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: Use of Harmonic in Breast Surgery

Summary: To compare harmonic scalpel with electrocautery for outcomes i.e. estimated blood loss (EBL), operating time, drain Volume and drain Days, seroma formation, surgical site infection and postoperative pain in adult females undergoing MRM at a tertiary care hospital. We hypothesized that harmonic yields better outcome than electrocautery dissection.

Detailed description: In this randomized controlled trial, adult females who underwent MRM between April 2010 and July 2011 were randomized to receive either intervention A (harmonic scalpel) or B (electrocautery). The procedure was standardized except elevation of flaps and axillary dissection, that was performed as per randomization. Patients were followed up in clinic for four weeks. The outcomes were estimated blood loss (EBL), operating time, drain Volume and drain Days, complications (seroma, surgical site infection, hematoma and flap necrosis) and postoperative pain.

Eligibility: Inclusion Criteria:
  -  Adult females with biopsy proven breast cancer underwent MRM
  Exclusion Criteria:
  -  Simultaneous procedure (Reconstruction, Sentinel lymph node biopsy)

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 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: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

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

Clinical trial: Uncovering Potential Breast Cancer Biomarkers Amp; Possible Drug Targets Using Advanced Quantitative Mass Spectrometry

Summary: The purpose of this study is to evaluate the use of advanced quantitative mass spectometry (Super SILAC) as a discovery platform to uncover novel protein biomarkers in tumor and to compare the protein profile between different subtypes of breast cancer (ER positive, HER2 positive, triple negative). A maximum of 100 breast tumor specimens will be obtained from the NUHS Tissue repository, comprising approximately equal proportion of ER positive, HER2 positive, and triple negative tumors. Samples will be analyzed using advanced Mass Spectrometry (Super SILAC) as a discovery platform to identify novel protein biomarkers that may be important in cancer. DNA and RNA will also be extracted from tumor samples for correlative analysis with the proteomics data. Genomics and proteomics data will be correlated with clinical data including treatment response and survival data. Importance of proposed research to science or medicine:Identification of tumor biomarkers may allow better prognostication, follow-up, and selection of treatment for cancer patients in the future. Potential benefits and risks: No direct benefit to the patient. Risk to the subjects is minimal as there is no direct patient contact, and analysis is done on previously donated tumor samples. Patients have previously provided consent to donate their samples for research into the NUHS Tissue Repository.
  Novel tumor biomarkers that determine tumor biology, including prognosis and treatment sensitivity, may be detectable using the novel advanced quantitative mass spectromy method (Super SILAC). Different subtypes of breast cancers will have different proteomic profiles analyzed using super SILAC.


Eligibility: Inclusion Criteria:
  -  Patients 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: 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
Patient case: 54-year-old female with Breast cancer. Genetic variant: PTEN Loss. Other conditions: Congestive Heart Failure.

Clinical trial: Sentinel Lymph Node Total Tumoral Load as a Predictor of Non Sentinel Node Involvement in Early Breast Cancer

Summary: This is a retrospective, multicentric cohort study of patient cases with cT1-3, N0 early breast cancer, who previously had intraoperative sentinel lymph node (SLN) evaluation by one-step nucleic acid amplification (OSNA) assay with a complete axillary dissection.
  The aim of the present study is to assess the intraoperative positive SLN total tumor load (TTL) obtained from the OSNA assay and to determine whether this TTL predicts non-SLN metastasis in patients with clinically node-negative early-stage breast cancer.


Eligibility: Inclusion Criteria:
  -  Pathologically confirmed invasive breast carcinoma
  -  Stage T1-3,N0 evaluated by physical exam or imaging according to AJCC v.7 and best clinical local practices
  -  Intraoperative evaluation of sentinel lymph node (SLN) by OSNA
  -  Complete dissection of axillary lymph nodes after the evaluation of the SLNs by OSNA
  -  Pathology report of the tumor and dissected lymph nodes that includes the following information:
  -  primary tumor size (mm), tumor grade (Scarff-Bloom Richardson), estrogen receptor status
  -  progesterone receptor status
  -  HER2 status (ASCO/CAP guidelines)
  -  Ki67 index
  -  presence/absence of lymphovascular invasion
  -  total number of sentinel and non-sentinel lymph nodes dissected during surgery
  -  total number of positive and negative sentinel and non-sentinel lymph nodes, *size of the metastasis in both sentinel and non-sentinel lymph nodes
  -  total tumoral load in each sentinel lymph node, expressed as number of CK19 mRNA copies per microliter.
  Exclusion Criteria:
  -  Patients who underwent neoadjuvant chemotherapy
  -  CK19-negative breast tumor
  -  ALND with <10 lymph nodes
  -  In situ carcinoma only
  -  Metastatic breast cancer at time of diagnosis

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: BRCA1-associated DNA Repair Dysfunction in Patients With Early Triple Negative Breast Cancer Treated With Neoadjuvant Platinum-based Chemotherapy

Summary: The purpose of this study is to assess efficacy of platinum-based neoadjuvant chemotherapy in correlation with BRCA1-associated DNA repair dysfunction in patients with early triple negative breast cancer.

