araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Biomarkers to Distinguish Benign From Malignant Thyroid Neoplasm

Summary: This protocol will evaluate microRNA biomarkers in blood and fine-needle aspirate biopsies (FNAB) of thyroid nodules. MicroRNA profiles will be determined and evaluated for their utility in pre-operative diagnosis, in particular to distinguish benign from malignant throid neoplasms. Post-surgical fresh-frozen thyroid cancer tissue will be assessed for somatic mutations, mRNA, and microRNA expression patterns. FFPE tissue will be used to obtain H&E and unstained slides to specific biomarker results using immunohistochemistry.

Detailed description: This protocol requires the collection of blood (5 ml), fine-needle aspirate biopsies (FNAB), and post-surgical thyroid cancer tissue. The post surgical tissue includes fresh-frozen tissue that is considered waste and in excess of that required for pathologic diagnosis, and archived formalin-fixed, paraffin-embedded tissue (FFPE). The blood will be used as a substrate for assessing known markers, including microRNA expression patterns that may be useful to predict disease and thyroid cancer morphotype. The FNABs will be used to screen the potential of markers for pre-operative diagnosis. The post-surgical fresh-frozen thyroid cancer tissue will be used to isolate DNA and RNA in order to assess somatic mutations (RAS and PAX8/PPAR-gamma rearrangement) and messenger RNA, and microRNA expression patterns. The FFPE tissue will be used to obtain H&E and unstained slides to validate results using immunohistochemistry. The goal of these studies is to define molecular markers that will accurately distinguish benign from malignant disease and the multiple thyroid cancer phenotypes. Current methods of distinguishing benign from malignant disease requires a detailed post-surgical analysis and no known markers have yet been identified to reliably differentiate the multiple thyroid cancer morphotypes.

Eligibility: Inclusion Criteria:
  -  Patient with palpable thyroid nodule suspicious for thyroid neoplasm
  -  Patient selected to undergo fine needle biopsy for cytologic diagnosis
  -  Male (18 years of age or older)
  -  Female (18 years of age or older)

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Triple Negative Breast Cancer: Study of Molecular and Genetic Factors

Summary: Breast cancer triples negatives (TN; 15 % of the cases) are characterized by a high histoprognostic grade, a strong proliferation, a strong metastatic power, and a worse prognosis than the other forms of breast cancer. It is however a heterogenous group for histological and molecular level, but also for evolution. Most of the TN is part of the basal breast cancer subcategory. Until now, the medical treatment is based on chemotherapy.
  Breast cancers by constitutional mutation of BRCA1 / BRCA2 (5 % of breast cancers) are mostly of basal type and their prognostic seems better that what could be expected from high grade tumours and without hormonal receptors. They would be much more frequent in the TN group. However, at this day, no prospective study was led to estimate this incidence, or to study the intervention of other genes of predisposition, as well to analyse the links between this phenotype and their consequences at the germinal or somatic level, in terms of associated molecular changes and prognosis.
  The purpose of this study is, on a prospective study, to lead a joined analysis at the germinal level, in search of mutations of the main genes of breast cancer predisposition (BRCA1/2, PALB2, PTEN, PALB2), and at the tumour level (tissue micro-array and transcriptome), by correlating these results to the main clinical parameters.
  The 5 years relapse-free survival will also be estimated.


Eligibility: Inclusion Criteria:
  -  women > 18
  -  non metastatic breast cancer
  -  triple negative
  -  5 years follow-up
  -  signed informed consent
  Exclusion Criteria:
  -  other cancer (except in situ)
  -  metastases at diagnosis
  -  impossibility of follow-up

Relevance to patient case: definitely relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Lipo-dox and Cyclophosphamide /5-Fluorouracil in Patients With Metastatic Breast Cancer

Summary: To determine the overall objective response rate of pegylated liposomal doxorubicin （Lipo-Dox）combined with cyclophosphamide/5-FU as second-line treatment in patients with metastatic breast cancer.


Eligibility: Inclusion Criteria:
  -  histologically proved breast cancer with metastatic disease
  Exclusion Criteria:
  -  life expectancy less than 3 months.

