araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

Clinical trial: Identifying Circulating Breast Cancer Cells in Women With Metastatic Breast Cancer

Summary: RATIONALE: Studying samples of blood and pleural or peritoneal fluid from patients with metastatic breast cancer in the laboratory may help doctors identify biomarkers related to breast cancer and learn more about how breast cancer begins and spreads in the body.
  PURPOSE: This research study is looking at a new way of identifying circulating breast cancer cells in blood and in pleural or peritoneal fluid in women with metastatic breast cancer.

Detailed description: OBJECTIVES:
  Primary
  -  To compare identification of circulating breast cancer cells (CBCCs) in blood or pleural or peritoneal fluid by a novel technique using stem cell marker retinaldehyde dehydrogenase (ALDH) and surface antigen expression (CD44+, CD24-) to the standard technique using the CellSearch® system in women with metastatic breast cancer.
  Secondary
  -  To determine whether CBCCs have the potential to grow into metastatic lesions.
  OUTLINE: Patients undergo sample collection to help develop a new technique using stem cell marker retinaldehyde dehydrogenase (ALDH) and surface antigen expression (CD44+, CD24-) in isolating circulating breast cancer cells (CBCCs) from blood and pleural or peritoneal fluid. Blood may also be drawn to measure the number of circulating tumor cells using the standard CellSearch® system.
  Mononuclear cells are isolated by density centrifugation. Cells are stained against surface antigens that provide specific expression patterns for CBCCs (CD44, CD24). Cells are analyzed on a fluorescence activated cell sorting (FACS) Calibur flow cytometer and sequentially gated (ALDHhigh→CD44+ vs CD24-/low or CD44+ vs CD24-/low→ALDHhigh) for detection of CBCCs. For further confirmation of epithelial origin, ALDHhighCD44+CD24-/low cells are isolated using a FACSAria flow sorter, cytocentrifuged onto glass slides then stained for the expression of epithelial-specific cytokeratins 5, 8, 14, 18 and 19 by standard immunohistochemical techniques. Using the phenotype that is found to most highly enrich for epithelial cells, cells are isolated by FACS and assayed for clonogenic growth.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed adenocarcinoma of the breast
  -  Metastatic disease (stage IV)
  -  Hormone receptor status not specified
  PATIENT CHARACTERISTICS:
  -  Female
  -  Menopausal status not specified
  PRIOR CONCURRENT THERAPY:
  -  Not specified

Relevance to patient case: not relevant
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

Clinical trial: Studying Blood Samples in Women With Breast Cancer or a History of Breast Cancer

Summary: RATIONALE: Studying samples of blood in the laboratory from patients with current or previous cancer may help doctors learn more about biomarkers related to cancer.
  PURPOSE: This research study is looking at blood samples in women with breast cancer or a history of breast cancer.

Detailed description: OBJECTIVES:
  Primary
  -  To compare peripheral blood (PB) concentrations of circulating endothelial cells (CEC) in women with measurable, active breast cancer to PB concentrations of CEC in a control population of women with a history of breast cancer who are currently without evidence of active disease.
  Secondary
  -  To compare in women with measurable breast cancer the relationship between PB concentrations of CEC prior to and at 3 and 6 weeks following initiation of a new chemotherapy or hormonal therapy, and correlate these values with clinical response to treatment to determine if CEC can be used as a tumor marker or indicator of disease burden.
  -  To compare PB concentrations of CEC to levels of plasma proteins associated with angiogenesis, including vascular endothelial growth factor, in women with active or a prior history of breast cancer.
  OUTLINE: Peripheral blood and plasma samples are collected for analysis of circulating endothelial cells (CEC) and angiogenic growth factor levels. Blood samples from patients initiating a new chemotherapy or hormonal therapy for breast cancer are collected at baseline and at 3 and 6 weeks following the start of treatment. CEC are quantified via flow cytometry and plasma angiogenic markers are assessed via ELISA.
  PROJECTED ACCRUAL: A total of 100 patients with active, measurable breast cancer and 100 patients with a prior history of breast cancer will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Meets 1 of the following criteria:
  -  Receiving treatment for measurable breast cancer at the Arizona Cancer Center Clinic
  -  Being followed for a prior history of breast cancer (with no evidence of active disease) at the Arizona Cancer Center
  -  Hormone receptor status not specified
  PATIENT CHARACTERISTICS:
  -  Menopausal status not specified
  -  Not pregnant or nursing
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

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: not relevant
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

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: 70-year-old female with breast cancer; genetic feature: AURKA amplification

Clinical trial: Breast Cancer Risk in Women Who Are BRCA1/BRCA2 Mutation Carriers

Summary: This research study is looking at breast cancer risk in women who are BRCA1/BRCA2 mutation carriers. Studying samples of DNA in the laboratory from women who are BRCA1/BRCA2 mutation carriers may help doctors identify biomarkers related to cancer.

