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

Clinical trial: Biomarkers in Predicting Response in Patients With Early-Stage Non-Small Cell Lung Cancer Previously Treated With Adjuvant Chemotherapy

Summary: This research trial studies prognostic and predictive markers in patients with early stage non-small cell lung cancer receiving chemotherapy. Prognostic markers are patient or tumor factors that predict patient survival independent of treatment. Predictive markers are factors that may influence and predict the outcome of treatment in terms of either response or survival benefit. Collecting and storing samples of tissue from patients with cancer to study in the laboratory may help doctors learn more about cancer and identify biomarkers related to cancer.

Detailed description: PRIMARY OBJECTIVES:
  I. Evaluate potential prognostic and predictive markers in patients receiving adjuvant chemotherapy for early stage non-small cell lung cancer (NSCLC).
  II. To perform cross-validation analyses for the predictive value of cyclin-dependent kinase inhibitor 1B (p27), excision repair cross-complementation group 1 (ERCC1), beta-tubulin and B-cell lymphoma 2 (BCL2)-associated X protein (BAX).
  III. To perform cross-validation analyses for the prognostic value of mucin and breast cancer (BRCA)1 expression.
  IV. To perform a pooled analysis for the prognostic impact of p53 protein expression by immunohistochemistry (IHC), tumor protein p53 (p53) mutation, ras mutation and epidermal growth factor receptor (EGFR) mutation, and Fas cell surface death receptor (Fas)/Fas ligand (FasL) expression by IHC.
  V. Validation of the 15-gene prognostic and predictive messenger ribonucleic acid (mRNA) signature on Lung Adjuvant Cisplatin Evaluation (LACE)-Bio formalin-fixed paraffin-embedded (FFPE) tumor samples.
  VI. Exploratory evaluation of the prognostic and predictive values of known potential oncogenic mutations using LACE-Bio FFPE.
  VII. Exploratory evaluation of the prognostic and predictive values of gene copy variation using LACE-Bio FFPE tumor samples.
  VIII. Exploratory identification and evaluation of prognostic and predictive value of novel genomic aberrations discovered by Next Generation Sequencing on LACE-Bio tumor samples.
  OUTLINE:
  Previously collected tissue samples are analyzed by IHC.

Eligibility: Inclusion Criteria:
  -  Registration to CALGB9633 for this study
  -  Institutional Review Board (IRB) review and approval at the institution where the laboratory work will be performed is required
  -  Informed consent:
  -  The subject population to be studied in this protocol includes patients selected from CALGB 9633 for whom an available specimen is present at the Alliance Ohio State University (OSU); all such patients have signed a written informed consent document meeting all federal, state, and institutional guidelines as part of entry into that trial
  -  Only cases with adequate tumor formalin FFPE material without depleting the available clinical block(s) are eligible

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

Clinical trial: Safety, Pharmacokinetics and Pharmacodynamics of BEZ235 Plus MEK162 in Selected Advanced Solid Tumor Patients

Summary: This is an open label, dose finding, phase Ib clinical trial to determine the maximum tolerated dose (MTD) and/or RP2D of the orally administered PI3K/mTOR inhibitor BEZ235 in combination with the MEK1/2 inhibitor MEK162. This combination will be explored in patients with EGFR mutant NSCLC which has progressed on EGFR inhibitors and triple negative breast cancer, as well as pancreatic cancer, colorectal cancer, malignant melanoma, NSCLC, and other advanced solid tumors with KRAS, NRAS, and/or BRAF mutations. Dose escalation will be guided by a Bayesian logistic regression model with overdose control. At MTD or RP2D, two expansion arms will be opened in order to further assess safety and preliminary anti-tumor activity of the combination of BEZ235 and MEK162.
  Study drugs will be administered orally on a continuous schedule, MEK162 bid and BEZ235 qd, a treatment cycle is defined as 28 days.


