araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: TD-1473 Long-Term Safety (LTS) Ulcerative Colitis (UC) Study

Summary: A 3-Year Multi-Center, Long-Term Safety (LTS) Study to Evaluate the Safety and Tolerability of TD−1473 in Subjects with Ulcerative Colitis who have participated in the Maintenance Study of Protocol 0157

Detailed description: This is a multi-center, long-term safety study to evaluate the safety and tolerability of TD-1473 for up to 156 weeks (3 years) + 4 week follow-up in subjects with moderate to severe UC exiting the preceding Maintenance Study of Protocol 0157 (NCT03758443).

Eligibility: Inclusion Criteria:
  To be eligible for the study, subjects are required to enter the LTS Study within 14 days of exiting the Maintenance Study of Protocol 0157 and must meet all the following criteria:
  -  Capable of providing informed consent, which must be obtained prior to any study related procedures.
  -  One of the following:
  -  Those who demonstrated persistent loss of response (no improvement 8 weeks after meeting loss of response criteria) OR
  -  Two Clinical Flares after an episode of loss of response during the Maintenance Study OR
  -  Those who have completed the Maintenance Study and confirmation of clinical remission status results are available
  -  During the study and for 7 days after receiving the last dose of the study drug, females of childbearing potential or men capable of fathering children must agree to use highly effective birth control measures (failure rate <1% when used consistently and correctly)) or agree to abstain from sexual intercourse. Females of childbearing potential must test negative for pregnancy at Day 1
  -  All male subjects must agree to refrain from semen donation during the study and for 7 days after the last dose of study drug.
  -  Must be able and willing to adhere to the study visit schedule and comply with other study requirements.
  Exclusion Criteria:
  -  Has symptoms suggestive of fulminant colitis, megacolon or intestinal perforation
  -  Likely to require surgery for UC or other major surgeries
  -  Has previously received / is currently receiving prohibited medications
  -  Has been diagnosed during Protocol 0157 with Crohn's disease, other colitis conditions or the subject has a current or past diagnosis of a fistula or abdominal abscess
  -  Has endoscopic findings during Protocol 0157 of colitis-associated colonic dysplasia (with the exception of subjects with non-colitis associated spontaneous adenomas that have been completely resected)
  -  Has clinically significant abnormalities in laboratory evaluations
  -  Additional exclusion criteria apply

Relevance to patient case: not relevant
Patient case: 45-year-old female with colon cancer; genetic feature: PIK3CA (E545K)

Clinical trial: INST 1204: PIK3CA Mutations as Biomarkers for Metastasis in Colon Cancer

Summary: This proposal seeks to further understand the contribution of the PIK3CA mutations in colon cancer, by correlating the type of hotspot mutation with the development of metastases in stage II and stage Ill patients.
  In order to do this, DNA will be extracted from either frozen or paraffin embedded colon cancer tissues to sequence PIK3CA, KRAS and BRAF. Clinical outcome data will be gathered to include metastases and survival to correlate with PIK3CA, KRAS and BRAF mutational status. Patients with stage II and stage Ill colon cancers will be identified in the University of New Mexico Human Tissue Repository and the NIH PLCO prevention trial biorepository.
  Existing banked tissues of stage II and Ill colon cancers will be collected. There will be no direct contact with living individuals. Epidemiological factors such as age, race, gender and outcome data of metastases and survival will be collected.

Detailed description: This proposal aims to identify PIK3CA mutations as a biomarker for metastasis.
  In order to do this, DNA will be extracted from either frozen or paraffin embedded colon cancer tissues to sequence PIK3CA, KRAS and BRAF. Clinical outcome data will be gathered to include metastases and survival to correlate with PIK3CA, KRAS and BRAF mutational status. Patients with stage II and stage Ill colon cancers will be identified in the University of New Mexico Human Tissue Repository and the NIH PLCO prevention trial biorepository.
  Existing banked tissues of stage II and Ill colon cancers will be collected. There will be no direct contact with living individuals. Epidemiological factors such as age, race, gender and outcome data of metastases and survival will be collected.
  Specific Aims:
  1. To develop and standardize methods for high throughput DNA extraction and analysis from colon tumors of patients with stage II and stage III disease harboring PIK3CA exon 9 and exon 20 mutations.
  2. To determine the correlation between wild type and PIK3CA, PIK3CA exon 9 and PIK3CA exon 20 mutations and development of metastatic disease and overall survival in stage II and stage III patients with colorectal cancer.