Detailed description: OBJECTIVE:
  I. To identify potential genetic modifiers of breast cancer risk in women who are carriers of the breast cancer susceptibility genes, BRCA1/2, by collecting data and genetic information from GOG-0199 and contributing it to the Consortium of Investigators of Modifiers of BRCA-Associated Breast Cancer (CIMBA), an international consortium of clinical cancer genetics investigators.
  OUTLINE: This is a multicenter study. Patients are stratified by study, country of residence, ethnicity, and birth cohort. Joint analyses of BRCA1 and BRCA2 mutation carriers are further stratified by mutation.
  Previously collected DNA samples and associated clinical information obtained from BRCA mutation-positive participants enrolled on GOG-0199 are studied. DNA samples are analyzed by mutation testing for variants (i.e., single nucleotide polymorphisms [SNPs]) in candidate genes of interest. Once genetic testing for a given set of variants has been completed, the coded laboratory data file is merged with selected demographic, clinical, and epidemiological data obtained from the GOG-0199 baseline questionnaire and submitted to the Consortium of Investigators of Modifiers of BRCA-Associated Breast Cancer (CIMBA) Central Database to analyze and publish the data. The epidemiological and SNP data contributed to the central database are then distributed to the investigators responsible for analysis of a particular SNP or set of SNPs from a candidate gene or genetic pathway.

Eligibility: Inclusion Criteria:
  -  Women with or without a personal history of breast cancer prior to enrollment in Gynecologic Oncology Group (GOG)-0199
  -  Known currently to be BRCA1/2 mutation carrier either by confirmed outside report or by research testing
  -  No BRCA1/2 mutation-negative or mutation-unknown status
  -  Enrolled on clinical trial GOG-0199 AND meets the following criteria:
  -  Completed baseline questionnaire (BQ-199)
  -  Provided information on previous breast cancer history, including date of diagnosis
  -  Provided complete data from the DNA analysis on the genetic variants of interest
  -  Available DNA samples for analysis
  -  Hormone receptor status not specified
  -  Pre- or post-menopausal status

Relevance to patient case: not relevant
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

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: 70-year-old female with breast cancer; genetic feature: AURKA amplification

Clinical trial: Study of Blood Samples From High-Risk Postmenopausal Women Who Received Treatment on Breast Cancer Prevention Clinical Trials NSABP-P-1 or NSABP-P-2

Summary: RATIONALE: Studying the genes expressed in samples of 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 blood samples from high-risk postmenopausal women who received treatment on breast cancer prevention clinical trials NSABP-P-1 or NSABP-P-2.

Detailed description: OBJECTIVES:
  Primary
  -  To identify genes associated with breast events (i.e., the occurrence of invasive breast cancer or ductal carcinoma in situ), in terms of single-nucleotide polymorphisms (SNPs) in a genome-wide association study, in Caucasian women at high risk of developing breast cancer who have received a selective estrogen receptor modulator (SERM) (i.e., tamoxifen or raloxifene) on the NSABP-P-1 OR NSABP-P-2 breast cancer prevention clinical trials.
  -  To determine the impact of CYP2D6 metabolizer status, which includes genotype and status of concurrent use of CYP2D6 inhibitors, on breast cancer events in participants receiving either tamoxifen or raloxifene.
  Secondary
  -  To explore whether multiple SNPs within a region are independently associated with a breast event.
  -  To explore whether there are interactions among SNPs that increase the risk for a breast event.
  -  To explore whether there is interaction of any SNPs identified in the primary objective with randomized treatment, in terms of the risk for a breast event.
  -  To identify rare variants that might affect estrogen-dependent expression of chromosomes (CTSO) 4 and 16 (ZNF423) and/or the relationship to BRCA1 expression.
  OUTLINE: Samples are stratified according to CYP2D6 genotype and CYP2D6 metabolizer status.
  DNA extracted from previously collected blood samples is analyzed in a genome-wide association study and compared with 2 control samples from patients who did not experience a breast event. DNA samples are used to identify and analyze single nucleotide polymorphisms.
  Also, exploratory analyses are conducted examining the impact of CYP2D6 metabolizer status on breast cancer events according to invasive vs non-invasive disease, ER status, PgR status, histologic type, and TMN stage.

Eligibility: DISEASE CHARACTERISTICS:
  -  Meets 1 of the following criteria:
  -  Previously treated on the NSABP-P-1 Breast Cancer Prevention clinical trial
  -  Caucasian women that did or did not experience an invasive breast cancer or ductal carcinoma in situ (DCIS)
  -  At least 50 years of age at time of entry to P-1
  -  Previously treated on the NSABP-P-2 Breast Cancer Prevention clinical trial
  -  Caucasian women that did or did not experience an invasive breast cancer or DCIS
  -  Hormone receptor status not specified
  PATIENT CHARACTERISTICS:
  -  Postmenopausal status
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

Clinical trial: A Study of Pertuzumab in Combination With Herceptin and Chemotherapy in Participants With HER2-Positive Breast Cancer

