors for benefit from EGFR-targeting agents. Rapid availability of these biomarker results is mandatory to prevent delayed or inferior treatments.
  Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is well-established for lung cancer diagnosis and staging. Next generation sequencing (NGS) via targeted resequencing allows simultaneous interrogation for multiple mutations, but has its limitations based on the amount of tumor tissue required and assay times. RT-PCR using Light-Cycler technology (LC-RTPCR) is a rapid and sensitive assay to detect somatic mutations in various tissues from NSCLC patients. The study's aim was to analyze if LC-RTPCR is feasible for rapid EGFRdelEx19 and KRAS Exon 2 mutation detection in EBUS-TBNA samples and to compare results with results obtained via standard NGS mutation analyses.

Eligibility: Inclusion Criteria:
  -  lung adenocarcinoma positive EBUS-TBNA specimen
  Exclusion Criteria:
  -  other diagnosis

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

Clinical trial: A Study of Rucaparib Versus Physician's Choice of Therapy in Patients With Metastatic Castration-resistant Prostate Cancer and Homologous Recombination Gene Deficiency

Summary: The purpose of this study is to determine how patients with metastatic castration-resistant prostate cancer, and evidence of a homologous recombination gene deficiency, respond to treatment with rucaparib versus treatment with physician's choice of abiraterone acetate, enzalutamide, or docetaxel.


Eligibility: Inclusion Criteria:
  -  Be 18 years old at the time the informed consent is signed
  -  Have a histologically or cytologically confirmed adenocarcinoma or poorly differentiated carcinoma of the prostate that is metastatic
  -  Be surgically or medically castrated, with serum testosterone levels of ≤ 50 ng/dL (1.73 nM)
  -  Be eligible for treatment with physician's choice of comparator treatment (abiraterone acetate, enzalutamide or docetaxel)
  -  Experienced disease progression after having received 1 prior next generation androgen receptor-targeted therapy for castration-resistant disease
  -  Have a deleterious mutation in a BRCA1/2 or ATM gene
  Exclusion Criteria:
  -  Active second malignancy, with the exception of curatively treated non melanoma skin cancer, carcinoma in situ, or superficial bladder cancer
  -  Prior treatment with any PARP inhibitor
  -  Prior treatment with chemotherapy for metastatic castration-resistant prostate cancer
  -  Symptomatic and/or untreated central nervous system metastases
  -  Pre-existing duodenal stent and/or any gastrointestinal disorder or defect that would, in the opinion of the investigator, interfere with absorption of study drug

Relevance to patient case: definitely relevant
Patient case: 50-year-old male with prostate cancer; genetic feature: ATM deletion

Clinical trial: Study of Olaparib (Lynparza™) Versus Enzalutamide or Abiraterone Acetate in Men With Metastatic Castration-Resistant Prostate Cancer (PROfound Study)

Summary: The purpose of this study is to evaluate the efficacy and safety of olaparib versus enzalutamide or abiraterone acetate in subjects with metastatic castration-resistant prostate cancer who have failed prior treatment with a new hormonal agent and have homologous recombination repair gene mutations.

Detailed description: This is a prospective, multicenter, randomized, open-label, phase 3 trial evaluating the efficacy and safety of olaparib versus enzalutamide or abiraterone in subjects with metastatic castration-resistant prostate cancer (mCRPC) who have failed prior treatment with a new hormonal agent (NHA) and have a qualifying tumor mutation in one of 15 genes involved in the homologous recombination repair (HRR) pathway. Subjects will be divided into two cohorts based on HRR gene mutation status.
  Approximately 340 subjects will be randomized 2:1 (olaparib : investigator choice of enzalutamide or abiraterone acetate) into the trial.

Eligibility: Inclusion criteria
  1. Histologically confirmed diagnosis of prostate cancer.
  2. Documented evidence of metastatic castration resistant prostate cancer (mCRPC).
  3. Subjects must have progressed on prior new hormonal agent (e.g. abiraterone acetate and/or enzalutamide) for the treatment of metastatic prostate cancer and/or CRPC .
  4. Ongoing therapy with LHRH analog or bilateral orchiectomy.
  5. Radiographic progression at study entry while on androgen deprivation therapy (or after bilateral orchiectomy).
  6. Qualifying HRR mutation in tumor tissue.
  Exclusion criteria
  1. Any previous treatment with PARP inhibitor, including olaparib.
  2. Subjects who have any previous treatment with DNA-damaging cytotoxic chemotherapy, except if for non-prostate cancer indication and last dose > 5 years prior to randomization.
  3. Other malignancy (including MDS and MGUS) within the last 5 years except: adequately treated non-melanoma skin cancer or other solid tumors curatively treated with no evidence of disease for ≥5 years.
  4. Subjects with known brain metastases.

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

Clinical trial: EGFR-TKI With/Without Chemotherapy in NSCLC Patients With Both EGFR Mutation and BIM Deletion Polymorphism

Summary: BIM deletion polymorphism might be associated with a poor clinical response to EGFR-TKIs in patients who had NSCLC with EGFR mutations. In the study, the investigators want to use EGFR-TKI with/without chemotherapy as first line treatment in stage IIIB/IV NSCLC patients with both EGFR mutation and BIM deletion polymorphism.