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Genetics, Brain Structure and Thinking Skills in Autism

Summary: The purpose of this research is to better understand the genetic, biochemical, cognitive and behavioral symptom abnormalities that contribute to autism spectrum disorders. The investigators anticipate recruiting at least 100 participants with autism spectrum disorder and large head size, at least 100 participants with autism spectrum disorder without large head size and at least 40 healthy siblings. Biological parents are expected to be recruited only as genetic changes are identified in individuals with autism spectrum disorders to better understand the nature of these genetic changes. Participants are asked to complete cognitive testing, a blood draw, urine collection and measurement of his/her height, weight and head circumference. Parents or caregivers may be asked to complete a diagnostic evaluation and will complete questionnaires that examine the participant's medical and family history as well as his/her current symptoms, functioning, and quality of life. A brief report simply listing and giving a basic description of any behavioral diagnostic information, autism symptoms, adaptive functioning, and a listing of results from cognitive testing will be provided as part of this study.


Eligibility: Inclusion Criteria:
  -  Clinical diagnosis of autism
  -  Consent from parents or guardians or an adult with or suspected of having an autism spectrum disorder that does not require a legal guardian or an adult who is the healthy sibling of an individual with an autism spectrum disorder.
  -  Youth ages 2-17 and adults ages 18-50. Youths and adults who are able (some young or severely impaired participants may not be able to provide assent) will be asked to provide assent.
  -  Families with multiple children who meet the above inclusion criteria will be permitted to have as many children participate as they wish.
  -  Youth ages 2-17 and adults ages 18-50 who do not have an autism spectrum disorder or are not suspected of having an autism spectrum disorder and who have a sibling with an autism spectrum disorder who has participated in the present study.
  Exclusion Criteria:
  -  Clinically significant medical disease that would prohibit participation in the study procedures.
  -  Children younger than 2 years old and adults older than 50 years old.

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Evaluation of Beauty Care Before Chemotherapy in Women With Breast Cancer

Summary: Evaluation of beauty care in women receiving adjuvant chemotherapy for breast cancer


Eligibility: Inclusion Criteria:
  -  breast cancer with no metastasis receiving adjuvant chemotherapy
  Exclusion Criteria:

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Biomarkers in Patients With Metastatic or Recurrent Head and Neck Cancer Treated With Cisplatin and Cetuximab on ECOG-E5397

Summary: RATIONALE: Studying samples of tissue from patients with cancer in the laboratory may help doctors predict how well patients will respond to treatment.
  PURPOSE: This research study is studying biomarkers in patients with metastatic or recurrent head and neck cancer treated with cisplatin and cetuximab on ECOG-E5397.

Detailed description: OBJECTIVES:
  Primary
  -  Compare cetuximab activity, as reflected in response rate (RR), in PTEN-deficient and PTEN-expressing cancers.
  Secondary
  -  Examine RR, progression-free survival (PFS), and overall survival (OS) in PTEN-deficient and PTEN-expressing cancers, by treatment arm.
  OUTLINE: Tissue microarray slides collected earlier from ECOG-E5397 are immunostained with PTEN antibody and analyzed with AQUA.

Eligibility: DISEASE CHARACTERISTICS:
  -  Treated on protocol ECOG-E5397
  PATIENT CHARACTERISTICS:
  -  Not specified
  PRIOR CONCURRENT THERAPY:
  -  See Disease Characteristics

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: An Observational Study to Register the Incidence of Breast Cancer and Current Clinical Care Patterns in Kenya

Summary: This observational study, conducted by the Kenya Society for Hematology and Oncology, will develop a Breast Cancer and Care Registry (BRECC) for Kenya. Data on demographic, clinical and pathological characteristics, treatment and clinical outcome will be collected from newly diagnosed breast cancer patients. Breast cancer patients will be recruited into this registry cohort and followed up for a period of not less than five years.