Eligibility: Inclusion Criteria:
  -  Specimen from patients with stage II and stage III colon cancer.
  Exclusion Criteria:
  -  Any other stage or type of disease outside of stage II and stage III colon cancer.

Relevance to patient case: definitely relevant
Patient case: 70-year-old female with breast cancer; genetic feature: AURKA amplification

Clinical trial: CD34 Selection of the Peripheral Blood Stem Cell Graft for Autologous Transplant

Summary: Evaluate the feasibility and safety of autologous transplantation of CD34+Thy-1+ hematopoietic stem cells afer high dose marrow ablative chemotherapy in patients with breast cancer.

Detailed description: Selection of CD34+THY-1 Positive Cells From Peripheral Blood Cells Procured for Autologous Hematopoietic Support Following High Dose Treatment with BCNU, Cyclophosphamide & Cisplatin for Stage IV Breast Cancer & Limited Prior Treatment

Eligibility: Inclusion Criteria:- stage IV breast cancer
  -  primary breast cancer does not express CD34+
  -  adequate organ function
  -  no evidence of active infection
  Exclusion Criteria:- chemotherapy within 4 weeks
  - CNS disease

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

Clinical trial: A Trial for HER2 Positive Breast Cancer Patients With Metastatic Disease

Summary: This phase II trial that includes Gemcitabine 1,250mg/m2 to be administered over approximately 30 minutes on days 1 and 8, every 21 days and Trastuzumab 8 mg/kg IV to be administered over 90 minutes on day 1 of the first cycle, then 6mg/kg as a 30 minute infusion administered on subsequent cycles.


Eligibility: Inclusion Criteria:
  -  Patients must have histologically or cytologically confirmed invasive breast cancer, with stage IV disease
  -  Tumors tested by IHC must be 3+ positive for HER2 overexpression. Tumors tested by FISH must be positive by the specific FISH assay for genetic amplification of HER2. Tumors that are 3+ by IHC but negative by FISH assay are ineligible
  -  Patients must have measurable disease
  -  Patients may NOT have received prior chemotherapy or prior trastuzumab therapy for metastatic breast cancer.
  -  Patients may have received prior chemotherapy and/or hormonal therapy for early stage breast cancer, including taxane-based chemotherapy regimens. Patients may NOT have received trastuzumab in the adjuvant setting unless disease free interval from completion of trastuzumab to time of relapse is greater than 12 months.
  Exclusion Criteria:
  -  Patients who have had prior gemcitabine chemotherapy and adjuvant trastuzumab and had less than 12- month disease free interval
  -  Patients with known leptomeningeal carcinomatosis

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

Clinical trial: Breast Cancer in Pregnancy Register Study

Summary: Women who were diagnosed with breast cancer during their pregnancy may be registered in this trial.
  Data is collected on the foetal outcome 4 weeks after delivery, maternal outcome of pregnancy as well as the breast cancer therapy applied (treatment, response to chemotherapy, type of surgery), diagnostic procedures applied (palpation, US, mammogram) and the outcome of mother and child after 5 years of therapy.

Detailed description: Breast cancer is the most common cancer malignancy in women of childbearing age after the age of 25 years. Since the incidence of breast cancer under the age of 40 is increasing, and women tend to delay pregnancy into later reproductive years, the coincidence of pregnancy and breast cancer is increasing. About 1 in 1,000 pregnancies is complicated by breast cancer. Nevertheless, little is known about the right therapy for the mother and the unborn child. We are therefore carrying out a trial, collecting prospective and retrospective data about pregnant women, with histological confirmed breast cancer. Data on the biology of the tumour and placenta tissues is also collected. The anonymous data is collected in a database.

