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

Clinical trial: Genetic & Pathological Studies of BRCA1/BRCA2: Associated Tumors & Blood Samples

Summary: The purpose of this study is to try to understand the biology of development of breast, ovarian, fallopian tube, peritoneal or endometrial cancer from persons at high genetic risk for these diseases. The influence of environmental factors on cancer development in individuals and families will be studied. The efficacy of treatments for these diseases will be evaluated.

Detailed description: 1. To establish a demographic database to evaluate the efficacy of medical interventions in patients and relatives who carry BRCA1 and 2 mutations and to compare these outcomes to patients who do not carry a BRCA1 or 2 mutation.
  2. To obtain blood samples from patients who undergo genetic testing to a) evaluate the incidence of genetic modifier polymorphisms involved in the development of cancer in BRCA1 and 2 mutation carriers and to compare this incidence to non-BRCA 1 and 2 carriers. b) to understand the interaction of genetic modifiers and BRCA1 and 2 in the development of cancer. c) to determine the effect of environmental influences on the incidence of polymorphisms in genetic modifiers and on the penetrance of BRCA1 and 2 mutations by linking information from our demographic database to blood samples and
  3. To obtain tumor tissue from BRCA1 and 2 carriers to utilize for gene expression studies.
  4. To establish a cohort of sporadic breast cancer patients, or women with no family history of cancer in a first degree relative, to serve as a comparison group to women with strong family history of breast cancer.
  5. To establish a cohort of healthy volunteers without personal or family history of cancer to serve as a comparison group to women with sporadic and familial breast cancer.

Eligibility: Inclusion Criteria:
  I. Women who have a high risk of developing breast or ovarian cancer due to a known germline mutation in the BRCA1/2, PTEN, CDH1, or TP53 cancer susceptibility genes, or due to strong family history of either breast or ovarian cancer, in the absence of known cancer susceptibility gene mutation.
  II. Women who are approaching surgery for resection of a pelvic mass, which is considered suspicious for neoplasia by radiologic or clinical criteria; such women may or may not also meet criteria for inclusion in group I.

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

Clinical trial: Detection of Amplification of Her2 Fluorescent in Situ Hybridization (FISH) in Breast Tissue Sections

Summary: The purpose of the study is the identification of amplification level in human breast tissue. The imaging system is intended for diagnostic use as an aid to the pathologist in the detection, counting and classification of Her2 FISH stained tissue samples.


Eligibility: Inclusion Criteria:
  -  Well stained breast tissue slides with bright Her2 signals
  Exclusion Criteria:
  -  Very old slides that were already bleached

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

Clinical trial: Breast Cancer Rehabilitation Program in Improving Quality of Life in Breast Cancer Survivors

Summary: RATIONALE: A breast cancer rehabilitation program and exercise therapy may help improve the quality of life of breast cancer survivors.
  PURPOSE: This clinical trial studies a breast cancer rehabilitation program in improving quality of life in breast cancer survivors.

Detailed description: PRIMARY OBJECTIVES:
  I. To estimate accrual, retention, adherence, and participation of breast cancer survivors to a breast cancer rehabilitation program.
  II. To estimate the variability of weight, six-minute walk, quality of life and other psychosocial and physical measures in women participating in the BCRP.
  SECONDARY OBJECTIVES:
  I. To assess changes in the anthropometric, psychosocial, and physical outcomes over the six-month period of the BCRP.
  II. To document the types and the rates of adverse events associated with the BCRP.
  OUTLINE:
  Patients attend exercise therapy sessions over 1 hour 3 times a week for 6 months. Exercise therapy sessions are comprised of a 10 minute warm-up of light stretching and aerobic type exercise (walking, cycling), 30 minutes of endurance type exercise (cycle, walking), and 20 minutes of resistance training exercise.

