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: Studying Tissue Samples From Women With Breast Cancer Who Were Treated on Clinical Trial NCCTG-N9831

Summary: This research study is looking at tissue samples from women with breast cancer who were treated on clinical trial NCCTG-N9831. Studying samples of 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. It may also help doctors predict how patients will respond to treatment.

Detailed description: PRIMARY OBJECTIVES:
  I. To determine the association between the primary breast tumor protein expression of MYC, IGF-1R, and PTEN and disease-free survival (DFS) in patients randomized on clinical trial NCCTG-N9831.
  II. To determine the association between the primary breast tumor amplification status of MYC and TOP2A and DFS in patients randomized on NCCTG-N9831.
  III. To determine the association between the primary breast tumor mutation status of PIK3 and DFS in patients randomized on NCCTG-N9831.
  SECONDARY OBJECTIVES:
  I. To determine the association between the primary breast tumor marker protein expression/amplification/mutation status of the aforementioned markers and overall survival in patients randomized on NCCTG-N9831.
  II. To investigate the predictive potential of multiple marker analyses on DFS and overall survival using multivariate analysis.
  III. To determine the correlation between the protein expression and amplification status of MYC in patients randomized on NCCTG-N9831.
  IV. To determine the correlation between marker protein expression/amplification/mutation status and known clinicopathological characteristics of the tumors.

Eligibility: Inclusion Criteria
  -  Diagnosed with breast cancer and treated on clinical trial NCCTG-N9831
  * Randomized to treatment
  -  HER-2 positive disease
  -  Whole tissue blocks and/or tissue microarray sections available
  -  Hormone receptor status:
  * ER/PR status known
  -  Any menopausal status

Relevance to patient case: definitely relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Biomarkers in Native American Women With Breast Cancer

Summary: RATIONALE: Studying samples of tumor tissue in the laboratory from Native American women with breast cancer may help doctors identify and learn more about biomarkers related to breast cancer in these patients. It may also help doctors learn more about the prognosis of these patients.
  PURPOSE: This laboratory study is looking at biomarkers in Native American women with breast cancer.

Detailed description: OBJECTIVES:
  -  Evaluate a selected panel of molecular markers in tissue specimens from Native American women with breast cancer.
  -  Determine which molecular markers provide independent prognostic information with respect to traditional prognostic factors in these patients.
  -  Compare and contrast the prevalence of positivity in Native American women with breast cancer with an age- and stage-matched cohort of Caucasian women with breast cancer enrolled on clinical trial NCCTG-77-30-51 or the Mayo Breast Cancer Registry.
  OUTLINE: Immunohistochemistry is performed on tumor samples to analyze the following molecular markers: estrogen receptor, progesterone receptor, c-erbB2, p53, Ki-67, Bcl-2, Bax, cyclin D-1, and insulin-like growth factor-1R.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of primary adenocarcinoma of the breast in Native American women
  -  Prior surgical treatment for breast cancer within the Aberdeen or Phoenix areas of the Indian Health Service or the Alaska area of the Native Health Service between 1990-2000
  -  Paraffin-embedded tissue available
  -  Paraffin-embedded tissue available from Caucasian women with breast cancer enrolled on NCCTG-77-30-51 or the Mayo Breast Cancer Registry
  PATIENT CHARACTERISTICS:
  Age
  -  18 and over
  Sex
  -  Female

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: Tamoxifen Resistance in Women With Stage I, Stage II, Stage IIIA, or Stage IIIB Breast Cancer

Summary: RATIONALE: Studying samples of blood from patients with breast cancer in the laboratory may help doctors identify and learn more about biomarkers related to tamoxifen resistance.
  PURPOSE: This laboratory study is looking at tamoxifen resistance in women with stage I, stage II, stage IIIA, or stage IIIB breast cancer.

Detailed description: OBJECTIVES:
  -  Identify women who are resistant to tamoxifen citrate and other drugs for the treatment of breast cancer by testing their plasma for the presence of proteins (e.g., macrophage migration inhibition factor) encoded by resistance-inducing genes (RIGs).
  -  Provide retrospective data on the predictive value of RIGs to serve as the basis for a prospective clinical trial of these genes as predictors of drug resistance.
  OUTLINE: This is a multicenter study. Patients are stratified according to response during tamoxifen citrate (TAM) therapy (resistant group [i.e., those who develop recurrent breast cancer while being treated with TAM] vs conditionally sensitive group [i.e., those who have disease-free survival for over 3 years after initial diagnosis while being treated with TAM]).
  Patients undergo blood collection at baseline, within 3 weeks of initiation of TAM therapy, and then every 6 months for 3 years or until relapse, whichever comes first. Samples are analyzed by enzyme-linked immunosorbent assay for expression of protein biomarkers (i.e., kallikrein gene 10, macrophage migration inhibition factor, prolyl carboxypeptidase, queuine tRNA-ribosyltransferase, and kinesin) encoded by resistance-inducing genes. An additional blood sample is obtained from patients at the time of relapse, if available.
  Patients also undergo assessment of medical history, personal habits, and characteristics of breast cancer (e.g., tumor histology, stage, and grade) at baseline.