Eligibility: Inclusion Criteria:
  -  Women with histologically confirmed breast cancer during pregnancy.
  -  Informed consent for data and specimen collection.
  Exclusion Criteria:
  -  Diagnosis of breast cancer outside the period of pregnancy.

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

Clinical trial: Study Evaluating HKI-272 (Neratinib) In Subjects With Advanced Breast Cancer

Summary: The purpose of this study is to learn whether neratinib is safe and effective in treating women with advanced human epidermal growth factor receptor 2 (HER2) positive breast cancer.

Detailed description: Arm A: HER2 gene amplification and disease progression following at least 6 weeks of standard doses of Herceptin; Arm B: HER2 gene amplification and no prior Herceptin or HER2-targeted treatment.

Eligibility: Inclusion Criteria:
  -  Pathologic diagnosis of breast cancer and current stage IIIB, IIIC, or IV
  -  Progression following at least 6 weeks of standard doses of Herceptin (Arm A only)
  -  Over-expression of HER2
  -  Tumor tissue available and adequate for analysis at screening
  -  At least one measurable lesion
  Exclusion Criteria:
  -  Prior treatment with Herceptin (Arm B only)
  -  More than 4 prior cytotoxic chemotherapy regimens
  -  Subjects with bone or skin as the only site of measurable disease
  -  Inadequate cardiac function
  -  Major surgery, chemotherapy, radiotherapy, investigational agents or other cancer therapy within 1 week of treatment day 1
  -  Active central nervous system metastases
  -  Pregnant or breastfeeding women
  -  Inability to swallow the HKI-272 capsules

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

Clinical trial: Skin Biopsies and DNA Analysis in Patients Receiving Irinotecan or Gemcitabine For Advanced Solid Tumors

Summary: RATIONALE: Studying samples of tumor tissue from patients with cancer in the laboratory may help doctors identify and learn more about biomarkers related to cancer.
  PURPOSE: This laboratory study is collecting skin biopsy specimens from patients receiving irinotecan or gemcitabine for advanced solid tumors and using them to study change in DNA due to this treatment.

Detailed description: OBJECTIVES:
  Primary
  -  Determine the level of p-Chk1 and phospho-histone 2AX (p-H2AX), an indicator of DNA damage, and possibly downstream pathway markers in hair follicles from skin biopsies of patients treated with gemcitabine hydrochloride or irinotecan hydrochloride for advanced solid tumors.
  Secondary
  -  Characterize the method for measurement (immunohistochemistry).
  -  Measure inter- and intra-patient variability for the biomarker.
  -  Partially characterize the dynamic time course of p-Chk1 and p-H2AX after administration of a DNA-damaging agent.
  OUTLINE: This is a multicenter study.
  Patients undergo collection of 2 skin biopsies with hair follicles at 4 and 8 hours or at 4 and 6 hours after the start of irinotecan hydrochloride or gemcitabine hydrochloride treatment on day 1 of course 1. Repeat biopsies will be taken at 4, 6, or 8 hours after the start of irinotecan hydrochloride or gemcitabine hydrochloride on day 1 of 2 successive courses.
  Tissue is examined by immunohistochemistry and possibly other methods for changes in p-Chk1 and pH2AX.
  PROJECTED ACCRUAL: A total of 60 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Diagnosis of advanced solid tumor malignancy (preferably colorectal, pancreatic, or breast cancer)
  -  Scheduled to receive a standard dose, weekly regimen of either irinotecan hydrochloride or gemcitabine hydrochloride
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  No DNA-damaging agent within the past 13 days

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

Clinical trial: Preoperative Bevacizumab and Trastuzumab With ABI-007 and Carboplatin in HER2+ Breast Cancer

Summary: This trial combines trastuzumab and bevacizumab monoclonal antibodies, with ABI-007 and carboplatin, as neoadjuvant therapy in previously untreated locally advanced breast cancers demonstrating HER2 gene amplification. It is hoped that this novel combination will result in increased pathologic response rates that will translate into long term outcome improvements in HER2 positive patients with locally advanced breast cancer.

