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: A Retrospective Study of Biomarkers in Non-Small Cell Lung Cancer

Summary: The purpose of this study is:
  1. To characterize the types and frequency of molecular alterations to the epidermal growth factor receptor (EGFR) pathway, FGFR4 and EML-ALK in Asian patients with non-small cell lung cancer
  2. To identify candidate biomarkers of importance in the EGFR and estrogen pathways
  Most, if not all, human malignancies including lung cancer are caused by somatic alterations of the genome, leading to activation of oncogenes or inactivation of tumor suppressor genes and their resultant oncogenic effects. In addition to mutations, increased chromosomal copy number (by amplification or polysomy) and DNA methylation are other mechanisms of oncogene activation and tumour suppressor gene inactivation respectively.
  Little is known about the relationship between these oncogenes of the EGFR family and the recently described oncogenes FGFR4 and fusion gene EML4-ALK. Recent data suggests molecularly defined subgroups of non-small cell lung cancer (NSCLC) exist and can be used to predict for sensitivity to targeted agents (erlotinib or gefitinib) or cytotoxic chemotherapy (pemetrexate, gemcitabine, platinum agents). The findings that estrogen receptors are present in lung tumours and that estrogen can stimulate growth and proliferation of lung cancers in vitro and in vivo are provocative. Further studies to evaluate the role of estrogens and other sex hormones in lung cancer are warranted.
  A further understanding of the molecular indicators of lung cancer prognosis and treatment prediction would improve drug development and patient treatment selection.
  Archived paraffin-embedded and fresh frozen NSCLC tumor tissue will be obtained via the Department of Pathology and the National University Tissue Repository respectively. Clinico-pathological characteristics will be obtained from the case records, Pathology and Tissue Repository. DNA will be isolated using standard techniques. Sequencing of genes in the EGFR signaling pathway: EGFR, KRAS, ErbB2, ErbB3, MET, PI3K, and BRAF as well as FGFR4. Unstained slides from the paraffin-embedded tissue will be obtained and subjected to fluoresce in vitro hybridization (FISH) for breakpoints in the EML4 and ALK genes as previously described. For cases that have been snap-frozen, RNA will be extracted and EML4-ALK fusions will be confirmed using RT-PCR and pre-specified primers. To analyse the expression of proteins of putative relevance to EGFR function (such as EGFR, ErbB2, ErbB3, AKT, MET, STAT, ERK, MAPK, cyclin D1, C/EBPa), downstream effects of EGFR: cell proliferation (Ki-67), angiogenesis (CD34, VEGF-A), apoptosis (bcl-2), metastasis, and hormonal influence (oestrogen and progesterone receptors, aromatase), TMA technology will be utilised. The status of the tumor suppressor genes PTEN and C/EBPa will be analysed.


Eligibility: Inclusion Criteria:
  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: Reducing Breast Cancer Recurrence With Weight Loss

Summary: The purpose of the ENERGY trial is to explore whether two different programs that are focused on weight management, through increased exercise and a healthy diet, are feasible, and have an impact on body weight, quality of life and fatigue. Since obesity among breast cancer survivors is associated with recurrence and other co-morbidities, those will be assessed and their impact calculated. Blood samples will be collected to enable analysis of potential mechanisms and differential response across subgroups.


Eligibility: Inclusion Criteria:
  -  Diagnosis of breast cancer (stages I (≥1 cm), stage II, or stage IIIA, B, C excluding distant metastasis) diagnosed between 6 months and 5 years earlier; after initial therapies are completed, diagnosed between six months and five years earlier
  -  BMI between 25 to 45 kg/m2
  -  Able to comply with all required study procedures and schedule
  Exclusion Criteria:
  -  Serious medical condition or psychiatric illness
  -  Inability to be moderately physically active
  -  Obesity of known endocrine origin (e.g., untreated hypothyroidism, PCOS)
  -  Currently enrolled in a weight loss program
  -  Current use of weight loss medication or supplements
  -  Previous surgical procedures for weight reduction
  -  Planning weight loss surgery in the next 2 years.
  -  6+ months use of meds likely to cause weight gain or prevent weight loss
  -  Planned surgical procedure that can impact the conduct of the study
  -  Currently pregnant/breastfeeding
  -  Planning to become pregnant within the next 2 years
  -  Have plans to relocate from area within 2 years
  -  Family relative or close friend is a trial staff member or a study participant
  -  Any condition which in the opinion of the investigator makes the subject unsuitable for inclusion in this study

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: Peritoneal Dialysis in Congestive Heart Failure