Eligibility: Inclusion Criteria:
  -  Histologically confirmed invasive breast cancer
  -  Initial pathologic stage I-IIIB disease
  -  No stage IV disease
  -  Meets the following criteria for breast cancer therapy:
  -  Received prior primary local therapy for breast cancer
  -  Scheduled to begin tamoxifen citrate as adjuvant therapy for breast cancer within 3 weeks
  -  Hormone receptor status:
  -  Estrogen-receptor positive tumor
  -  Female
  -  Pre- or post-menopausal
  -  Must be able to donate 20 mL of blood
  Exclusion Criteria:
  -  Severe anemia, defined as hemoglobin < 11 g/dL
  -  Psychiatric history that would preclude obtaining 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: Studying Tumor Tissue Samples From Patients With Early-Stage Breast Cancer

Summary: RATIONALE: 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.
  PURPOSE: This research study is looking at tumor tissue samples from patients with early-stage breast cancer.

Detailed description: OBJECTIVES:
  -  To characterize differences in tumor morphology and molecular features that exist in good- and poor-prognosis breast cancer as determined by Oncotype Dx assay (a reverse transcriptase-PCR-based assay).
  -  To develop a computer-aided design (CAD)-based system of analysis of digitized histological images that would perform as well as Oncotype Dx assay in stratifying estrogen receptor-positive (ER+) breast cancer into prognostic categories.
  -  To identify new therapeutic targets in the PI3-kinase signaling pathway for a subset of poor-prognosis ER+ breast cancers.
  OUTLINE: Patients who had Oncotype Dx assay (a reverse transcriptase-PCR-based assay) performed for their breast cancer are identified by review of medical records. Diagnostic H&E stained tumor tissue samples are reviewed by a pathologist. Relevant pathologic features of the tumor (size, stage, grade, estrogen receptor, progesterone receptor, and HER2 staining) and linked Oncotype Dx score are recorded.
  The H&E stained tumor tissue samples are scanned to create high-resolution digital images. The images from each tissue sample are subjected to image analysis algorithms to identify sets of image features that most clearly separate tumors with low recurrence scores from those with high recurrence scores.
  Unstained paraffin sections from each tumor tissue sample, when available, are processed using IHC to analyze PI3-kinase signaling pathway (PTEN expression). Staining for other components of the PI3-kinase signaling pathway, phospo-AKT, and other proteins of interest is also performed. DNA is extracted from the samples and subjected to pyrosequencing analysis on exons 9 and 20 of PI3KCA. Sequencing of other relevant potential oncogenes, such as AKT, is also performed. Statistical analysis is performed to look for a correlation between Oncotype Dx scores and the presence of PI3KCA mutations and/or loss of PTEN expression.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of early-stage breast cancer for which an Oncotype Dx assay has been performed
  -  Must have diagnostic H&E stained tumor tissue samples available
  -  Hormone receptor status:
  -  Estrogen receptor-positive tumor
  PATIENT CHARACTERISTICS:
  -  Menopausal status not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: definitely relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Efficacy and Safety of Adjuvant Metformin for Operable Breast Cancer Patients

Summary: The investigators hypothesize that adjuvant metformin use in breast cancer patients with overweight or pre-diabetes mellitus (DM) may improve their body condition including weight loss.
  In this study, the investigators aim to test the efficacy and safety of adjuvant metformin for operable breast cancer patients with overweight or pre-DM.


Eligibility: Inclusion Criteria:
  -  Operable Breast cancer patients with BMI ≥ 23 or 100 ≤ FBS < 126
  -  From 6 month to 2 years since breast cancer operation and at least 4 weeks since chemotherapy or radiotherapy
  -  No drug use except Tamoxifen
  -  Normal OTPT & Serum creatinine (<=ULN)
  -  ECOG performance status 0-2 or Karnofsky PS 60-100%
  -  Life expectancy > 12
  -  Absolute neutrophil count ≥ 1.5 x 10^9/L
  -  Platelets ≥ 100 x 10^9/L
  -  Pregnancy(-) & without plan for pregnancy
  -  Sign a written informed consent form
  Exclusion Criteria:
  -  Type I or II DM or concurrent use of DM control agents
  -  Prior use of Metformin
  -  Hypoglycemia (FBS< 70 with clinical symptom)
  -  Concurrent investigational or commercial agents
  -  Other diet or drug intervention for weight loss
  -  Concurrent use of steroid
  -  Abnormal liver and/or renal function
  -  Symptomatic congestive heart failure / Cardiac arrhythmia / Angina pectoris
  -  Ongoing or active infection
  -  lactic acidosis
  -  Pregnancy or ongoing breast feeding
  -  Anorexia, bulimia, nausea due to other disease for longer than 1 month
  -  Allergies or allergic reactions attributed to oral medications
  -  Inability to swallow or digest oral medications
  -  Physical or psychiatric illness that would limit compliance with study protocol
  -  Participants in other clinical trial

