20160714 data analytics platform yuan愿 song宋
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Yuan Song Professor, Clinical Data Scientist Duke university
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20160714 data analytics platform yuan愿 song宋
- 1. DATA ANALYTICS PLATFORM YUAN SONG PROFESSOR, CLINICAL DATA SCIENTIST DUKE UNIVERSITY COPYRIGHT BY YUAN SONG Jul. 14, 2016 1
- 2. REFERENCE: HTTP://WWW.SLIDESHARE.NET/EMARSHAD/EMERGING-TRENDS-IN-CLINICAL-DATA- MANAGEMENT Jul. 14, 2016COPYRIGHT BY YUAN SONG 2 Data Analytics Platform Work Flow – Clinical Trial
- 3. PHARMACOGENOMICS/PHARMACOGENETICS Jul. 14, 2016COPYRIGHT BY YUAN SONG 3
- 4. PHARMACOGENOMICS/GENETICS FINDINGS (PF) Jul. 14, 2016COPYRIGHT BY YUAN SONG 4 SDTM Sequence Number Genetic Target Reference Sequence Genetic Region of Interest Name of Pharmacogenomics Lab Test Vendor Name
- 5. Jul. 14, 2016COPYRIGHT BY YUAN SONG 5
- 6. DATA ANALYTICS PLATFORM WORK FLOW – GENOMIC LAB Jul. 14, 2016COPYRIGHT BY YUAN SONG 6
- 7. MODELING 3D FACIAL SHAPE FROM DNA CLAES, ET AL. (2014). PLOS GENETICS 10(3) Jul. 14, 2016COPYRIGHT BY YUAN SONG 7
- 8. • A federated ecosystem for sharing genomic, clinical data • The Global Alliance for Genomics and Health (June 9, 2016) • Science 352 (6291) Jul. 14, 2016COPYRIGHT BY YUAN SONG 8
- 9. CLIA & CAP CERTIFIED LABORATORY Jul. 14, 2016COPYRIGHT BY YUAN SONG 9
- 10. CLINICAL LABORATORY IMPROVEMENT AMENDMENTS (CLIA) CERTIFICATION • 3 federal agencies are responsible for CLIA: The Food and Drug Administration (FDA), Center for Medicaid Services (CMS) and the Center for Disease Control (CDC). Each agency has a unique role in assuring quality laboratory testing. (http://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/ IVDRegulatoryAssistance/ucm124105.htm) • Reference : How Obtain A CLIA Certificate file:///C:/Users/User/Desktop/wuxi%20nextcode/HowObtainCLIACe rtificate.pdf Jul. 14, 2016COPYRIGHT BY YUAN SONG 10
- 11. COLLEGE OF AMERICAN PATHOLOGISTS (CAP) LABORATORY ACCREDITATION PROGRAM • Reference: http://www.cap.org/web/home/lab/accreditation/laboratory- accreditation- program?_afrLoop=90302103728227#!%40%40%3F_afrLoop%3D90 302103728227%26_adf.ctrl-state%3Dgyms41b1v_30 Jul. 14, 2016COPYRIGHT BY YUAN SONG 11
- 12. DATA MANAGEMENT – CLINICALLY INTUITIVE • Genomically- Ordered Relational Database • Cloud based infrastructure • Reference datasets • SOP • Informed Consent • Internal Audit Jul. 14, 2016COPYRIGHT BY YUAN SONG 12 Reference: Wuxi Nextcode Tutorial https://www.youtube.com/watch?v=rMMPwoSYKO4
- 13. AUDITING WAR ROOM WHERE REQUESTS FOR INFORMATION, DOCUMENTATION, AND INTERVIEWS ARE PROCESSED AND MANAGED Jul. 14, 2016COPYRIGHT BY YUAN SONG 13
- 14. DATA INTERPRETATION – VISUALIZATION • Clinical Sequence Analyzer • Sequence Miner • Genome Browser Jul. 14, 2016COPYRIGHT BY YUAN SONG
- 15. DATA DELIVERY • RFI • BCL/FASTQ/BAM/VCF • Transfer Agreement • Transfer Schedule • Transfer Format • Data Validation Jul. 14, 2016COPYRIGHT BY YUAN SONG 15
- 16. THANK YOU Data Operation Security and Complian ce Acquisiti on Manageme nt Interpretatio n Delivery Jul. 14, 2016COPYRIGHT BY YUAN SONG 16
Editor's Notes
- • Preparation of Data Management Plan • CRF designing and Annotations • Database design and Validation programming • User Acceptance Testing • Scanning and Indexing (paper studies) • Double Data entry (paper studies) • Discrepancy management & Query Resolution • Dictionary Coding (TMS) • External Data Upload (Central Lab, e-Diaries) • Reconciliation of external data specialized in IVRS, Biomarker, Central lab, ECG, Holter, MRI, and PG Samples • SAE Reconciliation • Integration with a client's existing systems & processes • Handling of local lab and specialized lab settings • CDISC Compliant Data Transfers • Data extracts • Data base lock and Archiving of the study documentation with database • Database freeze
- In April 2015, DNAnexus and WuXi NextCODE announced a strategic alliance that will connect WuXi NextCODE’s sequence data analysis suite and their parent company WuXi AppTec’s global, open access drug discovery and development services through a single global cloud platform. This partnership also expands the DNAnexus genome informatics and data management platform to China. The DNAnexus global network for genomic medicine provides security, scalability, and collaboration for enterprises that are pursuing genomic-based approaches to health in order to accelerate medical discovery.
- The picture on the left side is a picture of a real human being; the one right next to it is a reconstructed from his 23andMe genotype so it's not a perfect likeness but I would say arguably it's better than a police sketch. And the technics are getting better all the time so I think this type of study that puts the lie for the idea that if we scrub the data hard enough if we remove enough identifiers, we will eventually be safe I don't think that's true I think there's a lot of information about you in the genome. So actually the more I can look at these 2 pictures, the more I think they look like. I am not sure if I am fooling myself.
- A FEDERATED DATA ECOSYSTEM. The Global Alliance for Genomics and Health (GA4GH) was established in 2013 to enable responsible and effective sharing of genomic and clinical data in a way that is as simple as using the World Wide Web. GA4GH, which now brings together hundreds of individuals and organizations, was built on the hypothesis that the data underlying genomic medicine must be federated. That is, whereas data may be distributed across many databases and computers around the world, they must be virtually connected through software interfaces that allow seamless, authorized access. In contrast to large centralized data repositories, a federated system will allow legal data control to remain within the originating jurisdiction (see the figure). International consortia such as the International Cancer Genome Consortium (ICGC) have already adopted federated databases because the model allows local databases to maintain autonomy (5).
- Instantaneous visualization of raw sequence reads. This example shows that by hitting the “Father BAM” button, the NextCODE Genome Browser instantaneously loads BAM sequences enabling users to check the assembly and variant calls between the affected patient and the father. This detailed display of raw reads provides rapid visual confirmation that the father is a heterozygous carrier of the mutant C and his affected child is homozygous for the mutation. Similar analysis can be done for other members of the family and even for large cohorts.