Detailed description: Recent gene expression profiling of breast cancer has identified specific subtypes with clinical, biologic, and therapeutic implications. The basal-like group of tumors is associated with aggressive behavior and poor prognosis, and typically do not express hormone receptors or HER-2 ("triple-negative" phenotype). Therefore, patients with basal-like cancers do not benefit from currently available targeted systemic therapy.
  There is a lot of evidence about a link between basal-like breast cancer and BRCA1 deficiency. Many clinical characteristics and molecular features are shared by basal-like breast cancers and tumors that arise in carriers of BRCA1 germline mutations.
  Some studies have indicated that BRCA1 mRNA expression was lower in basal-like sporadic cancers than in controls matched for age and grade. BRCA1 is rarely mutated in sporadic breast cancers and, therefore, it is believed that this may be a result of epigenetic mechanisms such as acquired methylation of the BRCA1 gene promoter or a dysfunction in the pathways that regulate BRCA1 expression, such as overexpression of ID4. The profound similarities between hereditary BRCA1-related breast tumors and basal-like tumors strongly implicate a fundamental defect in the BRCA1 or associated DNA-repair pathways (p53, PTEN) in sporadic basal-like tumors.
  There is increasing evidence that the BRCA1-related DNA-repair defects, especially defective homologous recombination, determines sensitivity to certain agents, such as platinum salts-based chemotherapy. The complexity in downregulation of BRCA1 expression suggests that these approaches may only be effective in the treatment of a subset of sporadic basal-like cancers. Identification of specific markers for these cancers will be essential to translate an understanding of defective DNA repair into targeted treatments for this poor prognosis subtype.

Eligibility: Inclusion Criteria:
  1. Female patients, age ≥18 years≤75;
  2. Histologically confirmed invasive ER-, PR-, and HER2-negative (triple- negative) adenocarcinoma of the breast;
  3. Clinical stage T1-2, N0-1, M0.
  Exclusion Criteria:
  1. Previous treatment for this breast cancer
  2. History of malignancy treated with curative intent within the previous 5 years with the exception of skin cancer, cervical carcinoma in situ, or follicular thyroid cancer. Patients with previous invasive cancers (including breast cancer) are eligible if the treatment was completed more than 5 years prior to initiating current study treatment, and there is no evidence of recurrent disease
  3. Pregnancy or breast-feeding

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 Internet-based Weight Loss and Exercise Intervention for Breast Cancer Survivors

Summary: The purpose of this study is to test the effectiveness of a behavioral weight loss and exercise intervention delivered via the internet at different cancer centers in New England. The investigators hypothesize that participants will lose 7% of their body weight. The research is being done because many women who are treated for breast cancer are overweight and treatment for breast cancer is often accompanied by weight gain. Individuals who are overweight may be more likely to have their breast cancer come back. Also women who exercise at least three hours a week seem to have less chance of their cancer coming back. The investigators hope to identify an effective weight loss and exercise intervention for breast cancer survivors that can be easily accessed by many people.
  This study is designed to determine the feasibility of conducting a distantly delivered-weight loss and exercise intervention for patients who have been treated for breast cancer at three cancer centers, and to evaluate the efficacy of an Internet-based behavioral weight loss and exercise intervention delivered to overweight/obese breast cancer survivors in three New England locations.
  Participants will be recruited from three New England Cancer Centers - the Vermont Cancer Center, Norris Cotton Cancer Center at Dartmouth University and the University of Massachusetts Cancer Center. Participants from each center will undergo baseline assessments that include diet assessment, body measurements (height, weight, etc), a physical activity assessment and be asked to complete a series of questionnaires.
  Patients that meet the minimum requirements will be enrolled on the study. They will participate in weekly on-line "chats" about behavioral and diet modifications led by a qualified facilitator. Participants will also engage in increasing amounts of aerobic activity (typically walking) throughout the course of the intervention. The intervention lasts 6 months. At the end of those 6 months, participants will have the same assessments that were collected at baseline. Following the collection of those assessments, participants will have completed the study.