Eligibility: Inclusion Criteria:
  -  histologically/cytologically confirmed, advanced non resectable solid tumors
  -  Measurable or non-measurable, but evaluable disease as determined by RECIST 1.0
  Exclusion Criteria:
  -  Patients with primary CNS tumor or CNS tumor involvement
  -  Diabetes mellitus - Unacceptable ocular/retinal conditions
  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: Safety, Pharmacokinetics and Pharmacodynamics of BKM120 Plus MEK162 in Selected Advanced Solid Tumor Patients

Summary: This is an open label, dose finding, phase Ib clinical trial to determine the maximum tolerated dose (MTD) and/or the recommended phase II dose (RP2D) of the orally administered phosphatidylinositol 3'-kinase (PI3K) inhibitor BKM120 in combination with the MEK1/2 inhibitor MEK162. This combination will be explored in patients with epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer (NSCLC) which has progressed on EGFR inhibitors and triple negative breast cancer, as well as pancreatic cancer, colorectal cancer, malignant melanoma, NSCLC, and other advanced solid tumors with KRAS, NRAS, and/or BRAF mutations. Dose escalation will be guided by a Bayesian logistic regression model with overdose control. At MTD or RP2D, two expansion arms will be opened in order to further assess safety and preliminary anti-tumor activity of the combination of BKM120 and MEK162.
  Study drugs will be administered once daily orally on a continuous schedule. A treatment cycle is defined as 28 days.


Eligibility: Inclusion Criteria:
  -  Histologically/ cytologically confirmed, advanced non resectable solid tumors
  -  Measurable or non-measurable, but evaluable disease as determined by RECIST
  Exclusion Criteria:
  -  Patients with primary CNS tumor or CNS tumor involvement.
  -  Diabetes mellitus
  -  Unacceptable ocular/retinal conditions

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

Clinical trial: A Study of Trastuzumab Emtansine in Comparison With Treatment of Physician's Choice in Participants With HER2-positive Breast Cancer Who Have Received at Least Two Prior Regimens of HER2-directed Therapy

Summary: This randomized, multicenter, 2-arm, open-label study (TH3RESA) will evaluate the efficacy and safety of trastuzumab emtansine (T-DM1) in comparison with treatment of the physician's choice in participants with metastatic or unresectable locally advanced/recurrent human epidermal growth factor receptor 2 (HER2)-positive breast cancer. Eligible participants will be randomized to receive either trastuzumab emtansine 3.6 mg/kg intravenously every 21 days or treatment of the physician's choice. Participants continue to receive study treatment until disease progression or unacceptable toxicity occurs. This study is also known under Roche study protocol number BO25734.


Eligibility: Inclusion Criteria:
  -  Adult participants ≥ 18 years of age.
  -  Histologically or cytologically documented breast cancer.
  -  Metastatic or unresectable locally advanced/recurrent breast cancer.
  -  HER2-positive disease by prospective laboratory confirmation.
  -  Disease progression on the last regimen received as defined by the investigator.
  -  Prior treatment with an trastuzumab, a taxane, and lapatinib.
  -  Disease progression after at least two regimens of HER2-directed therapy in the metastatic or unresectable locally advanced/recurrent setting.
  -  Adequate organ function, as evidenced by laboratory results.
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0, 1, or 2.
  -  Left ventricular ejection fraction (LVEF) ≥ 50% by echocardiogram or multi gated acquisition scan.
  Exclusion Criteria:
  -  Chemotherapy ≤ 21 days before first study treatment.
  -  Trastuzumab ≤ 21 days before first study treatment.
  -  Lapatinib ≤ 14 days before first study treatment.
  -  Prior enrollment in a trastuzumab emtansine containing study, regardless whether the patient received prior trastuzumab emtansine.
  -  Brain metastases that are untreated or symptomatic, or require any radiation, surgery or corticosteroid therapy to control symptoms within 1 month of randomization.

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

Clinical trial: Bioequivalence of 2 Formulations of TKI258 in Patients With Advanced Solid Tumors

Summary: This is a multi-center, open-label, two way crossover study designed to test the bioequivalence of 2 different oral forms of TKI258, FMI capsule and FMI tablet in patients with advanced solid tumors, excluding breast cancer. The aim of this test is to demonstrate that those 2 formulations are considered to be the same for all intents and purposes by making sure they are acting on the body with the same strength and are absorbed in similar amounts by the body. During the bioequivalence phase, patients will take orally at a daily dose of 500 mg one formulation of TKI258 during the first 3 weeks of treatment on a 5 days on/2days off dosing schedule, after which time, patients will switch to the alternate formulation for one additional week. After the bioequivalence phase, all patients may continue to take orally at a daily dose of 500 mg only TKI258 FMI capsule formulation until disease progression (assessed by RECIST 1.1), unacceptable toxicity, death or discontinuation from the study treatment for any other reason.


