araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Whole Exome Sequencing in Finding Causative Variants in Germline DNA Samples From Patients With Hypertension Receiving Bevacizumab for Breast Cancer

Summary: This research trial studies whole exome sequencing in finding causative variants in germline deoxyribonucleic acid (DNA) samples from patients with hypertension receiving bevacizumab for breast cancer. Studying samples of germline DNA in the laboratory from patients with hypertension receiving bevacizumab for breast cancer may help doctors learn about changes that occur in DNA and identify biomarkers related to hypertension.

Detailed description: PRIMARY OBJECTIVES:
  I. To identify, using next generation sequencing, rare variants of large effect size that impact the risk of hypertension in patients from the clinical trial Eastern Cooperative Oncology Group (ECOG)-5103 (E5103).
  OUTLINE:
  Previously collected germline DNA samples are analyzed via whole exome sequencing.

Eligibility: Inclusion Criteria:
  -  European American patients with deoxyribonucleic acid (DNA) available and designated case or control
  -  Patients who developed grade 3-4 bevacizumab-induced hypertension during their treatment with bevacizumab
  -  Patients who did not develop hypertension following a full course of treatment with bevacizumab

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Whole Exome Sequencing in Finding Causative Variants in Germline DNA Samples From Patients With Congestive Heart Failure Receiving Therapy for Breast Cancer

Summary: This research trial studies whole exome sequencing in finding causative variants in germline deoxyribonucleic acid (DNA) samples from patients with congestive heart failure receiving therapy for breast cancer. Studying samples of germline DNA in the laboratory from patients with congestive heart failure receiving therapy for breast cancer may help doctors learn more about changes that occur in DNA and identify biomarkers related to congestive heart failure.

Detailed description: PRIMARY OBJECTIVES:
  I. To identify, using next generation sequencing, rare variants of large effect size that impact the risk of congestive heart failure (CHF) in patients from the clinical trial ECOG-5103 (E5103).
  OUTLINE:
  Previously collected germline DNA samples are analyzed via whole exome sequencing.

Eligibility: Inclusion Criteria:
  -  European American patients with DNA available
  -  European American patients who developed CHF and patients who did not develop CHF following a full course of treatment with an anthracycline and bevacizumab
  -  African American cases (based on a drop in left ventricular ejection fraction [LVEF] < 50 or a drop from baseline > 20 points) and African American controls

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Whole Exome Sequencing in Finding Causative Variants in Germline DNA Samples From Patients With Peripheral Neuropathy Receiving Paclitaxel for Breast Cancer

Summary: This research trial studies whole exome sequencing in finding causative variants in germline deoxyribonucleic acid (DNA) samples from patients with peripheral neuropathy receiving chemotherapy for breast cancer. Studying samples of germline DNA in the laboratory from patients with peripheral neuropathy receiving paclitaxel for breast cancer may help doctors learn more about changes that occur in DNA and identify biomarkers related to peripheral neuropathy.

Detailed description: PRIMARY OBJECTIVES:
  I. To identify, using next generation sequencing, rare variants of large effect size that impact the risk of peripheral neuropathy in patients of African and European descent in the clinical trial ECOG-5103 (E5103).
  OUTLINE:
  Previously collected germline DNA samples are analyzed via whole exome sequencing.

Eligibility: Inclusion Criteria:
  -  European American patients with DNA available and designated case or control
  -  African American patients with DNA available and designated case or control status
  -  Patients who developed grade 2-4 for African American (AA) and grade 3-4 for European American (EA) peripheral neuropathy during their treatment with paclitaxel and who did not develop peripheral neuropathy following a full course of treatment with paclitaxel

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: A Sleep Intervention to Improve Outcomes Among Women at High Risk of Breast Cancer

Summary: Participants are asked to participate in a research study of the effect of a sleep intervention on improving sleep habits and reducing their risk of breast cancer.
  Participants are asked to participate in this research study because they have been identified as being at higher than average risk of developing breast cancer.
  The purpose of this study is to compare women who get a sleep intervention to women who do not get a sleep intervention. This study team will compare these two groups of women to see if the sleep intervention improves their sleep and if it lowers markers of inflammation that have been associated with an increased risk of breast cancer.

Detailed description: Objective 1: To test the effectiveness of the GO! To Sleep program at improving the sleep duration and sleep quality in women at high risk of breast cancer.
  Objective 2: To test the effectiveness of improvements in sleep quality and/or duration due to the GO! To Sleep program on biomarkers of inflammation in women at high risk of breast cancer.
  Objective 3: To evaluate the effectiveness of improvements in health-related quality of life after the GO! To Sleep in women at high risk of breast cancer.