Summary: This 3 arm study will assess the tolerability, safety and efficacy of 3 neoadjuvant treatment regimens in participants with locally advanced, inflammatory or early stage human epidermal growth factor receptor 2 (HER2)-positive breast cancer. Before surgery, participants will be randomized to receive either A) 6 cycles of pertuzumab plus trastuzumab (Herceptin), with 5-fluorouracil/epirubicin/cyclophosphamide (FEC) for cycles 1-3 and docetaxel for cycles 4-6, or B) FEC for cycles 1-3 followed by pertuzumab plus trastuzumab with docetaxel for cycles 4-6, or C) 6 cycles of pertuzumab plus trastuzumab with docetaxel and carboplatin. Pertuzumab will be administered at a loading dose of 840 mg intravenously (iv), then 420 mg iv 3-weekly, trastuzumab at a loading dose of 8 mg/kg iv, then 6 mg/kg iv 3-weekly, docetaxel at 75 mg/m^2 iv, increased to 100 mg/m^2 iv 3-weekly, and FEC and carboplatin iv 3-weekly at standard doses. Following surgery participants will receive trastuzumab 6 mg/kg iv 3-weekly for a total of 1 year, as well as adequate chemo-, radio- and hormone therapy. Anticipated time on study treatment is 4-12 months, and target sample size is 200-300.


Eligibility: Inclusion Criteria:
  -  female participants, age >/=18 years
  -  advanced, inflammatory or early stage unilateral invasive breast cancer
  -  HER2-positive breast cancer
  -  baseline left ventricular ejection fraction (LVEF) >/=55%
  Exclusion Criteria:
  -  metastatic disease (Stage IV) or bilateral breast cancer
  -  previous anticancer therapy or radiotherapy for any malignancy
  -  other malignancy, except for carcinoma in situ of the cervix, or basal cell carcinoma
  -  clinically relevant cardiovascular disease
  -  current chronic treatment with corticosteroids of >10mg methylprednisolone or equivalent

Relevance to patient case: not relevant
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

Clinical trial: Genetic Investigation of Solid Tumors Cohort

Summary: The objective of this study is to obtain blood samples, solid tumor and/or benign hyperplasia samples to learn more about genetic differences that are linked to the formation of solid tumors.

Detailed description: Recent studies in human genetics have discovered several intervals in the human genome containing inherited variants that are statistically associated with the propensity to develop solid tumors. Even though it has been firmly established that if an individual carries these DNA variants they have an increased chance of developing a solid tumor the underlying biological mechanisms for most of these associations are largely unknown.
  In addition to inherited DNA variants that are associated with the development of solid tumors it is well established that during the development and growth of solid tumors the DNA in these cancer cells undergo somatic changes (mutations). These somatic DNA changes have been studied over the past decade and frequently are specific chromosomal translocations and amplifications associated with the development of particular solid tumors. In some instances, examining the chromosomal translocation and amplification has lead to the discovery of proteins contributing to solid tumor pathology.
  the human 8q24 interval that has strong genetic associations with solid tumor development has also been noted as frequently amplified in solid tumors and serves as a predictor of poor survival in prostate cancers.

Eligibility: Inclusion Criteria:
  1. Age 18 years or older
  2. Eligible to have their blood drawn
  3. Be reliable, cooperative and willing to comply with all protocol-specified procedures
  4. Able to understand and grant informed consent
  5. Diagnosis of a solid tumor
  Exclusion Criteria:
  1. Has a significant chronic medical condition which would potentially confound interpretation of the individual's phenotype.
  2. Treatment with any investigational agents or devices within thirty days preceding enrollment in the study.
  3. Been administered or taken any CNS sedatives or depressants in the 12 hours prior to informed consent process

Relevance to patient case: not relevant
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

Clinical trial: The Potential for Oral Diindolylmethane (DIM) Supplementation to Increase the Production of the BRCA1 Protein in BRCA1 Mutation Carriers

Summary: Women with a BRCA1 mutation face a lifetime risk of breast cancer of approximately 70% and a lifetime risk of ovarian cancer of approximately 40%. A number of potential anti-cancer nutrients have been proposed, however, it is important that diet supplements be evaluated prior to general recommendation.
  The risk of breast and ovarian cancer in carriers of a BRCA1 mutation might be lowered by some nutritional supplements. For example, green tea, broccoli and vitamin D are of potential interest. One dietary supplement that is thought to have potential for BRCA1 carriers is diindolylmethane (DIM), which is an active ingredient in broccoli and other green vegetables. DIM - is found in vegetables like broccoli and is available as a supplement in health food stores. The investigators think that DIM may increase the production of the normal copy of BRCA1 and offset the effect of the mutation.
  The purpose of this study is to determine that there is a potential for oral DIM supplementation to result in the increased production of the BRCA1 protein in BRCA1 mutation carriers. The results of the study will also serve as an evaluation of the current use and success of preventive strategies for BRCA1 mutation carriers.


Eligibility: Inclusion Criteria:
  -  Carriers of a mutation in the BRCA1 gene
  -  Non-carriers of a mutation in the BRCA1 gene who come from a family with a BRCA1 mutation (a family in which at least one individual has tested positive for a BRCA1 mutation)
  -  Can participate after being free of DIM supplementation for one month
  Exclusion Criteria:
  -  Have a personal history of cancer
  -  Currently pregnant or breast-feeding

Relevance to patient case: not relevant