Eligibility: Inclusion
  -  First occurrence of breast cancer
  -  BMI >= 25
  -  Recently completed treatment(chemotherapy/radiation) for breast cancer (=< 8 weeks), but can be receiving adjuvant hormonal therapy
  -  Willing to comply with study visits, as outlined in the protocol
  -  Lives within 30 miles of study site, or willing to travel to study site if outside a 30-mile radius
  -  Ability to participate in a moderate exercise program, such as freedom from any orthopedic abnormalities that would prevent participation
  -  Ability to understand and the willingness to sign a written informed consent document
  Exclusion
  -  Unstable angina
  -  Cardiac conduction disturbances
  -  Plans to move from the study area
  -  Dementia that is medically documented or suspected
  -  Advanced arterial disease causing ischemia of any limb
  -  Physical immobility
  -  Homebound for medical reasons
  -  Dependent on wheelchair for mobility
  -  Chronic disease which significantly reduces 4-year survival
  -  Recurrent breast cancer

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

Clinical trial: A Study of RO5212054 (PLX3603) in Participants With BRAF V600-Mutated Advanced Solid Tumors

Summary: This open-label, multi-center study will evaluate the safety, tolerability, and pharmacokinetics of RO5212054 [PLX3603] in participants with BRAF V600-mutated advanced solid tumors. Cohorts of participants will receive escalating oral doses of RO5212054. Anticipated time on study treatment is until disease progression or unacceptable toxicity occurs.


Eligibility: Inclusion Criteria:
  -  Advanced solid tumor
  -  Dose-escalation phase: Histologically confirmed, newly diagnosed or relapsed/ refractory unresectable American Joint Committee on Cancer (AJCC) Stage IIIC or IV disease
  -  Eastern Cooperative Oncology Group (ECOG) performance status 0-1
  -  Adequate liver, renal and bone marrow function
  Exclusion Criteria:
  -  Participants for whom standard therapy exists and is considered appropriate by the investigator
  -  Prior treatment with an inhibitor of BRAF (sorafenib allowed)
  -  Active Central nervous system (CNS) lesions, or history of or known carcinomatous meningitis
  -  Treatment with any chemotherapy, radiotherapy, immunotherapy or investigational agent within 28 days prior to first dose of study drug
  -  Anticipated or ongoing anti-cancer therapies other than those administered in this study
  -  Serious cardiovascular illness within the 6 months prior to study drug administration

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

Clinical trial: Biomarkers in Tissue Samples From Patients With Breast Cancer Treated With Bevacizumab

Summary: RATIONALE: DNA analysis of tumor tissue may help doctors predict how well patients will respond to treatment.
  PURPOSE: This research study is studying biomarkers in tissue samples from patients with breast cancer treated with bevacizumab.

Detailed description: OBJECTIVES:
  Primary
  -  To demonstrate that vascular endothelial growth factor-A (VEGFA) haplotypes that are associated with an increased VEGFA expression will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab in ECOG-E2100 (but not for the control arm).
  -  To demonstrate that candidate single nucleotide polymorphisms (SNPs) will further improve the predictive capacity of outcome (efficacy and toxicity) in patients enrolled in ECOG-E2100.
  -  To demonstrate that tumor VEGFA amplification or borderline amplification (estimated 14% frequency) will predict superior outcome for patients with metastatic breast cancer receiving bevacizumab on ECOG-E2100 whereas those with VEGFA deletion (estimated 11% frequency) will predict inferior outcome.
  -  To demonstrate that VEGFA amplification/deletion will not predict outcome in the control arm of ECOG-E2100.
  Secondary
  -  To demonstrate that tumor VEGFA amplification will predict increased protein expression as ascertained by IHC.
  -  To demonstrate that a combined algorithm calculated from tumor-specific variability (VEGFA amplification/deletion) and host-specific variability (SNPs) will optimally predict outcome (efficacy) with bevacizumab in patients enrolled on ECOG-E2100.
  OUTLINE: This is a multicenter study.
  Previously collected tumor-derived DNA is analyzed for VEGFA amplification/deletion and haplotype as biomarkers for outcome after bevacizumab treatment. Gene expression, polymorphism, protein expression analysis, and IHC are performed on the samples.

Eligibility: DISEASE CHARACTERISTICS:
  -  Enrolled on ECOG-E2100
  PATIENT CHARACTERISTICS:
  -  Not specified
  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: Standard Neoadjuvant Chemotherapy Versus Genomic Driven Chemotherapy in Patients With Breast Cancer

Summary: This randomized trial is comparing a standard neoadjuvant chemotherapy with a genomic driven chemotherapy in patients with breast cancer.

