araag2/TREC_Precision-Medicine huggingface dataset:
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Efficacy and Safety of AZD4547 Versus Paclitaxel in Patients With Advanced Gastric or Gastro-oesophageal Cancer

Summary: The purpose of this study is to assess the efficacy, safety and tolerability of AZD4547 compared with paclitaxel in patients with advanced gastric or lower-oesophageal cancer whose tumours are found to have FGFR2 polysomy or gene amplification.

Detailed description: A Randomised Open-Label Phase IIa Study to Assess the Efficacy and Safety of AZD4547 monotherapy versus paclitaxel in Patients with Advanced Gastric or Gastro-oesophageal Junction Cancer with FGFR2 Polysomy or Gene Amplification (SHINE study). Patients were to be assigned to strata by FGFR2 status of: polysomy, low or high gene amplification.

Eligibility: Inclusion Criteria:
  -  Female or male aged 25 or over
  -  Histological diagnosis of locally advanced or metastatic gastro adenocarcinoma (including adenocarcinoma of the lower third of the oesophagus or the gastro oesophageal junction )
  -  Radiographically confirmed progression after 1 prior chemotherapy or chemoradiotherapy for gastric cancer. Suitable for and expected to benefit from paclitaxel monotherapy.
  -  At least one lesion, not previously irradiated, that has baseline at least 10mm in the longest diameter for non nodal lesions and is assessed by Computerised Tomography (CT) or Magnetic Resonance Imaging (MRI)
  -  Provision of either an archival tumour sample or a fresh tumour sample for confirmation of FGFR2 polysomy/gene amplification
  Exclusion Criteria:
  -  Prior exposure to AZD4547 or history of hypersensitivity other drugs similar in structure or class to AZD4547. Hypersensitivity to paclitaxel or formulated in cremophor EL (polyoxyethylated castor oil)
  -  Prior taxane treatment for gastric cancer with the exception of adjuvant/neo-adjuvant therapy given > 6 months; Major surgery, radiotherapy with wide field of radiation or any cancer treatment within 4 weeks before the first dose of the study treatment
  -  With the exception of alopecia, any unresolved toxicities from prior therapy with a Common Terminology Criteria for AE (CTCAE) grade >1 at the time of starting study treatment.
  -  Blood and Echocardiogram (ECG) readings that are deemed to be abnormal by falling outside of the reference ranges in the protocol inclusion/exclusion section.
  -  Taking other regular medication that are predicted to interact with AZD4547 due to their route of metabolism.

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

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: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Persistent Pain After Breast Cancer Treatment (PPBCT) - Risk Factors and Pathophysiological Mechanisms

Summary: The study is a prospective cohort study following breast cancer patients from before surgery to one year after. The aims of the study are to determine risk factors that predispose to the development of persistent pain.

Detailed description: The aim of the study is 1) to determine pre-, intra and post surgical risk factors for persistent pain after breast cancer treatment 2) to examine the prevalence of persistent pain 6 and 12 months after surgery 3) provide a quantitative sensory testing (QST) profile of the patient population, measured pre surgery, 1 week and 12 months after surgery.

Eligibility: Inclusion Criteria:
  -  Diagnosed with breast cancer
  -  18 years or older
  Exclusion Criteria:
  -  unable to give written consent
  -  unable to understand Danish
  -  Previous cosmetic surgery in the breast
  -  Previous surgery in ipsilateral breast
  -  Bilateral cancer
  -  Concomitant corrective surgery on contralateral side
  -  Pregnant
  -  Other disease or injury in the nervous system
  -  Psychiatric disease
  -  Alcohol or drug abuse

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: The Diagnosis of Biliary Tract Neoplasm by Diffusion Weighted Imaging and Magnetic Resonance Cholangiopancreatography

Summary: Researching the diagnostic significance of Biliary Tract Neoplasm under combining DWI sequence with MRCP versus MRCP only separately.

Detailed description: The purpose of the study is to evaluate the usefulness of diffusion weighted imaging(DWI) combined with MRCP of 3-T magnetic resonance imaging (MRI) in the evaluation of suspected malignant bile duct diseases.People with suspected Biliary Tract Neoplasm based on clinical symptoms(such as jaundice and thinness with unknown reasons)and CA-199 value raises are included.Diagnosis divided into two steps: the first one，only provide conventional MR sequences and MRCP images to make a diagnosis; the second step,provide the DWI images additionally, combining the image data before to make a diagnosis.Hypothesis is that DWI sequence should be regularly added into MRCP examination for improving diagnosis rate of Biliary Tract Neoplasm.