Detailed description: All eligible patients will receive induction chemotherapy prior to consideration of primary surgical intervention. If surgical intervention is deemed not to be in the best interest of the patient, patient will go off study at the time of evaluation for surgery. Upon completion of chemotherapy and surgery, all ER + and/or PR + patients will be placed on Tamoxifen 20 mg/qd or an aromatase inhibitor.
  Induction preoperative therapy:
  -  Bevacizumab
  -  Trastuzumab
  -  ABI-007
  -  Carboplatin
  Postoperative Adjuvant Therapy:
  -  Bevacizumab
  -  Trastuzumab

Eligibility: Inclusion Criteria:
  -  Female patients with histologically confirmed adenocarcinoma of the breast or inflammatory breast cancer
  -  Clinical stage T 1-4, N 0-3, M0
  -  FISH+ HER2 gene amplified breast cancer
  -  18 years or older
  -  Normal cardiac function
  -  Performance status 0-2
  -  Cannot have received any prior chemotherapy for this disease or cannot have received chemotherapy for any other cancer in the past 5 years.
  -  Previous diagnosis of noninvasive breast cancer is OK.
  -  Must have adequate bone marrow, renal and liver function.
  -  Pregnant or lactating females not allowed.
  -  Preexisting peripheral neuropathy must be equal to or less than grade 1
  -  Must have archived tumor tissue for tissue testing.
  Exclusion Criteria:
  You cannot be in this study if you any of the following:
  -  History of cardiac disease, with New York Heart Association Class II or greater with congestive heart failure
  -  Any heart attack, stroke or TIAs within the last 6 months or serious arrhythmias needing medication; no bleeding diathesis or coagulopathy.
  -  No prior investigational drug within the last 30 days
  -  No prior trastuzumab or bevacizumab therapy
  There are additional inclusion/exclusion criteria. The study center will determine if you meet all of the criteria. If you do not qualify for the trial, study personnel will explain the reasons.

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

Clinical trial: Magnetic Resonance Imaging for the Early Detection of CNS Metastases in Women With Stage IV Breast Cancer

Summary: RATIONALE: Diagnostic procedures, such as magnetic resonance imaging (MRI), may help doctors find CNS metastases and plan treatment.
  PURPOSE: This randomized clinical trial is studying how well MRI finds CNS metastases in women with stage IV breast cancer.

Detailed description: OBJECTIVES:
  Primary
  -  Determine survival (without neurological symptoms due to CNS metastases) in women with HER2/neu-overexpressing stage IV breast cancer who undergo gadolinium-enhanced magnetic resonance imaging (MRI) of the brain once every 4 months vs once every 12 months for early detection of CNS metastases.
  Secondary
  -  Determine the total number of therapeutic procedures (i.e., gamma-knife, radiotherapy, or surgery) required for the treatment of brain metastases in these women.
  -  Determine the total number of hospitalization days required in these women.
  -  Determine the overall survival of these women.
  -  Evaluate a cross-platform, manufacturer-independent MRI technique for diagnosis of brain metastases that could be used in future studies in the IRIS and ULB-Canceropôle networks.
  -  Compare 2D-SE vs 3D-GE thin sections methods for post-contrast brain imaging in these women.
  OUTLINE: This is a prospective, randomized study. Patients are randomized to 1 of 2 arms.
  -  Arm I: Patients undergo gadolinium-enhanced magnetic resonance imaging (MRI) of the brain at baseline (to exclude CNS involvement) and then once every 4 months (or earlier if symptoms possibly related to CNS involvement develop) in the absence of the development of CNS metastases.
  -  Arm II: Patients undergo gadolinium-enhanced MRI of the brain at baseline (to exclude CNS involvement) and then once every 12 months (or earlier if symptoms possibly related to CNS involvement develop) in the absence of the development of CNS metastases.
  Patients complete neurological symptoms questionnaires at baseline, every 6 weeks during study intervention, and at the completion of the study.
  PROJECTED ACCRUAL: A total of 96 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Histologically confirmed breast cancer
  -  Stage IV disease
  -  HER2/neu-overexpression (3+ by immunohistochemistry AND/OR gene amplification by fluorescence in situ hybridization)
  -  Undergoing treatment with trastuzumab (Herceptin®) (alone or together with chemotherapy) once weekly or 3 times weekly AND has achieved responding or stable disease for ≥ 12 weeks
  -  No CNS metastases (i.e., brain parenchymal lesions and/or leptomeningeal carcinomatosis)
  -  No uncontrolled metastatic disease at study entry
  -  Hormone receptor status
  -  Not specified
  PATIENT CHARACTERISTICS:
  -  Female
  -  Menopausal status not specified
  -  Karnofsky performance status 70-100%
  -  No contraindication to MRI scan
  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: Genetic Counseling in Women at Risk for BRCA1 or BRCA2 Mutations

