araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: A Safety Study Utilizing Yondelis and Doxorubicin in Patients With a Type of Cancer Called Soft Tissue Sarcoma

Summary: The purpose of the study is to determine the dose of the combination of trabectedin (Yondelis) and Doxorubicin for which neutropenia (low white blood cell counts) could be managed with filgrastim (a Granulocyte-Colony Stimulation Factor that is used to help control neutropenia) in patients with a type of cancer called soft tissue sarcoma.

Detailed description: This is a multicenter, open-label (identity of the assigned study treatments will be known to patients and study staff) study to determine the dose of the combination of trabectedin (Yondelis) and Doxorubicin for which the neutropenia (low white blood cell counts) is manageable with the use of filgrastim (an agent used to manage neutropenia) and associated with clinically acceptable number of side effects severe enough to continuation of treatment in patients with recurrent or persistent soft tissue sarcoma (STS, a malignant tumor that attacks the body's infrastructure of fat, muscles, nerves, joints, blood vessels, or deep skin tissues). Patients will be enrolled in the study after all study-specific entry criteria are met and informed consent is obtained. Patients will be required to attend regular clinic visits to receive study medication and have their status monitored. A detailed explanation can be provided by the study physician (Investigator) conducting this study. Doxorubicin (50 to 75 mg/m2) will be given as a 10-15 minute intravenous (i.v.) infusion on Day 1 via a central venous catheter which is a tube placed into a large vein. Trabectedin (0.9 to 1.3 mg/m2) will be given as a 3 hour i.v. infusion, immediately following the administration of doxorubicin. Dexamethasone 20 mg will be given within 1 hour before the start of each doxorubicin i.v. infusion and filgrastim will be administered according to manufacturer's instructions.

Eligibility: Inclusion Criteria:
  -  Have a diagnosis of soft tissue sarcoma, recurrent or persistent
  -  Signed informed consent obtained for all patients before performing any study-related procedures
  Exclusion Criteria:
  -  Patients treated with more than 1 prior chemotherapy regimen (including adjuvant (or other additional) therapy)
  -  Previous exposure to anthracyclines (a class of drugs used in cancer chemotherapy, example is Doxorubicin) or trabectedin
  -  Less than 4 weeks since radiation therapy
  -  Known metastases (spread) of cancer to the central nervous system
  -  Other ongoing serious illness present at the time of enrollment as determined by the Investigator

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: An Analysis of the Response of Human Tumor Microvascular Endothelium to Ionizing Radiation

Summary: Doctors will take some tissue from the tissue removed during surgery in order to study how the blood vessels of the tumor respond to radiation therapy. The tissue obtained will be used to determine how these tumor blood vessels respond to radiation therapy delivered to the tumor, after it has been removed. This radiation is delivered in the research lab. This research is being conducted in order to develop new methods to treat tumors by radiation therapy. No additional surgery will be performed to obtain these samples, and only materials that remain after all diagnostic testing has been completed will be used.

Detailed description: The goal of this study is to determine if concepts established in mouse models of the tumor microvascular response to ionizing radiation (IR) therapy are applicable to human tumors in order to begin to establish that the engagement of the endothelial response is a valid target for IR in human tumors. A portion of tumor will be isolated from individuals who have signed informed consent for this protocol and are undergoing surgery on the Neurosurgery, Colorectal, and Gynecology, Head and Neck, Urology, and Hepatobiliary Services at Memorial Sloan-Kettering Cancer Center. Tumor tissue will be obtained from the surgical sample in pathology after adequate specimens have been obtained for diagnostic purposes. Tumor tissue will be irradiated ex vivo and the microvascular endothelial response will be determined. From specimens of adequate size, a pure tumor endothelial cell population will be isolated and the response to IR will be determined.
  Primary Outcomes:
  -  To determine if human tumor microvascular endothelium displays similar dose parameters as mouse tumor endothelium.
  Secondary Outcomes:
  -  To determine if tumor endothelium isolated to near homogeneity demonstrates dose parameters similar to those used in single dose radiotherapy of brain tumors.
  -  To determine if the microvascular endothelium of tumors of different types behaves in a similar fashion in its response to IR.

Eligibility: Inclusion Criteria:
  -  Patients who are felt to have adequate tumor volume for these studies, at least a 2 x 2 x 2 cm3 tumor by physical exam, imaging studies or colonoscopy reports
  -  Primary or recurrent tumors are eligible
  -  Patients must be suitable candidates for surgery
  -  Patients who have signed the informed consent
  Exclusion Criteria:
  -  Patients who are not considered suitable candidates for surgery
  -  Patients who have received prior radiation therapy to the tumor being removed
  -  Patients who have received chemotherapy within 6 months of tumor removal
  -  Patients who are pregnant
  -  Patients may choose to be excluded at any time
  -  Minors are excluded from this study because there are expected to be very few minors with the tumor types which the investigators are evaluating in this study

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Molecular Mechanism of Trophinin in Cancer Invasion and Metastasis

Summary: Our study established a model combine the in silico biology and empirical methods to identify clinically useful biomarker from information of microarray gene expression profiles in public domain. Through this method, we found trophinin as a novel prognostic marker for early stage lung cancer, which provide insight towards the process of cancer metastasis and the potential target for treatment.