Eligibility: Inclusion Criteria:
  -  Informed consent
  -  Suspected Biliary Tract Neoplasm based on clinical symptoms(such as jaundice and thinness with unknown reasons)and CA-199 raises（＞37U/mL）
  -  No evidence of clinical symptoms or CA-199 increase by non-bile duct cancerous factors(hepatitis,cholangeitis,stones)
  -  Age ≥ 16
  Exclusion Criteria:
  -  Previous Biliary Tract Neoplasm surgery
  -  Contraindication for MRI (such as pacemaker or inner ear implant)
  -  Claustrophobia
  -  Age < 16

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Evaluation of Drug Activity in Women With Breast Cancer and no Previous Herceptin Treatment

Summary: To compare the activity of AZD8931 against placebo on the cell markers in cancer tumours

Detailed description: A Randomised Double-Blind Placebo-controlled Multicentre Phase I Study to Assess the Biological Activity of AZD8931 in Patients with Early Breast Cancer who are Ineligible for Treatment with trastuzumab as defined by IHC status

Eligibility: Inclusion Criteria:
  -  Females aged 18 or older Early stage breast cancer and planned surgery
  -  Ineligible for Trastuzumab (Herceptin) treatment as per local guidelines
  -  World health Organisation performance status of 0 to 1 Tumour size amenable to obtaining adequate biopsies pre dosing.
  Exclusion Criteria:
  -  Eligible for Trastuzumab (Herceptin) Treatment Known sensitivity to AZD8931, its excipients or drugs in its class;
  -  Including oral tyrosine kinase inhibitors History of eye conditions e.g. previous injury within 3 months or clinically significant eye disease
  -  Concurrent malignancy Unable to discontinue medication or herbal supplement known to inhibit CYP3A4 or CYP2D6

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: Depression Care for Hospitalized Coronary Heart Disease Patients: Prospective Cohort Study

Summary: The aims of this prospective, observational study are to assess the current use of depression care in Coronary Heart Disease (CHD) patients, and to provide estimates for the resources needed to implement guideline-oriented depression health care acceptable to CHD patients with comorbid depression.

Detailed description: In patients with established CHD, unipolar depression is up to three times more prevalent than in the general population and increases the risk for coronary events and mortality, higher health care consumption and decreased quality of life. Most hospitals in Germany have a unique infrastructure of psychiatric, psychosomatic and psychosocial services for CHD patients (psychiatric/psychosomatic consultation liaison services and a wide network of inpatient or outpatient cardiac rehabilitation centers). However, as of today, little is known about the current use and acceptability of depression health care from the perspective of CHD patients.
  This project has two main aims:
  1. to assess the current use of depression care in CHD patients who are hospitalized or receive ambulatory care at a cardiology clinic
  2. to provide estimates for the resources needed to implement guideline-oriented depression health care acceptable to CHD patients with comorbid depression.
  Specifically, the investigators will assess
  -  rates of and satisfaction with depression health care use in hospitalized CHD patients within one year after hospitalization
  -  perceived need for depression care and patient preferences for different types, settings and providers of these services
  -  correlates of depression health care use and patient preferences
  -  the amount of patients in need for depression health care according to existing recommendations
  The secondary objective is to assess direct and indirect costs associated with depressive symptoms and depression care use across 1 year (as indicated by quality of life, event-free survival, productivity, and health care costs).

Eligibility: Inclusion Criteria:
  -  chronic CHD (confirmed by a clinician)
  Exclusion Criteria:
  -  chart-documented dementia disorder
  -  cognitive impairment
  -  life expectancy < 1 year
  -  unavailability for follow-up
  -  insufficient proficiency in German or Turkish language

Relevance to patient case: not relevant
Patient case: 67-year-old female with Breast cancer. Genetic variant: FGFR1 Amplification, PTEN (Q171). Other conditions: Depression, Hypertension, Heart Disease.

Clinical trial: A Phase III Study of BKM120 With Fulvestrant in Patients With HR+,HER2-, AI Treated, Locally Advanced or Metastatic Breast Cancer Who Progressed on or After mTORi

Summary: This study will evaluate whether the addition of daily BKM120 to fulvestrant is effective and safe in treating patients with HR+, HER2-, AI treated locally advanced or metastatic breast cancer who progressed on or after mTor inhibitor based treatment.


Eligibility: Inclusion Criteria:
  -  Postmenopausal women
  -  Breast cancer that is locally advanced or metastatic
  -  HER2 negative disease, and a known positive hormone receptor status (common breast cancer classification tests)
  -  A tumor sample must be shipped to a central lab for identification of biomarkers (PI3K activation status) before randomization
  -  Prior treatment with AIs
  -  Evidence of progression to the combination of mTORi and endocrine therapy given as the last therapy prior to study entry
  -  Adequate bone marrow and organ function
  Exclusion Criteria:
  -  More than 1 prior chemotherapy given for locally advanced or metastatic disease
  -  Previous treatment with PI3K inhibitors, AKT inhibitors or fulvestrant
  -  Symptomatic CNS metastases
  -  Concurrent malignancy or malignancy within 3 years prior to start of study treatment
  -  Certain drugs or radiation within 2-4 weeks of enrollment
  -  Increasing or chronic treatment (> 5 days) with corticosteroids or another immunosuppressive agent
  -  Active heart (cardiac) disease or a history of cardiac dysfunction as defined in the protocol
  -  Hyper sensitivity to fulvestrant treatment excipients
  -  Certain scores on an anxiety and depression mood questionnaire given at screening
  -  Acute viral hepatitis or history of chronic or acute HBV, HCV, HAV, HDV, HEV
  -  Other protocol defined criteria may apply

Relevance to patient case: not relevant