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: Assessment of Candidate Protein Expression in Breast Cancer Specimens

Summary: RATIONALE: Studying the genes expressed in samples of tumor tissue from patients with cancer may help doctors identify biomarkers related to cancer.
  PURPOSE: This research study is looking at tumor tissue samples from patients who have undergone surgery for breast cancer.

Detailed description: OBJECTIVES:
  -  To determine if candidate genes display differential expression between normal and cancer breast tissues.
  OUTLINE: Previously collected breast cancer tissue samples (paraffin embedded blocks) and normal adjacent tissue are used for immunohistochemistry studies of expression of candidate genes.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of breast cancer
  -  Tissue samples available
  -  Samples are selected based on presence or absence of tumor receptors, (i.e.; estrogen, progesterone, and HER2 receptors) and grouped into following 4 categories:
  -  Estrogen receptor (ER)-positive/progesterone receptor (PR)-positive/HER2-negative
  -  ER-positive/PR-positive/ HER2-positive by FISH
  -  ER-negative/PR-negative/HER2-positive
  -  ER-negative/PR-negative/HER2-negative(triple negative or basal-type cancers)
  PATIENT CHARACTERISTICS:
  -  Menopausal status not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

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: Metformin Pre-Surgical Pilot Study

Summary: The purpose of this pilot study is to use a pre surgical intervention model to evaluate the biologic effects of metformin in women with newly diagnosed early invasive breast cancer. Metformin is a drug commonly used to treat patients with diabetes. This model will be used to evaluate the effects of metformin.

Detailed description: The purpose of this pilot study is to use a pre surgical intervention model to evaluate the biologic effects of metformin in women with newly diagnosed early invasive breast cancer. Metformin is a biguanide derivative which is commonly used to treat patients with diabetes. This model will be used to evaluate the effects of metformin on a specific molecular pathway called the AMPK/mTOR signaling pathway in the tumor. The effects of metformin on serum insulin levels and components of the insulin resistance syndrome will also be studied.

Eligibility: Inclusion Criteria:
  -  Histologically-confirmed operable invasive breast cancer or DCIS who undergo core needle biopsy followed by surgical excision at least 2 weeks after enrollment
  -  Body mass index > 25
  -  Age ≥ 21 years
  -  No prior chemotherapy, radiation therapy, or surgery within 6 months of study entry
  -  Signed informed consent
  Exclusion Criteria:
  -  History of diabetes mellitus requiring medical therapy
  -  Treatment with other investigational drugs within 6 months of study entry
  -  Significant renal impairment with a creatinine > 1.4 mg/dl
  -  Other serious intercurrent medical illness

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: Axillary Lymph Node Preservation Surgery in Reducing Lymphedema in Patients With Breast Cancer

Summary: This pilot phase I and randomized phase II trial studies the best way to perform axillary lymph node preservation surgery and to see how well it works in preventing lymphedema in patients with breast cancer. Lymph node mapping may help in planning surgery to remove breast cancer and affected lymph nodes. It is not yet known whether reverse mapping guided axillary lymph node dissection is more effective than standard axillary lymph node dissection in preventing lymphedema.

Detailed description: PRIMARY OBJECTIVES: I. To produce a map of the lymphatic drainage of the upper extremity as it relates to breast drainage, to determine the proportion of women undergoing axillary lymphadenectomy at risk for lymphedema. II. To determine if blue lymphatics contain lymph node metastases. III. To evaluate the incidence of lymphedema and associated other surgical related quality of life in those undergoing this procedure as compared to the current standard of care.
  OUTLINE: This is a phase I study followed by a randomized phase II study.
  PILOT PORTION: Patients receive isosulfan blue dye subcutaneously (SC) and then undergo reverse mapping-guided axillary lymph node dissection.
  RANDOMIZED PORTION: Patients are randomized to 1 of 2 treatment arms. ARM I: Patients receive isosulfan blue dye subcutaneously (SC) and then undergo reverse mapping-guided axillary lymph node dissection. ARM II: Patients undergo standard axillary lymph node dissection and then receive isosulfan blue dye SC.
  After completion of study treatment, patients are followed up periodically.