Summary: Rationale: End-stage congestive heart failure is a serious invalidating condition with a poor prognosis and increasing incidence. Non-randomized observations showed peritoneal dialysis (PD) in these patients to improve clinically from NYHA stadium III-IV to as low as NYHA stadium I-II. A randomized trial is needed to test whether PD improves symptoms in this condition and to find an optimal scheme.
  Objective: To improve symptomatology in severe chronic failure patients. Study design: Open, parallel intervention trial comparing 2 schemes of peritoneal dialysis with icodextrin (Extraneal®) with standard medical therapy..
  Study population: Patients with chronic refractory left ventricular congestive heart failure (LVEF < 30%, older than 18 years).
  Intervention: Peritoneal dialysis with one (night) or two (night and day) dwells with icodextrin (Extraneal®).
  Main study parameters/endpoints: Reduction in NYHA classification of symptomatic Congestive Heart Failure at 8 months after start of PD therapy. Burden of congestive heart failure: measured by reduction in unfavorable days (noted by patients in diaries and including days of hospitalization for CHF-deterioration and death).


Eligibility: Inclusion Criteria:
  -  Age > 18 years
  -  Refractory Left Ventricular Congestive Heart Failure: LVEF < 30%
  -  Diminished renal function: eGFR < 60 ml/min
  -  Clinically volume overloaded (Dyspnoea (NYHA III-IV), edema, and/or ascites)
  -  Hospitalization for CHF during the last 6 months
  -  Patient is on optimal cardiologic medical therapy, which has been stable for more than 4 weeks
  -  Suitable for PD
  Exclusion Criteria:
  -  Hypotension (SBP < 100 mmHg / MAP < 70) mmHg
  -  Instable AP or recent (< 6 months) myocardial infarction.
  -  Contraindications for PD (e.g. visual handicap, social)
  -  Liver failure
  -  COPD Gold class IV
  -  Malignancy with life expectancy < 2 years
  -  Non compliance
  -  No informed consent
  -  Poor mental health

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 Cardiac Safety in Patients With HER2 Positive Early Breast Cancer Treated With Herceptin

Summary: This is a single cohort observational safety study. All patients will be treated and monitored according to the local clinical practice. No additional procedures/patient visits in comparison with the usual clinical practice are planned for the study. Data will be collected from centre's medical records for up to 5 years or death.


Eligibility: Inclusion Criteria:
  -  All patients who are considered candidates to receive Herceptin for this indication
  Exclusion Criteria:
  -  Patients for whom Herceptin is contraindicated

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: Impact of Breast Magnetic Resonance Imaging (MRI) on Mastectomy Rates

Summary: The primary goal of this study is to determine if preoperative breast MRI findings resulted in more extensive surgery, i.e., mastectomy than breast conserving surgery, i.e., lumpectomy in early stage breast cancers at Summa Akron City Hospital. Early stage breast cancer is defined as breast tumor size less than 5 cm.
  The objectives are to:
  -  Review early stage breast cancer patient cases treated at Summa Akron City Hospital between 2006 and 2009 to evaluate clinical and pathological staging
  -  Determine the results of preoperative breast MRI and the impact on type of surgery performed
  -  Evaluate the decision to have mastectomy rather than lumpectomy, i.e., physician or patient decision and if this decision was based on breast MRI findings

Detailed description: Early stage breast cancer cases between 2006 and 2009 will be identified by the Summa Akron City Hospital cancer registry. The cases will be reviewed and abstracted. The abstracted data will include results of physical breast examinations, mammograms, sonograms, breast MRI reports, biopsy procedure notes and pathology reports to illustrate the clinical stage. Definitive surgical pathology reports will be included in the abstracted data to demonstrate the final pathologic stage of the breast cancer.
  A database will be developed to capture the abstracted data. Outcomes will be determined based on final pathology reports.

Eligibility: Inclusion Criteria:
  -  early stage breast cancer between 2006-2009
  -  preoperative MRI
  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: BCRL Prevention Pilot

Summary: The purpose of this study is to establish feasiblity of recruiting obese breast cancer survivors at the end of treatment, getting those survivors to lose weight and attend follow-up visits for 6 months.

Detailed description: Breast cancer related lymphedema occurs in 20-30% of survivors. Weight loss could prevent onset. We seek to do a pilot study to establish feasibility of 1) recruiting survivors at risk for lymphedema to do a weight loss intervention, 2) achieving 10-15% weight loss over 26 weeks in this population, and 3) attendance at follow-up visits 6 months.