Eligibility: Inclusion Criteria:
  1. Women at high risk of breast cancer due to one or more of the following:
  -  Carry deleterious mutations in the BRCA1, BRCA2, PTEN, TP53, STK11, or CDH1 genes
  -  Previous diagnosis of lobular carcinoma in situ (LCIS), atypical ductal hyperplasia (ADH) or atypical lobular hyperplasia (ALH)
  -  Lifetime risk of 20% or greater as calculated by the National Cancer Institute (NCI) Breast Cancer Risk Assessment Tool or the Tyrer-Cuzick IBIS Risk Assessment Tool
  2. Ability to access the internet and watch videos online.
  3. Valid email address.
  4. Self-reported sleep duration of 6 hours per night or less
  Exclusion Criteria:
  1. Previous diagnosis of cancer.
  2. Lack of ability to read and converse in English.
  3. Lack of ability to give informed consent.

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: PI3Kβ Selective Inhibitor With Paclitaxel, Advanced Gastric Adenocarcinoma

Summary: This is a Phase Ib/IIa, open-label, non-randomized, dose-escalation, multi-center study to evaluate the safety, tolerability, pharmacokinetics (PK), and clinical activity of oral GSK2636771 in combination with intravenous (IV) paclitaxel in two independent subject populations: subjects with PTEN-deficient, advanced gastric adenocarcinoma. This study will be conducted in two phases: the Dose Escalation Phase and the Dose Expansion Phase. The Dose Escalation Phase (Phase Ib) is designed to determine the maximum tolerated dose (MTD) and the recommended Phase II dose (RP2D) of GSK2636771 administered in combination with paclitaxel. The Dose Expansion Phase (Phase IIa) will further evaluate the safety and clinical activity of the RP2D as determined in the Dose Escalation Phase.


Eligibility: Inclusion criteria:
  1. histologically or cytologically confirmed diagnosis of advanced gastric adenocarcinoma
  2. Has a PTEN-deficient tumor as documented from archival or fresh (from biopsy) tumor tissue or has shown genomic alterations in PI3K pathway genes (PIK3CB, PI3KR1, PTEN, etc.) as assessed in a local laboratory.
  3. Has had no prior taxane exposure (preferred) or at least 6 months since last taxane exposure.
  4. Eastern Cooperative Oncology Group performance status of 0 or 1
  5. measurable or evaluable disease as determined by RECIST 1.1.
  6. Is able to swallow and retain orally administered medication
  7. adequate baseline organ function
  Exclusion criteria
  1. prior treatment with any AKT, mammalian target of rapamycin (mTOR) inhibitors or PI3K pathway inhibitors
  2. Has any unresolved Grade 2 (per CTCAE v4.0) toxicity from previous anti-cancer therapy at the time of enrollment such as neuropathy, except alopecia or Grade 2 anemia (if hemoglobin is ≥9.0 g/dL)
  3. Has CNS metastases
  4. Has a QTc interval >450 msec or QTc >480 msec for subjects with bundle branch block (BBB)
  5. Has a known immediate or delayed hypersensitivity reaction or idiosyncrasy to drugs chemically related to GSK2636771 or hypersensitivity to drug formulated in polyoxyl 35 castor oil, NF such as paclitaxel.

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Optimizing the Delineation of the Tumour Bed in Breast Irradiation

Summary: The aim of the present study is:
  1. to verify whether the delineation of the tumour bed, based on the combination of the visible postoperative changes and the position of the surgical clips on a CT scan in treatment position acquired 1 week before the start of the radiotherapy (RT), provides an accurate localisation of the boost volume compared to the localisation of the tumour on a pre-operative CT-scan.
  2. to document the changes that occur in the tumour bed as seen on a CT scan as a function of the delay between surgery and radiotherapy.
  3. to determine the ideal number and the positioning of the clips needed to reproduce the best treatment volume for the boost.
  4. to propose new guidelines for tumour bed definition and delineation based on the study findings.

Detailed description: Start of the study: february 2012

Eligibility: Inclusion Criteria:
  -  Breast Cancer patients, without metastases, who will undergo breast conserving surgery and probably will receive adjuvant chemotherapy and thereafter radiotherapy.
  Exclusion Criteria:
  -  Metastases at time of diagnosis

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Identification and Semi -Quantification of ER/PR Proteins Expression

Summary: The purpose of the study is the identification and quantification of proteins expression level in breast cancer tissues.
  The imaging system is intended for diagnostic use as an aid to the pathologist in the detection, counting and classifying ER/PR IHC stained samples.