Eligibility: Inclusion Criteria:
  -  Histologically or cytologically confirmed breast cancer
  -  No previous interventional therapy for breast cancer
  -  Ability to provide written informed consent as per GCP and local regulations
  Exclusion Criteria:
  -  Participation in other clinical study where the diagnosis and treatment protocol is stated prior to enrolment
  -  Inability to assess and follow up patient outcomes, for example quality of life due to psychiatric illness or WHO/ECOG performance status IV or worse

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Study of Ipatasertib or GDC-0980 With Abiraterone Acetate Versus Coralie in Participants With Castration-Resistant Prostate Cancer Previously Treated With Docetaxel Chemotherapy

Summary: This multicenter, international, Phase Ib/II trial consists of two stages: a Phase Ib, open-label stage in which the recommended Phase II dose will be determined for ipatasertib and GDC-0980 in combination with abiraterone and prednisone/prednisolone and a Phase II, 3-arm, double-blind, randomized comparison of ipatasertib with abiraterone and prednisone/prednisolone versus placebo with abiraterone and prednisone/prednisolone.


Eligibility: Inclusion Criteria:
  -  Histologically confirmed metastatic or advanced prostate adenocarcinoma that has been previously treated with docetaxel and has progressed during treatment of at least one hormonal therapy
  -  Two rising PSA levels greater than or equal to (>/=) 2 ng/mL measured >/= 1 week apart or radiographic evidence of disease progression in soft tissue or bone
  -  Eastern Cooperative Oncology Group (ECOG) performance status of 0 or 1 at screening
  -  Adequate hematologic and organ function
  -  Documented willingness to use an effective means of contraception
  Exclusion Criteria:
  -  History of Type I or Type II diabetes mellitus requiring insulin
  -  New York Heart Association Class III or IV heart failure or Left ventricular ejection fraction < 50% or ventricular arrhythmia requiring medication
  -  Significant atherosclerotic disease, as evidenced by: unstable angina, history of myocardial infarction within 6 months prior to Day 1, or cerebrovascular accident within 6 months prior to Day 1
  -  Active autoimmune disease that is not controlled by nonsteroidal anti-inflammatory drugs or active inflammatory disease which requires immunosuppressive therapy
  -  Clinically significant history of liver disease
  -  History of adrenal insufficiency or hyperaldosteronism
  -  Phase II only: Previous therapy for prostate cancer with 17 alpha-hydroxylase/C17,20-lyase inhibitors, including abiraterone
  -  Phase II only: Previous treatment for prostate cancer with Protein kinase B phosphatidylinositol 3 kinase and/or mammalian target of rapamycin inhibitors
  -  Need for chronic corticosteroid therapy of >/= 20 mg of prednisone per day or an equivalent dose of other anti inflammatory corticosteroids or immunosuppressant

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: The Immune System's Response to Young Women's Breast Cancer

Summary: This study plans to learn more about the immune system's response to breast cancer in young women.

Detailed description: The investigators will be looking at the level of immune suppression in different types of breast cancer. The investigators will use blood, urine, and tissue samples from patients with Pregnancy Associated Breast Cancer (PABC) versus non-PABC, as well as comparing different types of breast cancer. If tissue sampling permits, the investigators may use some of the breast cancer tissue to develop models for human cancer for drug targeting. Understanding the immune response and suppression in different types of cancer will help us understand mechanisms involved in breast cancer better and help the investigators in developing new treatment in the future.

Eligibility: Inclusion Criteria:
  -  Females 50 or younger
  -  Histological or cytological confirmation of breast cancer
  -  Any clinical stage is allowed
  Exclusion Criteria:
  -  Any known autoimmune condition, chronic steroid use, underlying immune disease (other than breast cancer), use of immunomodulatory prescription drugs for any medical condition.
  -  The presence of other comorbid conditions known to impact immune function, (such as: type I diabetes, uncontrolled adult onset diabetes, severe chronic obstructive pulmonary disease (COPD), uncontrolled infection or known HIV infection.)
  -  Underlying psychiatric condition which would, in the opinion of the investigator, preclude compliance with study requirements
  -  Diagnosed with another type of cancer within 5 years except for breast cancer, cervical or non-melanomatous skin cancer.

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Palliative Care for Heart Failure Patients

Summary: The purpose of this study is to assess the impact of palliative care consultation on quality of life and symptom management for patients hospitalized with acute heart failure with a randomized control trial at Abbott Northwestern Hospital.

Detailed description: Research questions:
  Q1. Does the provision of palliative care to heart failure patients yield higher quality of life, increased symptom management, or reduced depression compared to heart failure patients not receiving palliative care?
  Q2. Does the provision of palliative care to heart failure patients result in differential use of medical services (lower hospital days and readmission) compared to heart failure patients not receiving systematic palliative care?