Eligibility: Inclusion Criteria:
  -  Women
  -  Breast Cancer Survivors who had 5 or more lymph nodes removed and radiation to lymph nodes as part of treatment.
  -  Completed all treatments - no metastatic cancers
  -  Overweight or obese (BMI greater than or equal to 25 kg/m2)
  -  Medically and logistically able to participate in a weight loss and exercise program over 6 months.
  -  Diagnosed with breast cancer within the past 2 years.
  Exclusion Criteria:
  -  More than 2 years since breast cancer diagnosis
  -  Medical status that would preclude safety of participation in a weight loss and exercise program
  -  Metastatic cancer
  -  Already enrolled in a weight loss program

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: Lung Inflammation and Lung Metastases From Breast Cancer

Summary: The purpose of this study is to find out if there is a link between cigarette smoking, inflammation and the spread of breast cancer to the lung. We think that women who are current or former smokers may be at increased risk for breast cancer spreading to the lung compared to women who have never smoked. Smoking causes inflammation in the lung in some women. Researchers at Memorial Sloan-Kettering (MSKCC) think that smoking-related lung inflammation may increase the chance of breast cancer spreading to the lung. In order to find out whether inflammation plays a role in breast cancer spreading to the lung, we will measure a urinary marker of lung inflammation. This will allow us to determine if this marker is more commonly elevated in women with breast cancer that has spread to the lung compared to those without breast cancer in the lung. We will also collect DNA from blood to have the opportunity to determine if there are differences in DNA in women with or without breast cancer that has spread to the other sites including the lung. We will also collect blood to determine if we can identify risk factors for the spread of breast cancer to the lungs.


Eligibility: Inclusion Criteria:
  -  Registered patient at MSKCC
  -  Histologically proven breast cancer. It is not necessary that pathology be reviewed at MSKCC
  -  Age ≥18 years Group 1 (A and B)
  -  Diagnosed with metastatic breast cancer on biopsy or imaging study.
  -  Patients will be considered to have lung metastases, and will be assigned to group 1A if any of the following criteria are met, otherwise patients will be assigned to group 1B "No known Lung Metastases," Biopsy-proven lung metastasis.
  -  Pleural effusion with cytologic evidence of malignancy.
  -  Pleural effusion, exudative in character, without alternative explanation and attributed, in the opinion of the clinician to metastatic disease.
  -  Symptoms attributable to lung metastases and a radiological pattern interpreted by a radiologist as suspicious for metastatic disease.
  -  Any pulmonary nodule on chest radiograph, CT scan, PET-CT or MRI, which is interpreted by the clinician and radiologist to be metastatic in etiology, whether or not a biopsy was performed, and regardless of symptoms.
  -  A radiographic pattern interpreted by a radiologist as consistent with lymphangitic carcinomatosis.
  Group 2 (Controls)
  -  History of early breast cancer and currently no evidence of disease
  Exclusion Criteria:
  -  Inability to provide written informed consent.
  -  Inability to complete smoking and NSAID questionnaire.
  -  Steroid use within the previous 4 weeks.
  -  Radiotherapy to the breast, chest wall or axilla within the previous 3 months.
  -  Men with breast 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: Congestive Heart Failure Weight Study

Summary: Early morning weights to monitor CHF patient's fluid status is common practice but there is a lack of evidence that this is the best practice. The purpose of this study is to determine if there is a difference in net weight gain or loss for hospitalized patients with CHF who are weighed in the evening instead of early morning.

Detailed description: This is a quasi-experimental pilot study with prospective cohort design. Study subjects will be weighed in the early morning and then again in the evening for a minimum of three days. Analysis will be accomplished on data by analysis within-subjects data utilizing the paired t test. Other data to be collected includes dates of hospitalization, demographics, dose and timing of medications, lab results and documentation of comorbid conditions.

Eligibility: Inclusion Criteria:
  -  18-85 years old
  -  Admitted to hospital with a primary diagnosis of heart failure or fluid overload
  -  Ambulatory with a medical order to be out of bed
  -  Able to stand on a scale
  -  Have no problems with balance
  Exclusion Criteria:
  -  Patients with a primary diagnosis other than heart failure or fluid overload
  -  Patients diagnosed with renal failure
  -  Non-English speaking
  -  Unable to follow directions or consent due to cognitive impairment
  -  Medical order for bed rest
  -  Involved in another study

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 Bimatoprost Gel on Eyelash Growth

Summary: A internally controlled, single-blinded, randomized controlled trial to investigate the use of Bimatoprost eyelash gel on eyelash growth and appearance in breast cancer patients who suffer from madarosis (loss of eyelashes) due to the side effects of chemotherapy. IND and IRB approval have been obtained.