Eligibility: Inclusion Criteria:
  1. Patients with a histopathologically or cytopathologically confirmed diagnosis of an advanced solid tumor, excluding breast cancer, who have progressed despite standard therapy, or for which no standard therapy exists
  2. ECOG performance status (PS) 0, 1 or 2
  3. Patients must meet protocol-specified laboratory values
  Exclusion Criteria:
  1. Patients with brain metastases
  2. Patients who have concurrent severe and/or uncontrolled medical conditions which could compromise participation in the study
  3. Patients who have not recovered from previous anti-cancer therapies
  4. Patients who are expected to receive any prohibited medications during the bioequivalence phase of the study
  5. Female patients who are pregnant, breast feeding
  6. Fertile male or women of child-bearing potential not willing to use two highly effective methods of contraception
  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: Phase Ib/II Trial of BEZ235 With Paclitaxel in Patients With HER2 Negative, Locally Advanced or Metastatic Breast Cancer

Summary: This is a prospective, multi-center, open-label, phase Ib/ II study (two parts) with patients that have locally advanced or metastatic HER2 negative breast cancer. The first part (phase Ib) will investigate the MTD / Recommended Phase 2 Dose (RP2D) of the combination therapy of BEZ235 twice daily (b.i.d.) and weekly paclitaxel using a Bayesian model. When MTD/ RP2D is established the second part (phase II) will start. Phase II will evaluate the efficacy and the safety of weekly paclitaxel alone compared to weekly paclitaxel plus BEZ235 bid.


Eligibility: Inclusion Criteria (phase lb):
  -  Females with Breast cancer that is histologically or cytologically confirmed, HER2 negative and locally advanced or metastatic as confirmed by radiology
  -  ECOG performance status 0 and 1
  -  Adequate bone marrow and organ function
  Exclusion Criteria (Phase lb):
  -  Previous treatment with PI3K and/or mTOR inhibitors
  -  Symptomatic Central Nervous System (CNS) metastases
  -  Concurrent malignancy or malignancy in the last 5 years prior to start of study treatment
  -  Wide field radiotherapy ≤ 28 days or limited field radiation for palliation ≤ 14 days prior to starting study drug
  -  Active cardiac disease (e.g. LVEF less than institutional lower limit of normal, QTcF > 480 msec, unstable angina pectoris, ventricular, supraventricular or nodal arrhythmias)
  -  Inadequately controlled hypertension
  -  Impairment of gastrointestinal (GI) function or GI disease that may significantly alter the absorption of BEZ235 and/or paclitaxel
  -  Treatment at start of study treatment with drugs with a known risk to induce Torsades de Pointes, moderate and strong inhibitors or inducers of isoenzyme CYP3A4, warfarin and coumadin analogues, LHRH agonists
  -  Sensitivity to paclitaxel treatment
  -  Uncontrolled diabetes mellitus
  -  Pregnant or nursing (lactating) woman
  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: Phosphoproteomic Patterns as a Novel Biomarker for Aurora and Polo-like Kinase Inhibitors in Non-Small Cell Lung Cancer

Summary: The investigators have characterized in preclinical Non-Small Cell Lung Cancer (NSCLC) models the proteomic expression profile associated with exposure to Aurora and Polo-like kinase inhibitors. The identification of proteomic expression patterns in patients with NSCLC would be an important step in defining the possible role of these agents as potential targeted therapies for this clinically important disease. This study proposes to evaluate resected non-small cell lung cancer specimens for these proteomic expression profiles.


Eligibility: Inclusion Criteria:
  -  Subjects undergoing or who have undergone thoracic surgery for presumed lung cancer
  -  Wedge resection, lobectomy, bilobectomy, segmentectomy and pneumonectomy thoracic surgical operations are permitted.
  -  Age ≥ 18 years.
  -  Subject meets criteria for thoracic surgery as determined by the thoracic surgeon.
  -  Able to provide written informed consent.
  Exclusion Criteria:
  -  Subjects undergoing or who have undergone thoracic surgery for metastatic disease from other primary sources such as colorectal cancer, sarcoma, melanoma, breast cancer, bladder cancer, prostate cancer, esophageal cancer, pancreatic cancer, or gastric cancer will be excluded.
  -  Subjects who have received prior preoperative lung cancer anticancer therapy will be excluded.