Eligibility: Inclusion Criteria:
  - Patients diagnosed with breast cancer with a planned axillary lymph node dissection planned for breast cancer
  Exclusion Criteria:
  -  Prior lymphedema in either arm
  -  Prior history of axillary surgery (except for sentinel node biopsies)
  -  Prior history of chest/axillary radiation
  -  Need for bilateral axillary node dissection surgery
  -  Prior neurologic deficits (either motor or sensory) in ipsilateral arm
  -  Known allergy to vital blue dyes
  -  No prior diagnosis of inflammatory breast cancer
  -  Cannot be pregnant or planning to continue breast-feeding immediately after surgery

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 Study of Trastuzumab-MCC-DM1 Administered Intravenously to Patients With HER2-Positive Metastatic Breast Cancer Who Have Previously Received a Trastuzumab-Containing Regimen

Summary: This is a phase I, multicenter, open-label, dose-escalation study of single-agent trastuzumab-MCC-DM1 administered by intravenous (IV) infusion in patients with HER2-positive metastatic breast cancer (MBC) who have previously received trastuzumab. The study will assess the safety, tolerability, and pharmacokinetics of trastuzumab-MCC-DM1 and determine the dose and schedule to be used in Phase II.


Eligibility: Inclusion Criteria:
  -  Histologically documented, incurable, locally advanced or metastatic breast cancer
  -  Evaluable or measurable HER2-positive disease
  -  History of progression during or within 60 days after treatment with any prior trastuzumab-containing chemotherapy regimen for HER2-positive breast cancer
  -  Previous treatment with chemotherapy for MBC
  -  Granulocyte count ≥ 1,500/μL, platelet count ≥ 100,000/μL, and hemoglobin ≥ 9 g/dL
  -  Serum bilirubin ≤ 1.5 mg/dL; AST, ALT, and alkaline phosphatase ≤ 2.5 × upper limit of normal (ULN) except for: Patients with hepatic metastases: ALT and AST ≤ 5 × ULN Patients with hepatic and/or bone metastases: alkaline phosphatase ≤ 5 × ULN
  -  Serum creatinine ≤ 1.5 mg/dL or creatinine clearance of ≥ 60 mL/min based on a 24-hour urine collection
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status of 0, 1, or 2
  -  Women of childbearing potential and men must agree to use an effective method of birth control (e.g., hormonal, barrier) while receiving study treatment
  Exclusion Criteria:
  -  History of significant cardiac disease, unstable angina, CHF, myocardial infarction, or ventricular arrhythmia requiring medication
  -  History of Grade ≥ 3 hypersensitivity reaction to trastuzumab
  -  History of any toxicity to trastuzumab that resulted in trastuzumab being permanently discontinued
  -  Symptomatic brain metastases or any radiation or surgery for brain metastases within 3 months of first study treatment
  -  Require supplemental oxygen for daily activities
  -  Grade ≥ 2 peripheral neuropathy
  -  Bisphosphonate therapy for symptomatic hypercalcemia
  -  Any chemotherapy, hormonal therapy, radiotherapy, immunotherapy, or biologic therapy for the treatment of breast cancer within 4 weeks of first study treatment
  -  Any experimental therapy within 4 weeks of first study treatment
  -  Any major surgical procedure within 4 weeks of first study treatment
  -  History of clinically symptomatic liver disease, including viral or other hepatitis, current or history of alcoholism, or cirrhosis
  -  Pregnancy or lactation
  -  Cardiac troponin I ≥ 0.2 ng/mL
  -  Ejection fraction < 50% or below the lower limit of normal determined by echocardiogram or MUGA scan
  -  Prior cumulative doxorubicin dose of > 360 mg/m2 or equivalent

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: Analysis of Surgery in Patients Presenting With Stage IV Breast Cancer

Summary: The purpose of this study is to study patients presenting with stage IV breast cancer. Stage IV means that the breast cancer has spread to another part of the body outside the breast. This study is important because in different parts of the country some patients are being offered surgical treatment for the breast tumor and some are not. The doctors do not know if surgery for the breast tumor is helpful in patients with stage IV breast cancer. The doctors will collect information about the patient and their treatment to learn more about how patients and doctors make treatment decisions. The doctor will also collect blood samples and tissue samples for laboratory studies to learn more about tumors that have spread to other parts of the body.


Eligibility: Inclusion Criteria:
  -  Age 18 years or older
  -  Known or suspected Stage IV breast cancer with intact primary tumor
  -  Known or suspected Stage IV breast cancer with intact primary tumor, having begun systemic therapy within the past 12 months
  -  Known or suspected Stage IV breast cancer within 3 months of local breast surgery
  -  Known or suspected Stage IV breast cancer within 3 months of local breast surgery, having begun systemic therapy within the past 12 months
  Exclusion Criteria:
  -  Primary breast cancer diagnosis made by FNA only and no pre-treatment core biopsy planned for diagnostic or research purposes.
  -  Failure of MSKCC or participating site to confirm Stage IV breast cancer diagnosis by biopsy within 30 days of study enrollment

Relevance to patient case: not relevant