Detailed description: This study was to combine the in silico biology and empirical methods to identify clinically useful biomarker of lung cancer from microarray gene expression profiles in public database.
  Using the expression profile of a known metastasis suppressor, CRMP-1, as a template to search for and compare transcriptome expressions in publicly accessible microarray datasets, trophinin (TRO) was identified as the best correlated gene. The expression pattern of trophinin in a lung cancer cell lines of invasion model was investigated using quantitative RT-PCR. The role of trophinin in cancer metastasis was investigated by measuring the change of invasion activity in trophinin gene-transfected cell lines. The relationship of trophinin and the clinicopathological characteristics of lung cancer were further examined by immunohistochemical staining.

Eligibility: Inclusion Criteria:
  -  patients who underwent surgery for non-small-cell lung cancer at the National Taiwan University Hospital from 1991 to 2000 with available stored tissue blocks were included as potential subjects in this study.
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Randomized Evaluation of Long Term Anticoagulant Therapy (RE-LY) With Dabigatran Etexilate

Summary: The primary objective of this trial is to demonstrate the efficacy and safety of dabigatran etexilate in patients with non-valvular atrial fibrillation for the prevention of stroke and systemic embolism.


Eligibility: Inclusion criteria Patients with non-valvular atrial fibrillation (AF), at moderate to high risk of stroke, or systemic embolism with at least one additional risk factor (i.e. previous ischemic stroke, TIA, or systemic embolism, left ventricular dysfunction, age >=75 years, age >=65 with either diabetes mellitus, history of coronary artery disease or hypertension)
  Exclusion criteria
  1. Prosthetic heart valves requiring anticoagulation per se, or hemodynamically relevant valve disease that is expected to require surgical intervention during the course of the study
  2. Severe, disabling stroke within the previous 6 months, or any stroke within the previous 14 days
  3. Conditions associated with an increased risk of bleeding
  4. Contraindication to warfarin treatment
  5. Reversible causes of atrial fibrillation (e.g., cardiac surgery, pulmonary embolism, untreated hyperthyroidism).
  6. Plan to perform a pulmonary vein ablation or surgery for cure of the AF
  7. Severe renal impairment (estimated creatinine clearance <=30 mL/min)
  8. Active infective endocarditis
  9. Active liver disease
  10. Women who are pregnant, lactating, or of childbearing potential who refuse to use a medically acceptable form of contraception throughout the study
  11. Anaemia (haemoglobin <100g/L) or thrombocytopenia (platelet count <100 x 109/L)
  12. Patients who have developed transaminase elevations upon exposure to ximelagatran
  13. Patients who have received an investigational drug in the past 30 days or are participating in another drug study
  14. Patients considered unreliable by the investigator concerning the requirements for follow-up during the study and/or compliance with study drug administration, has a life expectancy less than the expected duration of the trial due to concomitant disease, or has any condition which in the opinion of the investigator, would not allow safe participation in the study (e.g., drug addiction, alcohol abuse)
  15. Any known hypersensitivity to galactose if the warfarin used contains galactose.

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Assessment of EGFR Genomic Alterations as Prognostic Markers in Cervical Cancer

Summary: The Tissue Repository will search for cases, pull slides, Paraffin-embedded tissue (PET) blocks.

Detailed description: This study is done to gather preliminary data for determining the best way to test EGFR expression in patients with cervical cancer who will receive treatment with EGFR inhibitors in the future.
  This study is designed to obtain preliminary data of genomic and phenotypic alterations of the EGFR pathway in high grade cervical intraepithelial lesions (HG-SIL) and invasive cervical cancers (CC) to be used later for therapeutic guidance and to evaluate genomic (over-expression, amplification, point mutations, etc.) and phenotypic alterations of other transduction pathways interacting with the EGFR pathway.

Eligibility: Inclusion Criteria:
  -  Samples from patients diagnosed with HG-SIL (n=300) and CC (n=300) with a follow-up of at least 24 months, existing at the Department of Pathology will be retrieved by the Tissue Repository, de-identified them and provided with code numbers that will not be linked to patient's data.
  Exclusion Criteria:
  -  None Specified.

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: DNA Array Analysis of Patients With Cervical Cancer

Summary: The goal of this clinical research study is to find out if the expression of certain genes is linked with the response of cervical cancer to radiation. Researchers will study a large number of genes located in tumor material to learn this information.

