Introduction to the Partners Biobank Portal. December 2016

Transcription

1 Introduction to the Partners Biobank Portal December 2016

2 Agenda About the Partners Biobank About the Biobank Portal Data Types in the Biobank Sample types DNA. Plasma and Serum Consent Genomic Data Health Information Survey Phenotypes (Curated Disease Populations) Clinical\EMR Data Healthy Controls Live Demonstration of the Biobank Portal Navigating the Ontology Running a Query / Running a Temporal Query Downloading Data Sample, Identified data and Genomic Data Requests Help and Support Options 2

3 What is the Partners Biobank? The Partners HealthCare Biobank is a large research data and sample repository which aims to: Advance our understanding of the causes of common diseases, and advance the practice of medicine. By using consented, annotated, and high quality samples, investigators can generate high-quality data that advances personalized genetic medicine. Reduce the cost of research by supplying samples that are significantly less expensive. Consented DNA, plasma, and serum samples cost $20-35 per sample, depending on type/volume. Without the Biobank, samples typically cost 300-$1,000 per subject Consent More than 53,674 patients have consented to join the Partners Biobank at Brigham and Women s Hospital (BWH), Massachusetts General Hospital (MGH), Spaulding Rehabilitation Hospital (SRH), Faulkner Hospital (FH) and McLean Hospital (MCL) The target is to reach 75,000 consented patients by Samples To date there are a total of 30,103 plasma samples, 30,190 serum samples and 37,694 DNA samples available to researchers. 3

4 4 What is the Biobank Portal? The Biobank Portal is a web-based tool designed to allow investigators to create queries using a variety of data in order to define sets of patients for which to request samples from the Partners Biobank (

5 5 Biobank Consent Information Biobank consent information in the Biobank Portal provides information about Biobank patient consent but most importantly if they have agreed to be re-contacted. All Biobank subjects have provided their consent to join the Partners Biobank, which includes agreeing to provide a blood sample linked to the electronic medical record. Subjects may also agree to be recontacted by the Partners Biobank staff as needed.

6 6 Biobank Genomics The Biobank Genomics folder in the Biobank Portal indicates which patients' DNA has been genotyped. The Biobank is in the process of genotyping 25,000 Biobank subjects. To date, genotyping on 10,097 subjects is complete and is available to Partnersaffiliated investigators. The remaining subjects will be genotyped over the next two years. The subjects were genotyped using the Illumina Multi-Ethnic GWAS/Exome SNP Array (MEGArray and MEGA EX chip). Chip details and manifest files are available on the Portal wiki. An IRB protocol is not required to request deidentified genomic data. You will, however, need to sign a Data Use Agreement for use of a limited data set. An IRB protocol is required to request identified genomic data

7 Biobank Health Information Survey The Biobank Health Information Survey in the Biobank Portal provides patient-reported lifestyle, environment and family history information. All Biobank subjects are asked to fill out an online health information survey on a comprehensive list of health-related topics: Age at time of survey Language preference Education Employment Height, Weight and BMI Sun Sensitivity Smoking Alcohol Physical Activity Sleep Habits Female Reproductive History Family History (Twin/Adopted) Family History of Cancer Family History of Heart Disease Family History of Other Medical Problems 7

8 8 Biobank Curated Disease Populations Curated Disease Populations in the Biobank Portal are validated disease definitions, or phenotypes, for the Biobank subjects. The phenotypes were developed by the Biobank Portal team using both structured and unstructured electronic medical record (EMR) data. Natural Language Processing (NLP) was used to extract data from narrative text. Chart reviews by clinical experts helped identify features and variables associated with particular phenotypes and were used to train and validate the algorithms. The process produced robust phenotype algorithms that were evaluated using metrics such as sensitivity, the proportion of true positives correctly identified as such, and positive predictive value (PPV), the proportion of individuals classified as cases by the algorithm. Current Phenotypes Bipolar Disease (BD) Congestive Heart Failure (CHF) Coronary Artery Disease (CAD) Crohn s Disease (CD) Multiple Sclerosis (MS) Rheumatoid Arthritis (RA) Type-ll Diabetes Mellitus (T2DM) Ulcerative Colitis (UC) Asthma Breast Cancer Depression Epilepsy Gout Hypertension Obesity Type-I Diabetes

9 9 Biobank Healthcare Data The Biobank Portal provides visibility into Electronic Medical Record (EMR) data. Queries may be made based on this clinical data, such as diagnosis, medication, or lab results. Healthcare Data in the Biobank Portal contains electronic medical record (EMR) data on Biobank subjects, organized into subject folders. This data comes from the RPDR. In order to obtain Identified data for a patient set with clinical data associated with a set of samples, you'll need to make a detailed data request in the RPDR Query Tool.

10 10 Biobank Healthy Populations (Controls) The Healthy Population (Controls) category in the Biobank Portal is designed to help you select relatively healthy controls from the Biobank population. The calculations are based on the Charlson Age-Comorbidity Index divided into 10- year survival probability classes. The Charlson Index combines the presence and severity of co-morbidities with age to predict the 10- year survival probability for Biobank Portal subjects. It may be used to find relatively healthy subjects for control populations. It is important to note that the Charlson Index may be used to assess the severity of illness for individuals or a population of subjects; however, it will not provide a population completely free of disease or chronic conditions

11 11 Getting Access to the Biobank To get access to the Biobank Portal, you must first be a registered user of the Research Patient Data Registry (RPDR) at Once you have RPDR access, you may go to the Biobank Portal link at : ( OR your Partners Application menu, enter your Partners username + password and electronically sign a Data Use Agreement (DUA) The Biobank Portal is also available from the RPDR Query Tool

12 Additional Resources Biobank Portal Biobank Portal Wiki For Biobank Portal assistance contact: Stacey Duey - Project Specialist (617) sduey@partners.org or biobankportalhelp@partners.org Partners Healthcare Biobank biobank@partners.org 12

13 Live Demonstration How to use the Biobank Portal. The following will be covered in the live demonstration: Main portal page description including :Navigate terms, Find terms, Groups, Workplace, Previous Queries, Show Query Status, Graph Results, Query Report, Download Results Creating a query (dates constrain, Occurs >0, Exclude, New group) Illustrate temporal query (defining events, define sequence of events) Display reports/graphs/download results Explain previous queries ( functionality, helpfulness) Workplace tab and shared folder ( how to use, helps to share queries with other portal user) Use Curated disease population in a query Explain how to request samples/identified data Explain how to request genomic information Help and support 13