Eligibility: Inclusion Criteria:
  -  18-80 YO females
  -  madarosis or hypotrichosis (loss of eyelashes) due to chemotherapy used to treat breast cancer
  -  only breast cancer patients
  Exclusion Criteria:
  -  inability to follow up, apply gel
  -  active eye/eyelid infection or inflammatory process
  -  cancer not related to breast cancer, healthy patients
  -  males

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: Prognostic Biomarkers in Patients With Endometrial Cancer

Summary: This research study is studying prognostic biomarkers in tissue samples from patients with endometrial cancer. Studying samples of tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer.

Detailed description: PRIMARY OBJECTIVES:
  I. To validate the clinicopathologic associations and prognostic significance of ATR mutation in endometrioid endometrial cancer cases with defective DNA mismatch repair.
  OUTLINE: This is a multicenter study.
  DNA extracted from previously collected tumor samples is analyzed to validate the clinicopathologic associations and prognostic significance of ATR mutation.

Eligibility: Inclusion Criteria:
  -  Women who were eligible and evaluable for the GOG-0210 molecular staging protocol in women with endometrial cancer
  -  Women who were registered during the unrestricted enrollment period (through 9/23/07) will automatically qualify
  -  Women who were registered during the restricted enrollment period (after 9/23/07) will only be considered if needed
  -  Women who had histologically confirmed endometrioid endometrial adenocarcinoma regardless of stage or grade
  -  Women who have defective DNA mismatch repair and are microsatellite instability positive (MSI+ and MSI-low)
  -  Women who consented to allow their specimens and clinical data to be used for future cancer research
  -  Women who have sufficient high-quality genomic DNA from tumor available for mutation analysis of ATR

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: Safety, Tolerability & Potential Anti-cancer Activity of Increasing Doses of AZD5363 in Different Treatment Schedules

Summary: This study is designed to investigate the safety and tolerability of a new drug, AZD5363, in patients with advanced cancer - and to identify a dose and schedule that can be used in the future. This study will also investigate how the body handles AZD5363 (ie, how quickly the body absorbs and removes the drug). This study will also investigate anti-tumour activity of AZD5363 in patients with advanced / metastatic breast, gynaecological cancers or other solid cancers bearing either AKT1 / PIK3CA or PTEN mutation.

Detailed description: A Phase I, Open-Label, Multicentre Study to Assess the Safety, Tolerability, Pharmacokinetics and Preliminary Anti-tumour Activity of Ascending Doses of AZD5363 under Adaptable Dosing Schedules in Patients with Advanced Solid Malignancies.

Eligibility: Inclusion Criteria:
  -  Aged at least 18 years.
  -  Parts A,B: The presence of a solid, malignant tumour, excluding lymphoma, that is resistance to standard therapies or for which no standard therapies exist.
  -  ER+/HER2+ breast, ovarian, cervical, endometrial cancer, or other solid cancers, resistance to standard therapies with a PIK3CA gene mutation (Part C), AKT1 gene mutation (Part D) or a dysregulatory aberration on the PIK/AKT pathway (Part D), advanced or metastatic ER+ positive breast cancer that has an AKT1 gene mutation (Part E) or advanced or metastatic ER+ positive breast cancer that has a PTEN gene mutation (Part F).
  -  The presence of at least one lesion that can be accurately assessed at baseline by CT, MRI or plain X-ray and is suitable for repeated assessment. Estimated life expectancy of more than 12 weeks.
  -  Estimated life expectancy of more than 12 weeks.
  Exclusion Criteria:
  -  Clinically significant abnormalities of glucose metabolism.
  -  Spinal cord compression or brain metastases unless asymptomatic, treated and stable (not requiring steroids).
  -  Evidence of severe or uncontrolled systemic diseases, including active bleeding diatheses or active infections including hepatitis B, C and HIV.
  -  Evidence of clinically significant cardiac abnormalities, uncontrolled hypotension, left ventricular ejection fraction below the lower limit of normal for the site or experience of significant cardiac interventional procedures.
  -  A bad reaction to AZD5363 or any drugs similar to it in structure or class.

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

Clinical trial: Breast Cancer Registry - National University Health System, Singapore

Summary: The Breast Cancer Registry aims to collect clinical data of all breast cancer patients diagnosed and/or treated in the National University Hospital, with the goal of understanding risk factors, presenting symptoms, diagnosis, treatment, and outcome data of breast cancer in Singapore. This information will contribute to improving management of breast cancer patients.


Eligibility: Inclusion Criteria:
  - All breast cancer patients who were diagnosed or managed in NUH.
  Exclusion Criteria:
  - Non breast cancer patients.

Relevance to patient case: not relevant