Summary: RATIONALE: Genetic counseling and using an interactive computer program may help women at risk for breast cancer make medical decisions about treatment.
  PURPOSE: This randomized clinical trial is studying standard genetic counseling to see how well it works when given together with or without a medical decision-making computer program in women at risk for BRCA1 or BRCA2 mutations.

Detailed description: OBJECTIVES:
  -  Evaluate the impact of BRCA1/BRCA2 testing among members of hereditary breast-ovarian cancer families.
  -  Evaluate the long-term impact of genetic counseling and testing on psychosocial and behavioral outcomes.
  -  Evaluate the relative impact of standard genetic counseling (SGC) versus SGC plus the interactive decision-aid (IDA) on medical decision-making.
  -  Evaluate the relative impact of SGC vs SGC + IDA on psychological well-being.
  -  Explore the mechanisms by which the SGC + IDA intervention impacts on psychosocial and behavioral outcomes.
  OUTLINE: This is a multicenter study.
  Eligible women are asked to participate in a baseline telephone interview over 30 minutes and then invited to a genetic counseling session over 1.5-2 hours that includes information about BRCA1/2 testing. Patients are then offered BRCA1/2 testing, and the test results (i.e., mutation carrier vs noncarrier) are presented at a subsequent in-person individual genetic counseling session over 1.5-2 hours. Patients who tested positive for BRCA1 or 2 mutation are randomized to 1 of 2 counseling arms. All other patients proceed to follow up.
  -  Arm I (standard genetic counseling): No further counselor-initiated contact is scheduled.
  -  Arm II (individualized decision aid): Patients are asked to view an interactive computer program that is designed to help the patients make medical decisions based on their breast cancer risk.
  Outcome assessments, including quality of life assessment, are conducted at 2, 6, and 12 months.
  PROJECTED ACCRUAL: A total of 950 patients will be accrued for this study.

Eligibility: DISEASE CHARACTERISTICS:
  -  Members of hereditary breast/ovarian cancer families (in which there is at least a 10-20% prior probability of a BRCA1/2 mutation) OR who have a first-degree relative with a known BRCA1 or BRCA2 mutation
  -  Prior diagnosis of breast cancer allowed
  -  Must not be undergoing active treatment
  -  Patients with prior bilateral mastectomy are eligible for study but not eligible for randomization
  PATIENT CHARACTERISTICS:
  -  Female only
  -  No psychiatric or cognitive disorder that would preclude giving informed consent
  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: Safety and Efficacy Study of MK0974 in the Acute Migraine (0974-016)

Summary: The purpose of this study is to investigate the efficacy and safety of MK0974 compared to a placebo for acute migraine.


Eligibility: Inclusion Criteria:
  -  Patient has at least 1 year history of migraine (with or without aura)
  -  Females of childbearing years must use acceptable contraception throughout trial
  Exclusion Criteria:
  -  Patient is pregnant/breast-feeding (or is a female expecting to conceive during the study period)
  -  Patient has history or evidence of uncontrolled diabetes, or Human Immunodeficiency Virus (HIV) disease. Patient has uncontrolled cardiovascular disease
  -  Patient has major depression, other pain syndromes that might interfere with study assessments, psychiatric conditions, dementia, or significant neurological disorders (other than migraine)
  -  Patient has a history of gastric or small intestinal surgery or has a disease that causes malabsorption
  -  Patient has a history of cancer within the last 5 years

Relevance to patient case: not relevant