Detailed description: Patients in this study are already scheduled to begin radiation therapy. Researchers will get tumor cells by taking two biopsies of the cervix. The first biopsy of the cervical tumor will be done before any treatment is given. The second biopsy will be performed about 48 hours after the radiation treatment has begun. They will then study the cells in the lab with a new technique for studying gene expression called DNA array, as well as HPV analysis, quantification of apoptosis levels, hematoxylin and eosin staining, and storage of tissue for future research..
  The patterns of gene expression in the biopsies will be compared with the success of radiation treatments.
  Some of the material will also be stored and used in the future for other research projects.
  This is an investigational study. A total of 18 patients will take part in this study. All will be enrolled at UTMDACC.

Eligibility: Inclusion Criteria:
  1. Newly diagnosed cervical cancer: clinical Stage IB -IIIB
  2. Invasive pure squamous cell carcinoma
  3. Planned treatment with concurrent cisplatinum/5-fluorouracil chemotherapy and pelvic radiation
  Exclusion Criteria:
  1. Previous cervical cancer treatment including but not limited to transvaginal cone irradiation

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Phase II Study of Neoadjuvant Chemotherapy With Doxorubicin Followed by Docetaxel-Cisplatin in Locally Advanced Breast Cancer

Summary: Phase II study of neoadjuvant chemotherapy with Doxorubicin followed by Docetaxel-Cisplatin in locally advanced breast cancer


Eligibility: Inclusion Criteria:
  -  Patients with locally advanced breast cancer
  Exclusion Criteria:
  -  Patients with metastatic breast cancer

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Safety and Efficacy Study of Trabectedin for the Treatment of Localized Myxoid / Round Cell Liposarcoma

Summary: The purpose of this study is to evaluate the safety and efficacy of trabectedin for the treatment of localized (non-metastatic) myxoid / round cell liposarcoma (malignant tumor derived from primitive or embryonal lipoblastic cells).

Detailed description: This is an open-label (all people know the identity of the intervention), prospective (study following participants forward in time), multicenter (when more than one hospital or medical school team work on a medical research study) study of trabectedin for the treatment of localized myxoid / round cell liposarcoma (MRCL). Trabectedin will be given at 1.5 milligram per meter square (mg/m^2) over a 24-hour intravenous (iv) infusion every 3 weeks for a minimum of 3 and a maximum of 6 cycles along with dexamethasone 20 mg iv which will be given within 30 minutes before start of each trabectedin iv infusion. Participants whose myxoid/round cell liposarcoma (MRCL) do not progress at the end of the neoadjuvant treatment will be followed every 6 weeks for disease progression or until 6 months post definitive surgery, in the absence of unacceptable toxicity and/or disease progression. Efficacy will be assessed by determining the pathologic Complete Response (pCR) rate assessed in the tumor surgical specimen by a central pathology review. Participants' safety will be monitored throughout the trial.

Eligibility: Inclusion Criteria:
  -  Pathological diagnosis of myxoid / round cell liposarcoma (MRCL) and availability of pathology specimens for central review and pharmacogenomic studies
  -  Clinical evidence of locally advanced (Stage III), non-metastatic tumor, including locally recurring disease after initial surgery
  -  Measurable disease (by Response Evaluation Criteria In Solid Tumors [RECIST])
  -  No prior chemotherapy or radiation (except for adjuvant post-operative radiotherapy)
  -  Eastern Cooperative Oncology Group (ECOG) Performance Status (PS) 0-2
  Exclusion Criteria:
  -  Known hypersensitivity to any of the components of the trabectedin intravenous (iv) formulation or dexamethasone
  -  Pregnant or lactating women and women of reproductive potential who are not using effective contraceptive methods
  -  History of another neoplastic disease (except basal cell carcinoma or cervical carcinoma in situ adequately treated) unless in remission for 5 years or longer
  -  Known distant metastases
  -  Other serious illnesses such as congestive heart failure or angina pectoris, myocardial infarction within 1 year before enrollment, uncontrolled arterial hypertension or arrhythmias

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Registry for Patients With Acquired Resistance to Small Molecule Kinase Inhibitors in Non-Small-Cell Lung Cancer

Summary: The purpose of this study is to try to learn more about how small molecule kinase inhibitors work in treating lung cancer. Some early studies have shown that gefitinib, erlotinib and similar drugs are more likely to work if a particular DNA change (also known as a mutation) is found in a protein that is important in lung cancer. This protein is called the epidermal growth factor receptor (EGFR). Since small molecule kinase inhibitors sometimes stop working, we would like to examine your tumor to learn why these medicines are not working as well. Your tumor will be examined for a variety of things including changes in the DNA of the EGFR. We will also sequence parts of the genes for HER2, HER3, HER4, and KRAS, other proteins thought to be important in lung cancer.