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

Clinical trial: Mechanical Stimulation in Preventing Bone Density Loss in Patients Undergoing Donor Stem Cell Transplant

Summary: This pilot clinical trial studies mechanical stimulation in preventing bone density loss in patients undergoing donor stem cell transplant. Mechanical stimulation may limit, prevent, or reverse bone loss, increase muscle and cardiac performance, and improve overall health

Detailed description: PRIMARY OBJECTIVES:
  I. To determine the feasibility of a mechanical stimulation regimen in hematopoietic cell transplant (HCT) patients.
  SECONDARY OBJECTIVES:
  I. To evaluate the data collection tools to prepare for a larger phase II trial.
  OUTLINE:
  Patients undergo mechanical stimulation over 20 minutes once daily (QD) beginning on date of hospital admission and continuing through day 100 post-HCT, except for day 0 (date of transplant).

Eligibility: Inclusion Criteria:
  -  Meet eligibility criteria for first allogeneic HCT, and are scheduled to undergo allogeneic HCT
  -  Pre-transplant Karnofsky Performance Status (KPS) >= 70
  -  Patient or legal representative must understand the investigational nature of this study and sign an Institutional Review Board approved written informed consent form prior to receiving any study related procedure
  Exclusion Criteria:
  -  Any prior allogeneic HCT
  -  Pre-transplant weight >= 280 lbs
  -  Body mass index (BMI) < l8kg/m^2
  -  Human leukocyte antigen (HLA)-mismatched HCT
  -  Cord blood transplant
  -  Osteopenia or osteoporosis (T-score =< -1.0)
  -  Multiple myeloma diagnosis
  -  Any prior history of a central nervous system (CNS) hemorrhage
  -  Currently treated with a therapeutic dose of anti-coagulation for a recent pulmonary embolism or deep vein thrombosis
  -  Current or previous bisphosphonate use
  -  Prior history of non-traumatic fracture
  -  Any screws, pins, rods, or other metal objects in the body
  -  Total joint replacement
  -  History of kidney stones or gall stones
  -  Any artificial limbs
  -  Pregnant or nursing female patients
  -  Unwilling or unable to follow protocol requirements
  -  Any condition which in the Investigator's opinion deems the patient an unsuitable candidate to receive study intervention

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 Trastuzumab (Herceptin) and a Taxane in First-Line Treatment in Participants With Human Epidermal Growth Factor 2 (HER2)-Positive Advanced Breast Cancer

Summary: This multicenter, open-label, single-arm, Phase IIIb study will evaluate the safety and tolerability of pertuzumab in combination with trastuzumab (Herceptin) and a taxane (docetaxel, paclitaxel or nab-paclitaxel) in first-line treatment in participants with metastatic or locally recurrent HER2-positive breast cancer. Participants will receive pertuzumab intravenously (IV) and trastuzumab (Herceptin) IV plus a taxane in cycles of 3 weeks each until predefined study end, unacceptable toxicity, withdrawal of consent, disease progression, or death, whichever occurs first.


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed adenocarcinoma of the breast with metastatic or locally recurrent disease not amenable to curative resection
  -  HER2-positive breast cancer
  -  Eastern cooperative Oncology Group (ECOG) performance status 0, 1 or 2
  -  LVEF of at least 50 percent (%)
  Exclusion Criteria:
  -  Previous systemic non-hormonal anti-cancer therapy for metastatic or locally recurrent disease
  -  Disease-free interval from completion of adjuvant or neoadjuvant systemic non-hormonal treatment to recurrence less than or equal to (</=) 6 months
  -  Previous approved or investigative anti-HER2 agents in any breast cancer treatment setting, except for trastuzumab and/or lapatinib in the adjuvant or neoadjuvant setting
  -  Disease progression while receiving trastuzumab and/or lapatinib in the adjuvant or neoadjuvant setting
  -  History of persistent Grade 2 or higher (National Cancer Institute Common Toxicity Criteria [NCI-CTC], Version 4.0) hematological toxicity resulting from previous adjuvant or neoadjuvant therapy
  -  Central nervous system (CNS) metastases
  -  Current peripheral neuropathy of Grade 3 or greater (NCI-CTC, version 4.0)
  -  History of other malignancy within the last 5 years prior to first study drug administration, except for carcinoma in situ of the cervix or basal cell carcinoma
  -  Inadequate bone marrow, liver or renal function
  -  Uncontrolled hypertension
  -  Hepatitis B, hepatitis C or Human Immunodeficiency Virus (HIV) infection