Detailed description: After a core biopsy, each tumor is profiled using Affymetrix U133plus2 gene expression array. DLD30 score (Hess, JCO, 2006) and TOP2A expression are quantified. Patients are then either treated with 4FEC followed by 4 docetaxel (standard arm) or by a genomic-driven regimen (experiemental arm). In the experimental arm, patients with high DLD30 receive 3 months weekly paclitaxel followed by 4 FEC, patients with high TOP2A receive 4FEC then 4 docetaxel, patients with low DLD30 and low TOP2A are treated with 6 cycles of docetaxel-capecitabine.

Eligibility: Inclusion Criteria:
  -  Invasive breast cancer not eligible for conservative surgery
  -  Her2 negative
  -  Amount of tumor cells >30% on HES slides
  -  RIN>6 and amount of RNA>1 ug
  -  No metastases
  -  Subject, age > 18 years and <65 years old
  -  Signed written informed consent
  -  PS 0-1
  -  No previous treatment for breast cancer
  -  Adequate organ function
  -  FEVG >50%
  Exclusion Criteria:
  -  In situ carcinoma
  -  Multifocal cancers
  -  Her2+
  -  Presence of metastasis
  -  Genomic testing not feasible because of tumor cells <30%, RIN<6, insufficient amount of RNA
  -  Organ dysfunction that contraindicates chemotherapy

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

Clinical trial: Lung Inflammation and Lung Metastases From Breast Cancer

Summary: The purpose of this study is to find out if there is a link between cigarette smoking, inflammation and the spread of breast cancer to the lung. We think that women who are current or former smokers may be at increased risk for breast cancer spreading to the lung compared to women who have never smoked. Smoking causes inflammation in the lung in some women. Researchers at Memorial Sloan-Kettering (MSKCC) think that smoking-related lung inflammation may increase the chance of breast cancer spreading to the lung. In order to find out whether inflammation plays a role in breast cancer spreading to the lung, we will measure a urinary marker of lung inflammation. This will allow us to determine if this marker is more commonly elevated in women with breast cancer that has spread to the lung compared to those without breast cancer in the lung. We will also collect DNA from blood to have the opportunity to determine if there are differences in DNA in women with or without breast cancer that has spread to the other sites including the lung. We will also collect blood to determine if we can identify risk factors for the spread of breast cancer to the lungs.


Eligibility: Inclusion Criteria:
  -  Registered patient at MSKCC
  -  Histologically proven breast cancer. It is not necessary that pathology be reviewed at MSKCC
  -  Age ≥18 years Group 1 (A and B)
  -  Diagnosed with metastatic breast cancer on biopsy or imaging study.
  -  Patients will be considered to have lung metastases, and will be assigned to group 1A if any of the following criteria are met, otherwise patients will be assigned to group 1B "No known Lung Metastases," Biopsy-proven lung metastasis.
  -  Pleural effusion with cytologic evidence of malignancy.
  -  Pleural effusion, exudative in character, without alternative explanation and attributed, in the opinion of the clinician to metastatic disease.
  -  Symptoms attributable to lung metastases and a radiological pattern interpreted by a radiologist as suspicious for metastatic disease.
  -  Any pulmonary nodule on chest radiograph, CT scan, PET-CT or MRI, which is interpreted by the clinician and radiologist to be metastatic in etiology, whether or not a biopsy was performed, and regardless of symptoms.
  -  A radiographic pattern interpreted by a radiologist as consistent with lymphangitic carcinomatosis.
  Group 2 (Controls)
  -  History of early breast cancer and currently no evidence of disease
  Exclusion Criteria:
  -  Inability to provide written informed consent.
  -  Inability to complete smoking and NSAID questionnaire.
  -  Steroid use within the previous 4 weeks.
  -  Radiotherapy to the breast, chest wall or axilla within the previous 3 months.
  -  Men with breast cancer.