Detailed description: The goal of this protocol is to determine mechanisms of resistance to epidermal growth factor (EGFR) tyrosine kinase inhibitors (EGFR-TKI) in non-small cell lung cancer (NSCLC). A number of trials have shown small molecule kinase inhibitors to be active agents in the treatment of NSCLC [1]. Clinically these drugs have been noted to produce dramatic but infrequent responses. Mutations in the epidermal growth factor receptor have been shown to correlate with sensitivity to gefitinib and erlotinib[2,3]. However, we know that most patients who have initial responses to EGFR-TKI eventually progress. The mechanism of acquired clinical resistance to these inhibitors in patients incompletely understood.
  This is a protocol to study clinical characteristics and biopsy tissue of patients with non-small cell lung cancer who have had previous clinical response to small molecule kinase inhibitors and subsequently experience progression of disease. The tissues and other specimens will be used to carry out laboratory studies to explore the molecular basis of sensitivity and resistance to small molecule kinase inhibitors.

Eligibility: Inclusion Criteria:
  Patients diagnosed with unresectable or metastatic non-small cell lung cancer (NSCLC) and who fulfill the following eligibility criteria will be considered eligible for this study.
  -  Patient must have previously received treatment with small molecule kinase inhibitors targeting at least, in part, EGFR patients may have received other treatments since treatment with small molecule kinase inhibitors including radiation or chemotherapy)
  -  Development of disease progression while actively receiving tyrosine kinase inhibitor
  -  Signed informed consent
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: Environmental Pollutants and the Risk of Soft Tissue Sarcoma: A Pilot Study

Summary: The purpose of this study is to assess the feasibility of conducting a large hospital based case control study of the role of dioxins and dioxinlike polychlorinated dibenzofurans (PCDFs) and polychlorinated biphenyls (PCBs).


Eligibility: Inclusion Criteria:
  -  Patients with Soft tissue sarcoma at MSKCC are eligible for this study if they meet the following criteria:
  -  Between 18 and 79 years of age
  -  were diagnosed within the previous 6 months with primary soft tissue sarcoma of one of the following histologic subtypes: liposarcoma, leiomyoscaroma, MFH, or synovial sarcoma
  -  are enrolled in protocol 02-060 ("Novel Biochemical and Molecularr Determinants for Soft Tissue Sarcoma"; PI, Dr. Samuel Singer)
  -  controls will be eligibile for this study if they meet the following criteria
  -  are b/w 18-79 years of age
  -  have no prior history of cancer (other than non melanoma skin cancer)
  Exclusion Criteria:
  -  Individuals will be excluded if they
  -  are unable to sign informed consent for medical or other reasons
  -  do not speak english

Relevance to patient case: not relevant
Patient case: 26-year-old male with Liposarcoma. Genetic variant: MDM2 Amplification. Other conditions: None.

Clinical trial: DNA Repair and Genetic Susceptibility to Lung Cancer

Summary: The purpose of this study is to help us better understand the cellular changes that may lead to the development of lung cancer. We want to compare people with a second primary lung cancer with those who have only a first primary lung cancer. We hope to use the information obtained in this study as the basis for future studies and will not regard the results from this study as final.
  We will analyze your blood cells and DNA to measure the changes in several genes that we believe may be involved in lung cancer. We also want to evaluate the capacity for your DNA to repair itself.


Eligibility: Inclusion Criteria:
  -  Cases will be eligible for inclusion if:
  -  They have been diagnosed with a second primary lung cancer, and
  -  They speak English or a language for which we have a translated consent form, and
  -  They understand and agree to sign informed consent, and
  -  They agree to give us a blood sample, and
  -  They agree to give us a tissue sample when part of normal clinical procedures, and
  -  They agree to complete the study questionnaires, and
  -  They agree to have their pathology information reviewed. This could include biopsy specimens.
  Controls will be eligible for inclusion if
  -  They have been diagnosed with a first primary lung cancer, and
  -  They speak English or a language for which we have a translated consent form, and
  -  They understand and agree to sign informed consent, and
  -  They agree to give us a blood sample, and
  -  They agree to give us a tissue sample when part of normal clinical procedures, and
  -  They agree to complete the study questionnaires,
  -  They agree to have their pathology information reviewed. This will could include biopsy specimens.
  Exclusion Criteria:
  -  Subjects who do not meet the inclusion criteria as either cases or controls will not be eligible for this study.
  -  Control subjects who have a history of another cancer, other than nonmelanoma skin cancer or a first primary lung cancer, will not be eligible for this study.
  -  Control subjects who otherwise meet the eligibility requirements above but who have had chemotherapy and/or are currently being treated with chemotherapy will be excluded from the functional assay, but not from the genotyping.

Relevance to patient case: not relevant