Eligibility: Inclusion Criteria:
  -  Abbott Northwestern Hospital inpatient adults with a diagnosis of acute heart failure
  Exclusion Criteria:
  -  Are not an inpatient at Abbott Northwestern Hospital
  -  Are in the ICU
  -  On a ventilator
  -  Are pre-or post heart transplant
  -  Have a ventricular assist device (VAD)
  -  Determined to be actively dying
  -  Have cognitive impairments such that informed consent would not be possible,
  -  Are not proficient in the English language

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: The Psychosocial and Economic Burden of Genital Warts

Summary: Considering the importance of HPV(human papilomavirus) and related diseases in Brazil, and the lack of studies about both the economic and the psychosocial burden of these diseases, BEMFAM, a Brazilian non-governmental organization that provides reproductive health services and technical support to local governments proposes a study to measure the psychosocial and economic burden of genital warts.

Detailed description: Cervical cancer is a public health issue in Brazil. The Cancer National Institute estimates that cervical cancer will be the second most incident among women, with 18.430 new cases in 2010. Human papillomavirus (HPV) is related to cervical cancer and is also responsible for benign lesions, such as genital warts.The Brazilian Ministry of Health estimates the prevalence of genital warts to be 5,7% among pregnant women and 21,5% among women attending sexually transmitted infections treatment clinics.The study will measure the psychosocial burden of genital warts using HPV Impact Profile questionnaire and the economic burden of genital warts among women attending its six reproductive health clinics.
  There are two study objectives:
  1 - to measure the psychosocial burden of genital warts in women attending six reproductive health clinics in Brazil. 2- to measure the economic burden of genital warts treatment for women attending six reproductive health clinics in Brazil.
  Hypothesis testing:
  For objective 1, the experiment compare differences on psychosocial burden of Genital Warts among subgroups and therefore does not include any formal hypothesis testing about the psychosocial burden of the disease in agreement with the extant literature on the subject (Xingshu Zhu et al., 2009).
  Objective 2 aims to measure differentials in the economic burden of the disease among subgroups with different type of genital warts (newly diagnosed, recurrent and resistant), site of the lesion, age, duration of treatment, number of medical visits, type and number of medical procedures. No formal hypothesis will be tested.

Eligibility: Inclusion Criteria:
  -  women aged 18 to 45 years, who had a Pap-smear in the preceding 90 days or were diagnosed with genital warts during physical examination.
  -  good health
  Exclusion Criteria:
  -  women self reported HIV-positive
  -  women undergoing antiretro-viral treatment
  -  illiteracy
  -  pregnancy

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Predictive Clinical and Biological Parameters in Breast Cancer

Summary: Research of predictive clinical and biological factors in breast cancer :
  genomic, proteomic, mutation


Eligibility: Inclusion Criteria:
  -  breast cancer
  -  age > 18
  -  signed informed consent
  Exclusion Criteria:
  -  emergency

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Studying Blood and DNA Samples From Patients With Breast Cancer Treated With Chemotherapy With or Without Trastuzumab

Summary: RATIONALE: Studying samples of blood and DNA in the laboratory from patients who received chemotherapy with or without trastuzumab may help doctors learn more about the effects of trastuzumab on cells. It may also help doctors understand how well patients respond to treatment.
  PURPOSE: This research trial studies blood and DNA samples from patients with breast cancer treated with chemotherapy with or without trastuzumab.

Detailed description: OBJECTIVES:
  -  To determine the role of trastuzumab in the generation of HER2-specific antibodies in breast cancer patients undergoing adjuvant combination therapy.
  -  To determine whether the improved disease-free period and overall survival of patients treated in the adjuvant setting with combination of chemotherapy and trastuzumab is dependent on the Fcγ receptor genotype of the patient.
  OUTLINE: Previously collected serum and DNA samples are analyzed for HER2-specific antibodies and FcγR genotype by enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR).

Eligibility: • Patients with HER-2-overexpressing node-positive or high-risk node-negative breast cancer enrolled on NCCTG-N9831
  * Pre- and post-treatment serum and DNA samples of patients treated with doxorubicin and cyclophosphamide followed by paclitaxel with or without trastuzumab (Herceptin®)

Relevance to patient case: not relevant
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

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: definitely relevant