araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Molecular Mechanisms of Clinical Resistance to Targeted Therapy Among Patients With Breast Cancer

Summary: The purpose of this study is to learn why certain drugs stop working in patients.In lab studies, tumors become resistant in several ways. Specific molecules seem to change and this may be why therapy stops working. However, we do not know if the same molecules change in patients. This study is being done to see if they do change. If we learn more about how patients become resistant, we may be able to offer better treatment in the future.


Eligibility: Inclusion Criteria:
  All patients:
  -  Diagnosed with progressive, recurrent or metastatic HER2+ or ER+ breast cancer.
  Cohort 1
  -  Patients who previously received treatment with anti-HER2 therapy (including trastuzumab, pertuzumab, TDM1, or lapatinib) as part of adjuvant chemotherapy and now have progressive or recurrent breast cancer or, patients who previously (or currently) received anti-HER2 therapy as part of a regimen for metastatic breast cancer and subsequently experienced.
  -  Evidence of disease progression or recurrence after prior therapy (e.g. radiologic progression by RECIST criteria or new metastasis).
  -  Prior tumor biopsy (may be original) defined as HER2+ by amplification by FISH (>1.9 gene copy number) or IHC 3+.
  Cohort 2
  -  Patients who previously received treatment with hormonal therapy (including tamoxifen, toremifene, raloxifene, anastrozole, letrozole, exemestane, fulvestrant, ARN-810) as a part of adjuvant therapy and now have progressive or recurrent breast cancer or patients who previously (or currently) receive hormonal therapy as part of a regimen for metastatic breast cancer and subsequently experienced evidence of disease progression.
  Cohort 3
  -  Patients not eligible for Cohorts 1 or 2, but previously received treatment of any other kind for breast cancer.
  Exclusion Criteria:
  -  Patients who are unable to consent to a biopsy.
  -  Patients for whom a repeat biopsy would be medically unsafe

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Study of Tumor and Blood Samples From Women With Breast Cancer

Summary: RATIONALE: Studying samples of tumor tissue and blood 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 and blood samples from women with breast cancer.

Detailed description: OBJECTIVES:
  Primary
  -  Assess relapse locally or remotely using biomarkers collected from primary tumor and blood samples from women with breast cancer during the first 2 years after diagnosis.
  Secondary
  -  Evaluate all relapses.
  -  Assess survival without relapse.
  -  Determine correlation between biomarkers and relapse.
  OUTLINE: Primary tumor and blood samples collected during usual care of patients during the first 2 years after diagnosis are analyzed for biomarkers useful in monitoring and diagnosing breast cancer.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of infiltrating unilateral breast cancer
  -  No in situ disease (ductal or lobular)
  -  No invasive bilateral synchronous disease
  -  Breast cancer at high risk, defined by at least 2 of the following factors:
  -  Hormone receptor negative (HR-)
  -  Axillary node positive
  -  Histopathologic grade III
  -  High mitotic index (as defined by the Curie Institute as > 20 mitoses per 10 high-power fields [HPF])
  -  Tumor size ≥ 2 cm
  -  HER2-positive (3 + IHC or FISH/ICHS positive)
  -  Triple-negative tumors (HR- and HER2-negative)
  -  Initial thoracic-abdomino-pelvic and bone scans must be negative
  -  Underwent initial surgery
  PATIENT CHARACTERISTICS:
  -  Menopausal status not specified
  -  Serum calcium normal (15.3 mg/dL) or normalized within 8 weeks after surgery
  -  No other invasive cancer within the past 5 years
  -  Not pregnant or nursing
  -  No psychological, familial, social, or geographical reasons that make monitoring impossible
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Phase I Open Label Trial to Assess Safety of BIBW 2992 (Afatinib) in Combination With Herceptin® in Patients With HER2-positive Advanced Breast Cancer.

Summary: Study to determine the Maximum Tolerated dose of BIBW 2992 given in combination with Herceptin®


Eligibility: Inclusion criteria:
  1. Female patients aged >18 years.
  2. Advanced or metastatic breast cancer that over-expresses HER2 (immunohistochemistry 3+ or 2+ and gene amplification by FISH). Prior treatment with Herceptin® or Lapatinib® (in the adjuvant or metastatic settings) is permitted but not required.
  Exclusion criteria:
  Patients with untreated or symptomatic brain metastases. Prior treatment with EGFR targeting therapies or treatment with EGFR- or HER2 inhibiting drugs within the past four weeks before the start of therapy or concomitantly with this study.

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Safety and Efficacy of TKI258 in FGFR1 Amplified and Non-amplified Metastatic HER2 Negative Breast Cancer

Summary: The purpose of this trial is to determine the efficacy and safety profile of TKI258 in 4 groups of patients with metastatic HER2 negative breast cancer (BC) stratified by FGFR1 and hormone receptor (HR) status.


Eligibility: Inclusion Criteria:
  1. Female presenting with metastatic breast cancer.
  2. Tumor must have been tested by FISH/CISH for FGFR1 amplification.
  3. HER2 and HR status must have been determined.
  4. Patients must have HER2 negative breast cancer.
  5. Patients must have a documented disease progression as define by RECIST at baseline.
  6. Patients with HR+ disease:
  -  Must have received at least one prior endocrine therapy in the metastatic setting.
  -  Must have received no more than three lines of chemotherapy in the metastatic setting.
  7. Patients with HR- disease must have received at least one and no more than three lines of chemotherapy in metastatic setting.
  Exclusion Criteria:
  1. Patients with known brain metastases or who have signs/symptoms attributable to brain metastases and have not been assessed with radiologic imaging to rule out the presence of brain metastases.
  2. Impaired cardiac function or clinically significant cardiac diseases, including any of the following:
  -  History or presence of serious uncontrolled ventricular arrhythmias or presence of atrial fibrillation.
  -  Clinically significant resting bradycardia (< 50 beats per minute).
  -  LVEF assessed by 2-D echocardiogram (ECHO) or Multiple gated acquisition scanning (MUGA)< 45%.
  3. Any of the following within 6 months prior to study entry: myocardial infarction (MI), severe/unstable angina, Coronary Artery Bypass Graft (CABG), Congestive Heart Failure (CHF), Cerebrovascular Accident (CVA), Transient Ischemic Attack (TIA), Pulmonary Embolism (PE).
  4. Uncontrolled hypertension defined by a SBP > 150mm Hg and/or DBP > 100mm Hg, with or without anti-hypertensive medication.
  Other protocol-defined inclusion/exclusion criteria may apply

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Study of Blood Samples in Patients With Breast Cancer

Summary: RATIONALE: Studying the genes expressed in samples of blood from patients with cancer may help doctors identify biomarkers related to cancer. It may also help doctors predict how patients will respond to chemotherapy.
  PURPOSE: This clinical trial is studying blood samples in patients with breast cancer.

Detailed description: OBJECTIVES:
  -  Identify constitutional gene variants associated with a change in response.
  OUTLINE: Blood samples are collected periodically for analysis of genetic factors.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed breast carcinoma
  -  Received first-line chemotherapy (in neoadjuvant or metastatic setting) comprising anthracyclines and/or taxanes, including for a second primary cancer
  -  Patient agrees to conservative surgery
  -  Hormone receptor status not specified
  PATIENT CHARACTERISTICS:
  -  Menopausal status not specified
  -  No contraindication for chemotherapy comprising anthracyclines and/or taxanes
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics
  -  No prior adjuvant therapy

Relevance to patient case: not relevant