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

Clinical trial: A Study of the Experimental Drug BKM120 With Paclitaxel in Patients With HER2 Negative, Locally Advanced or Metastatic Breast Cancer, With or Without PI3K Activation

Summary: This study evaluated whether the addition of daily BKM120 to weekly paclitaxel was effective and safe in treating patients with HER2- locally advanced or metastatic breast cancer.

Detailed description: Based on the efficacy results at the time of the interim analyses, the DMC recommended stopping the study at Phase II during the interim as it met the protocol pre-specified futility criteria. Consequently, the Phase III portion of the study was not conducted.

Eligibility: Inclusion Criteria:
  -  Breast cancer that is locally advanced or metastatic
  -  HER2 negative disease, and a known hormone receptor status - ER/PgR (common breast cancer classification tests)
  -  A tumor sample must be shipped to a central lab for identification of biomarkers (PI3K activation status) before randomization
  -  Adequate bone marrow and organ function
  -  Measurable or non-measurable disease
  Exclusion Criteria:
  -  Prior chemotherapy for locally advanced or metastatic disease
  -  Previous treatment with PI3K or AKT inhibitors
  -  Patient has symptomatic CNS metastases
  -  Concurrent malignancy or malignancy within 3 years of study enrollment
  -  Hematopoietic colony-stimulating growth factors or radiation within 2-4 weeks prior to starting study drug
  -  Increasing or chronic treatment (> 5 days) with corticosteroids or another immunosuppressive agent
  -  Active heart (cardiac) disease as defined in the protocol
  -  Known hypersensitivity or contraindications to use paclitaxel
  -  Pregnant or nursing (lactating) woman
  -  Certain scores on an anxiety and depression mood questionaire given at screening
  -  Other protocol defined criteria may apply

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

Clinical trial: Open-Label,Non-Randomized Trial of Cisplatin Chemotherapy in BRCA1-Positive Metastatic Breast Cancer Patients

Summary: Among women with a BRCA1 mutation and breast cancer, choice of chemotherapy is a critical issue. There are emerging data which suggest that mutation carriers may respond differently than non-carriers to particular agents. BRCA1-associated cancers differ from non-hereditary cancers for a range of pathologic and molecular factors, including tumor grade and histologic appearance. Several studies have shown that the response to treatment for women with a BRCA1-associated breast cancer reflects the underlying tumor biology, in particular, the impairment of the DNA damage response and repair pathways, and that it is possible to exploit the sensitivity of BRCA1-associated cancers to DNA damage.
  It is equally important that the investigators evaluate the benefit of cisplatin in women with disseminated breast cancer, including those who have previously been treated with one or more chemotherapy regimens. This study is undertaken to evaluate the efficacy of cisplatin chemotherapy in BRCA1 carriers with metastatic breast cancer. The primary objective is to determine the objective response rate of cisplatin in BRCA1 carriers with metastatic breast cancer. The secondary objectives are to determine 3-year survival and to evaluate the toxicities of cisplatin in BRCA1 carriers with metastatic breast cancer.


Eligibility: Inclusion Criteria:
  -  Female patients aged ≥ 18 years, with measurable (defined by Response Evaluation Criteria in Solid Tumors (RECIST) criteria (14)) metastatic (stage IV) breast cancer, and who are known to carry a BRCA1 mutation, are eligible.
  -  In addition, the following are required:
  -  adequate hematologic
  -  renal, and hepatic function
  -  adequate recovery from recent surgery and/or radiation therapy
  -  recovery from all prior treatment-related toxicities (to grade < 2 according to National Cancer Institute Common Toxicity Criteria, Version3.0, except alopecia)
  -  life expectancy of at least 12 weeks
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1. -
  -  Patients could have received up to four prior chemotherapies for metastatic disease.
  Exclusion Criteria:
  -  Patients with known brain metastases are not eligible.
  -  Patients previously treated with a platinum-based chemotherapy are not eligible.

Relevance to patient case: not relevant