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

Clinical trial: Clinical Study to Evaluate the Maximum Tolerated Dose of BAY1000394 Given in a 3 Days on / 4 Days Off Schedule in Subjects With Advanced Malignancies

Summary: Clinical study to determine safety, tolerability, to measure how the drug is metabolized by the body and to determine the maximum tolerated dose of BAY1000394 given in an intermittent 3 days on / 4 days off schedule to patients with advanced malignancies


Eligibility: Inclusion Criteria:
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 - 1
  -  Life expectancy of at least 12 weeks
  -  Subjects with advanced, histologically or cytologically confirmed solid tumors, refractory to any standard therapy, have no standard therapy available, or subjects must have actively refused any treatment which would be regarded standard, and / or if in the judgment of the investigator, experimental treatment is clinically and ethically acceptable
  -  At least 1 tumor lesion measurable by computer tomography (CT) scan or magnetic resonance imaging (MRI) according to RECIST 1.1
  -  Adequate bone marrow, liver, and renal functions as assessed by the following laboratory requirements to be conducted within 14 days prior to the first dose of study drug
  Exclusion Criteria:
  -  History of cardiac disease: congestive heart failure > NYHA Class II, unstable angina (anginal symptoms at rest), any episodes of angina or history of myocardial infarction, cardiac arrhythmias requiring anti-arrhythmic therapy (beta blockers or digoxin are permitted), previous venous or arterial thrombotic events, pulmonary embolism
  -  Moderate or severe hepatic impairment, i.e. Child-Pugh class B or C(3)
  -  History of human immunodeficiency virus (HIV) infection or chronic hepatitis B or C
  -  Active clinically serious infections of CTCAE > Grade 2 (CTCAE v4.02)
  -  Symptomatic metastatic brain or meningeal tumors unless the subject is > 3 months from definitive therapy, has no evidence of tumor growth on an imaging study within 4 weeks prior to study entry, and is clinically stable with respect to the tumor at the time of study entry. Subjects must not be on acute steroid therapy or taper off steroid therapy (chronic steroid therapy is acceptable provided that the dose is stable for 4 weeks prior to study entry and following screening CT / MRI scan). Subjects with neurological symptoms should undergo a CT / MRI scan of the brain to exclude new or progressive brain metastases. Spinal cord metastasis is acceptable
  -  Seizure disorder requiring therapy (such as steroids or anti-epileptics)
  -  History of organ allograft
  -  Evidence or history of bleeding disorder, i.e. any hemorrhage / bleeding event of CTCAE > Grade 2 within 4 weeks prior to prior to the first dose of study drug

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 AZD4547 in Combination With Fulvestrant vs. Fulvestrant Alone in ER+ Breast Cancer Patients

Summary: The purpose of this study is to assess the safety and effectiveness of AZD4547 in combination with fulvestrant vs. fulvestrant alone in ER+ breast cancer patients with FGFR1 polysomy (FISH4/5) or gene amplification (FISH 6)


Eligibility: Inclusion Criteria:
  -  Post-menopausal women (either through bilateral oophorectomy or amenorrhoeic for 24 months)
  -  Histological confirmation of Breast Cancer with documented ER+ receptor status
  -  Safety run-in: Relapsing during/within 12 months of completion of a single regimen of adjuvant endocrine therapy with non-steroidal AI and/ tamoxifen or progression following 1st line endocrine therapy with non-steroidal AL
  -  Rand phase IIa: Received at least 1 prior endocrine therapy in the metastatic setting or have relapsed during/ within 6 months of completion of adjuvant endocrine therapy (either non-steroidal AI or tamoxifen or a combination of both). Chemotherapy administered in the adjuvant setting is permitted.
  -  Rand phase IIa: Mandatory provision of tumour sample to confirm FGFR1 polysomy or gene amplification. At least one measurable lesion that can be accurately assessed by CT/MRI/x-ray at baseline and follow up visits
  Exclusion Criteria:
  -  Prior exposure to exemestane (safety run-in) / fulvestrant (randomized phase IIa), or any agent known to inhibit FGFRs.
  -  More than 1 prior regimen of chemotherapy for breast cancer
  -  ECG recordings that demonstrate significant abnormalities in cardiac rate, rhythm or conduction
  -  History of hypersensitivity to active or inactive excipients of AZD4547 or exemestane (safety run-in ) or fulvestrant (Randomized phase), including castor oil, or drugs with a similar chemical structure or class to AZD4547 or exemestane or fulvestrant.
  -  Randomized phase IIa: bleeding/blood clotting conditions that would prevent the administration of the fulvestrant injection into the buttocks