Eligibility: Inclusion Criteria:
  -  breast cancer diagnosis
  -  Completion of surgery, chemotherapy +/- radiation for stage I, II, or III breast cancer 2-12 months prior to study initiation
  -  BMI between 27 and 50
  -  patient self-report of ability to walk for 10 minutes without interruption or pain
  -  access to computer and the internet
  Exclusion Criteria:
  -  metastatic disease
  -  prior receipt of chemotherapy for other malignancy
  -  pregnancy at the time of study entry
  -  limited food choices due to celiac sprue or inflammatory bowel disease
  -  illiteracy
  -  non-English speaking

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: Relationship Between PTEN and Glycemic Variability and Outcome in Critically Ill Patients

Summary: Glycemic variability in critically ill patients is a recognized negative prognostic factor. The molecular mechanisms determining inter-patients variability in glucose metabolism during stress are not fully understood. The Phosphatase and Tensin homolog (PTEN) is known to influence glucose homeostasis by interfering in intracellular insulin signaling.
  Aim of this study is to ascertain whether differential expression of PTEN in critically ill patients correlates with glycemic variability and clinical outcome.


Eligibility: Inclusion Criteria:
  -  trauma
  -  provision informed consent
  Exclusion Criteria:
  -  diabetes
  -  impaired fasting glucose levels

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 Association Between Alpha 1 Acid Glycoprotein Level and Outcome Metastatic Cancer Treated With Docetaxel

Summary: Docetaxel based chemotherapy is a standard therapy in various metastatic cancers including lung cancer, breast cancer, gastric cancer, prostate cancer, and bladder cancer.
  One of the main plasma protein carriers of docetaxel is Alpha 1 acid glycoprotein.
  Retrospective data suggests that plasma level of alpha 1 acid glycoprotein is associated with the outcome of docetaxel based therapy in cancer patients.
  The investigators aim to prospectively study the association between the plasma level of alpha 1 acid glycoprotein and the outcome of docetaxel based therapy in cancer patients.

Detailed description: Docetaxel based chemotherapy is a standard therapy in various metastatic cancers including non small cell lung cancer, breast cancer, gastric cancer, prostate cancer, and bladder cancer.
  One of the main plasma protein carriers of docetaxel is Alpha 1 acid glycoprotein
  Retrospective data suggests that plasma level of alpha 1 acid glycoprotein is associated with the outcome of docetaxel based therapy in non small cell lung cancer patients.
  The investigators aim to prospectively study the association between the baseline plasma level of alpha 1 acid glycoprotein (measured on the first day of the first cycle of docetaxel) and the outcome (response rete, progression free survival, overall survival) of docetaxel based therapy in patients with metastatic non small cell lung cancer, breast cancer, stomach cancer, prostate cancer, and bladder cancer.

Eligibility: Inclusion Criteria
  -  patients with metastatic cancer from lung, breast, gastric, prostate, and bladder origin
  -  patients must be treated with docetaxel based chemotherapy
  -  patients must sign an informed consent form
  Exclusion Criteria
  -  patients with metastatic cancer other than lung, breast, gastric, prostate, and bladder origin
  -  patients treated with chemotherapy other than docetaxel
  -  patients that did not sign an informed consent form

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 Trial of a Comprehensive Breast Cancer Treatment Patient Decision Tool

Summary: This study examines the impact of an online decision tool for patients with early stage invasive breast cancer. The study is a randomized controlled trial (RCT) of 444 newly diagnosed patients, recruited from multiple surgical practices in two SEER catchment areas. Participants will be randomized to receive either a basic version of a decision tool (similar to existing website with breast cancer information) or an enhanced version (featuring a knowledge building component, a values clarification exercise, and a patient activation module). Our hypothesis is that patients who use the enhanced version of the tool will have greater knowledge of their test and treatment options, have a higher rate of high quality (i.e., informed, preference-concordant) decisions, and report more positive appraisal of the decision-making process.

Detailed description: Patients newly diagnosed with breast cancer face a series of complex decisions regarding locoregional and systemic treatment. Currently many of these decisions do not meet the definition of a high quality decision, defined as one that is both informed (i.e., based on an accurate understanding of the treatment risks and benefits) and preference-concordant (i.e., consistent with the patients' underlying preferences). Moreover, the introduction of evaluative tests has made these decisions more complicated for many patients. There is a need to improve the quality of locoregional and systemic treatment decisions for breast cancer patients, and to help patients understand the role of evaluative tests in this decision process. Ensuring patients can deliberate effectively about these decisions, assert their views and communicate with their clinicians is likely to improve their overall decision preparedness and satisfaction. This study will focus on the third pillar of individualized care by evaluating the impact of an innovative decision tool on locoregional and systemic therapy decision making for newly diagnosed breast cancer patients. The innovative online decision tool has been developed and tested over the past two years by the CanSORT team (R21 CA129859). Pilot data suggests that this tool has a positive impact on patient knowledge and decision outcomes. The goal of this study is to evaluate the impact of this tool, after it is enhanced in collaboration with our Communication and Dissemination Core, on the quality of decision making for locoregional and systemic breast cancer treatment decision making.

Eligibility: Inclusion Criteria:
  -  Stage 1-2 invasive breast cancer diagnosis,
  -  DCIS
  -  Ability to read English
  Exclusion Criteria:
  -  Male

Relevance to patient case: not relevant