Detailed description: The anti ER/PR Kit is a semi-quantitative immunohistochemical (IHC) assay to identify the progesterone (PR) and estrogen (ER) expressions in formalin-fixed, paraffin-embedded human breast cancer tissue specimens. Results from the ER/PR test is indicated as an aid in the assessment of the hormones status of breast cancer patients. While the ER/PR kit provides the antibodies that offer direct visualization and semi-quantification of the protein expression through a brightfield microscope, the GenASIs GoPath system is designed to complement the routine workflow of the pathologist in the review of immunohistochemically stained histologic slides.

Eligibility: Inclusion Criteria:
  -  Women having breast cancer
  Exclusion Criteria:
  -  others

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Identification and Semi-Quantification of Ki-67 Protein Expression Status

Summary: The purpose of the study is the identification and semi-quantification of Ki-67 protein expression level in breast cancer tissues by the GenASIs GoPth system as compared to manual reading of the same slides.
  The imaging system is intended for diagnostic use as an aid to the pathologist in the detection, counting and classifying ER/PR IHC stained samples

Detailed description: The anti Ki-67 is a semi-quantitative immunohistochemical (IHC) assay to identify the Ki-67 protein expressions in formalin-fixed, paraffin-embedded human breast cancer tissue specimens. Results from the Ki-67 test is indicated as an aid in the assessment of the protein status of breast cancer patients. While the p53 kit provides the antibody that offer direct visualization and semi-quantification of the protein expression through a brightfield microscope, the GenASIs GoPath system is designed to complement the routine workflow of the pathologist in the analysis and review of immunohistochemically stained histologic slides.

Eligibility: Inclusion Criteria:
  -  Slides with nuclear borders of tumor nuclei that is distinguishable, and having good integrity.
  Exclusion Criteria:
  -  Slides that have lots of background that interfere with the analysis

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Bright Light on Fatigue in Women Being Treated for Breast Cancer

Summary: This proposed study will examine feasibility and implement therapeutic bright light that is tailored to the individual's circadian typology to estimate its therapeutic effects on sleep/wake patterns and fatigue in breast cancer patients undergoing chemotherapy.


Eligibility: Inclusion Criteria:
  -  21 years of age or older
  -  Newly diagnosed with stage I-III breast cancer
  -  Scheduled to receive 21-day cycles of intravenous chemotherapy
  -  Experiencing disrupted sleep (determined by Pittsburgh Sleep Quality Index)
  -  Morning or evening types (determined by Horne-Ostberg Morningness-Eveningness Questionnaire (MEQ)
  -  Sighted
  -  Mentally competent to consent
  -  Able to under English
  Exclusion Criteria:
  -  Concurrent malignancy
  -  Undergoing other cancer treatments
  -  Engage in shift work or travel across more than 3 time zones within 2 weeks prior to study
  -  Known history of seasonal affective disorder or substance abuse
  -  Current diagnosis of major Axis I psychiatric disorders, neurological impairments, or muscular dystrophies
  -  Regularly use steroid or other immunosuppressive medications
  -  Take prescribed sedative hypnotics or sleep medications because these conditions may affect fatigue and/or sleep/wake patterns.
  -  Have eye conditions (glaucoma or retinal disease), problems triggered by bright light (e.g. migraine), or take photosensitizing medications (e.g. some porphyrin drugs, antipsychotics, antiarrhythmic agents)

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Targeted Next-generation Sequencing Panel for Identification of Germline Mutations in Early Onset Cancers With Sporadic or Hereditary Presentation

Summary: Despite relevant clinical and/or familial presentations suggesting a hereditary predisposition (early-onset, multiple primary tumors, familial aggregation), targeted genomic analysis based on the phenotype are often non contributive. As somatic cancer genes are limited, the hypothesis is that the targeted next-generation sequencing of 200 genes, selected for their implications in cancers may contribute to the understanding of many selected patients' presentation by the identification of germline deleterious mutations, and may identified phenotype overlapping and/or mosaicisms. The focus will be put on early-onset breast, ovarian, colorectal cancer or pediatric cancers and multiple primary tumors.