Detailed description: BIM deletion polymorphism was a poor clinical response marker to EGFR-TKIs in NSCLC patients who had EGFR mutations. In the study, the investigators want to use EGFR-TKI with chemotherapy as 1 st treatment in stage IIIB/IV NSCLC patients with both EGFR mutation and BIM deletion polymorphism.

Eligibility: Inclusion Criteria:
  1. Signed informed consent
  2. Histologically documented, unresectable, inoperable, locally advanced, recurrent or metastatic Stage IV Non-Small Cell Lung Cancer (NSCLC)
  3. Must have measurable or non-measurable disease
  4. Must be able to comply with study and follow-up procedures
  Exclusion Criteria:
  1. Small cell, carcinoid, or mixed small cell lung cancer
  2. Malignancies within 3 years except for adequately treated carcinoma in situ of the cervix or basal or squamous cell skin cancer
  3. Symptomatic or untreated brain metastases Prior systemic chemotherapy for NSCLC
  4. Unstable systemic disease, including active infection, uncontrolled hypertension, unstable angina, congestive heart failure, or myocardial infarction within 6 months prior to Day 1, or serious cardiac arrhythmia requiring medication
  5. History of other diseases, metabolic dysfunction, physical examination finding, or clinical laboratory finding giving reasonable suspicion of a disease or condition that contraindicates the use of an investigational drug or that might affect the interpretation of the results of the study or render the patient at high risk from treatment complications
  6. Gastrointestinal tract disease resulting in an inability to take oral medication or a requirement for intravenous (IV) alimentation, or prior surgical procedures affecting absorption
  7. Pregnancy or lactation

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

Clinical trial: Ultrasound-Based Imaging Using the Aixplorer System in Diagnosing Prostate Cancer in Patients Undergoing Biopsy

Summary: This clinical trial studies an ultrasound-based imaging procedure called elastography using the Aixplorer system in diagnosing prostate cancer in patients undergoing biopsy. Ultrasound is a non-invasive imaging technique that uses high-frequency sound waves to produce images of internal structures. Elastography uses ultrasound imaging techniques to examine the stiffness or elasticity of a tissue and may enhance the detection of prostate cancer. It is not yet known whether elastography imaging using the Aixplorer system works better than standard ultrasound imaging in detecting prostate cancer.

Detailed description: PRIMARY OBJECTIVES:
  I. To evaluate the detection of prostate cancer with elastography using the Aixplorer scanner.
  SECONDARY OBJECTIVES:
  I. To obtain quantitative data on the elastic properties of normal and malignant tissue in the prostate of patients referred for ultrasound guided biopsy.
  II. To compare the Gleason grade of prostate cancers detected with elastography to the Gleason grade of tumors detected by conventional systematic biopsy.

Eligibility: Inclusion Criteria:
  -  Be scheduled for a clinically indicated biopsy of the prostate
  -  Agree to an ultrasound examination using the Aixplorer system
  -  Sign an institutional review board (IRB) approved informed consent prior to any study procedures
  Exclusion Criteria:
  • Recent prostate biopsy within 90 days

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

Clinical trial: K-BASKET, TAS-117, PI3K/AKT Gene Aberration

Summary: The phosphatidylinositol 3-kinase (PI3K)-v-akt murine thymoma viral oncogene homolog (AKT)-mammalian target of rapamycin (mTOR) signaling pathway is one of the most frequently aberrantly regulated pathways in human tumors. TAS-117 is a highly potent and selective oral allosteric AKT inhibitor. It has high affinity for AKT1, 2, and 3 and shows potent anti-proliferative activity against multiple tumor cell lines in vivo. Therefore, we propose to conduct a phase II trial of TAS-117, potent and selective AKT inhibitor, in patients with advanced solid tumor with PI3K/AKT genetic aberrancy by NGS focusing panel in part of K-BASKET trial.


Eligibility: Inclusion Criteria:
  1. Histologically or cytologically confirmed recurrent or advanced solid cancers with PI3K/ATK aberration
  2. Progressive disease who failed to previous standard treatment.
  3. At least one measurable lesion according to Response Evaluation Criteria in Solid Tumors version 1.1 criteria
  4. Eastern Cooperative Oncology Group performance status 0 or 1
  5. Able to take medications orally
  6. Adequate organ function
  7. A life expectancy of at least 60 days
  Exclusion Criteria:
  1. Previous treatment with anti-PI3K or AKT directed therapies
  2. Known hypersensitivity to any drugs similar to TAS-117 in structure or class.
  3. History or current evidence of type 1 or type 2 diabetes mellitus that requires insulin and/or oral antidiabetic therapy.
  4. Current evidence of retinopathy that requires ophthalmological therapy.
  5. History or current evidence of cardiac arrhythmia and/or conduction abnormality.
  6. Treatment with any of the following within the specified time frame prior to study drug administration:
  -  Major surgery within prior 4 weeks
  -  Radiation therapy for extended field within 4 weeks prior to study drug administration or limited field radiation therapy within 2 weeks prior to study drug administration.
  -  Any anticancer treatment within 3 weeks prior to study drug administration (mitomycin within prior 5 weeks).
  7. A serious illness or medical condition(s)
  8. Unresolved toxicity of Grade >1 attributed to any prior therapies (excluding alopecia, skin pigmentation and anemia).
  9. Patients with the risk of hypokalemia
  10. Receiving oral steroid medication.
  11. Pregnant or lactating female

Relevance to patient case: not relevant