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

Clinical trial: A Study of BYL719 in Adult Patients With Advanced Solid Malignancies, Whose Tumors Have an Alteration of the PIK3CA Gene

Summary: This is a first-in-man trial, in which BYL719 will be administered to adult patients with advanced solid tumors, whose tumors have an alteration of the PIK3CA gene and whose disease has progressed despite standard therapy or for whom no standard therapy exists. A combination of BYL719 with fulvestrant will also be investigated in post-menopausal patients with locally advanced or metastatic breast cancer whose tumors have an alteration of the PIK3CA gene. The single agent MTD dose expansion cohort and the fulvestrant combination MTD dose expansion cohort will also include ER+/HER2- breast cancer patients whose tumors have the wild type PIK3CA gene


Eligibility: Inclusion Criteria:
  -  Patients with histologically-confirmed, advanced unresectable solid tumors who have progressed within three months before screening/baseline visit Only patients who have confirmed PIK3CA status (wild type, mutation or amplification) will be allowed for screening (patients participating in the combination arm must be eligible for treatment with fulvestrant)
  -  Availability of a representative formalin fixed paraffin embedded tumor tissue sample
  -  At least one measurable or non-measurable lesion
  -  Age ≥ 18 years
  -  World Health Organization (WHO) Performance Status ≤ 2
  -  Good organ (hepatic, kidney, BM) function at screening/baseline visit
  Exclusion Criteria:
  -  Brain metastasis unless treated and free of signs/symptoms attributable to brain metastasis in the absence of corticosteroid therapy (anti-epileptic therapy is allowed).
  -  Prior treatment with PI3K, AKT or mTOR inhibitor and failure to benefit
  -  Patient with peripheral neuropathy NCI-CTC Grade ≥ 3
  -  Patient with diarrhea NCI-CTC Grade ≥ 2
  -  Patient with acute or chronic pancreatitis
  -  Impaired cardiac function or clinically significant cardiac disease incl. unstable angina pectoris ≤ 3 months prior to starting study drug and Acute Myocardial Infarction (AMI) ≤ 3 months prior to starting study drug.
  -  Patients with clinically manifest diabetes mellitus, history of gestational diabetes mellitus or documented steroid-induced diabetes mellitus
  -  Women who are pregnant or breast feeding or adults of reproductive potential not employing an effective method of birth control
  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: Endoscopic Breast Surgery in Treating Patients With Breast Cancer

Summary: RATIONALE: Endoscopic breast surgery (EBS) is a less invasive type of surgery for breast cancer and may have fewer side effects and improve recovery. PURPOSE: This clinical trial studies endoscopic breast surgery in treating patients with breast cancer.

Detailed description: PRIMARY OBJECTIVES: I. To determine the surgical complication rate in patients undergoing EBS for benign or malignant disease and the 5-year local recurrence rate following endoscopic breast surgery among subjects undergoing EBS for breast cancer at USC. SECONDARY OBJECTIVES: I. To evaluate the safety, breast cosmesis and patient quality of life following EBS. OUTLINE: Patients undergo endoscopic breast surgery. After completion of study treatment, patients are followed up every 6 months for 5 years.

Eligibility: Inclusion Criteria:
  -  Breast cancer or prophylactic mastectomy requiring axillary nodal staging
  -  Breast disease (e.g., fibroadenoma, ADH)
  -  Ability to read and/or comprehend consent form and questionnaires
  -  Ability to follow-up per protocol
  -  Not pregnant or breastfeeding
  Exclusion Criteria:
  -  Pregnant or breastfeeding
  -  Evidence of chest wall or skin* involvement
  -  NOTE: *may be endoscopy-assisted

Relevance to patient case: not relevant