Eligibility: Inclusion Criteria :
  -  Older than 18 or parental agreement in case of children.
  For patient with early-onset breast cancer :
  -  Invasive breast cancer, regardless of histological type or stage, diagnosed before 31 years.
  -  Sporadic or familial presentation
  -  No genomic alterations of BRCA1, BRCA2 or TP53
  For patient with early-onset ovarian cancer :
  -  Invasive ovarian cancer, regardless of histological type or stage, diagnosed before 41 years.
  -  Sporadic or familial presentation
  -  No genomic alterations of BRCA1, BRCA2
  Patient with early-onset colorectal cancer :
  -  Invasive colorectal cancer diagnosed before 31 years.
  -  Sporadic or familial presentation
  -  No genomic alteration of MSH2, MLH1 or MSH6 in case of HNPCC presentation
  -  No genomic alteration of APC, MUTYH, SMAD4, BMPR1A, PTEN or STK11 in case of adenomatous polyposis or hamartoma presentation
  Patient with pediatric cancer :
  -  Non haematological tumour diagnosed before 16 years, with Li-Fraumeni presentation.
  -  No genomic alteration of TP53
  Patient with Multiple primary malignant tumours :
  -  Multiple synchronous or metachronous primary malignant tumors with early-onset
  -  No syndromic presentation
  Exclusion Criteria:
  -  Any already known deleterious mutations according to the patient's phenotype

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Mutation of BRCA1/2 and Other Potential Genes in Triple-negative Breast Cancer

Summary: The study is to determine the prevalence of potential chemo-response related genes mutation in TNBC patients between pCR and SD/PD group, which achieved after NAC; and to evaluate potential relationship between these gene mutations and NAC-response in TNBC patients.Based on the results,we can further characterize TNBC from a phenotypical and molecular perspective, in order to identify potential new target agents and to individualize the treatment.

Detailed description: This is single centre，exploratory，parallel and retrospective study to analysis the mutation and expression of tBRCA1/2 and other potential genes in triple-negative breast cancer. Patients received neoadjuvant chemotherapy with paclitaxel and carboplation are enrolled in this study. The participants are required to have clinical stage II or III breast cancer with a clinical or radiographically measurable residual tumor after core biopsy. We will enroll the patients of pCR or SD/PD, which achieved after complete NAC. Every group will enroll 50 patients. This study is to identify relationship between different gene mutations and expression, which may be targeted with currently available investigational drugs, and chemo-response.
  Patients who will fulfil all inclusion/exclusion criteria. We conducted a retrospective chart review of the 100 patients.

Eligibility: Inclusion Criteria:
  Patients receiving neoadjuvant chemotherapy with paclitaxel and carboplation are enrolled in this study.
  -  (1) histologically confirmed mainly invasive breast carcinoma
  -  (2) a unilateral and non-inflammatory tumors
  -  (3) status of ER, PR and HER-2 are available and negative
  -  (4) The participants are required to have clinical stage II or III breast cancer with a clinical or radiographically measurable residual tumor after core biopsy.
  -  (5)patients had pathological evaluation after NAC
  -  (6) the pathologic tissues are available for immunohistochemistry and next generation sequencing
  Exclusion Criteria:
  -  (1) carcinoma in situ
  -  (2) received less than 4 cycles neoadjuvant chemotherapy

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Phase 1 Study of DS-6051b in Japanese Subjects With Advanced Solid Malignant Tumors

Summary: This is a Phase 1 study to evaluate the safety, tolerability, and pharmacokinetics of DS-6051b in Japanese subjects with advanced solid malignant tumors harboring either a ROS1 or NTRK fusion gene.

Detailed description: This study is single arm study with DS-6051b in approximately 9 subjects with advanced solid malignant tumors harboring either a ROS1 or NTRK fusion gene. Safety and tolerability, pharmacokinetics (PK), MTD/RP2D (maximum tolerated dose/recommended phase 2 dose) and preliminary efficacy of DS-6051b will be evaluated.

Eligibility: Inclusion Criteria:
  -  Advanced solid malignant tumors that are refractory to standard therapy or for which no standard therapy is available.
  -  An Eastern Cooperative Oncology Group (ECOG) performance status (PS) 0-1.
  Exclusion Criteria:
  -  Previously had or currently has any of the following diseases:
  Cardiac failure (NYHA Functional Classification ≥ Class III), myocardial infarction, cerebral infarction, unstable angina, arrhythmia requiring treatment, coronary/peripheral artery disease, pulmonary thrombosis, uncontrolled deep vein thrombosis, clinically severe thromboembolic event, or autoimmune disease requiring treatment.
  -  Previously had or currently has clinically severe pulmonary disease (eg, interstitial pneumonia, pneumonitis, pulmonary fibrosis, radiation pneumonia).
  -  Severe or uncontrolled concomitant disease.
  -  Clinically active brain metastases or central nervous system tumor requiring steroid or anticonvulsant treatment.

Relevance to patient case: not relevant