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Lessons Learned & Future Directions in Human Genome Sequencing

This panel discussion explores the challenges, lessons learned, and future directions in human genome sequencing, focusing on data standardization, process optimizations, and the use of innovative research tools.

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Lessons Learned & Future Directions in Human Genome Sequencing

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  1. EHRI Working Group Panel Lessons Learned & Future Directions Human Genome Sequencing Center Baylor College of Medicine eMERGE Centralized Sequencing & Genotyping (CSG) Facility Mullai Murugan, M.S. Director of Software Engineering Human Genome Sequencing Center Baylor College of Medicine murugan@bcm.edu

  2. Disclosure Mullai Murugan: I and my spouse/partner have no relevant relationships with commercial interests to disclose. Baylor College of Medicine has a minority equity interest in Codified Genomics.

  3. BCM Challenges • Complexity of eMERGE • World of heterogeneity • Stay flexible & innovate • To harmonize both – • Data • Delivery • Retrofit current pipeline • Seamlessly • Innovation with • Research tools

  4. Lessons Learned • Importance of Data Standardization and Harmonization • Process Optimizations and Change Management • Need for Tracking, Dashboard & Analysis Tools • Managing Variant Reclassification

  5. Lessons Learned 1. Why is Data Standardization/Harmonization so crucial? • Importance of data standardization and harmonization

  6. The Multi-Institutional eMERGE Network Biorepository eMERGE Study Sites EHRs BCM Data Generation Variant Confirmation Interpretation Reporting Annotation Filtration Sample Prep Variant Calling GeneInsight DCR eDAP • DNAnexusData Commons • (raw data – enables discovery analyses) DNAnexusClinical Reports EMR Delivery DNAnexus Baylor Sample Accessioning Variant Harmonization e Broad Institute LMM CSGs transfer raw data, vcf, annotations to enable discovery analyses Data Generation Variant Confirmation • GeneInsight • Knowledge Base • Reporting Tool Annotation Filtration Sample Prep Interpretation Reporting Variant Calling

  7. 1. CSGs Data Standardization & Harmonization Biorepository eMERGE Study Sites EHRs BCM Data Generation Variant Confirmation Interpretation Reporting Annotation Filtration Sample Prep Variant Calling GeneInsight DCR eDAP • DNAnexusData Commons • (raw data – enables discovery analyses) DNAnexusClinical Reports EMR Delivery DNAnexus Baylor Sample Accessioning Variant Harmonization e Broad Institute LMM CSGs transfer raw data, vcf, annotations to enable discovery analyses Data Generation Variant Confirmation • GeneInsight • Knowledge Base • Reporting Tool Annotation Filtration Sample Prep Interpretation Reporting Variant Calling • Variant harmonization • Structure & Content of accessioning and report data • Ontologies/Coding Systems • Data Delivery

  8. EHRI Survey *CCMC, CHOP, Columbia, Geisinger, Harvard, KPW/UW, Marshfield, Mt. Sinai, NU, VUMC * Data collected from May to July 2018 • Survey – 10 respondents, 7 structured data • Emphasizes need for Reporting Standard - • Structure & Content • Vocabulary & Ontologies • Easier integration/interoperability • Easier communication • GI XML Format was identified

  9. CSGs Data Harmonization – BCM Pipeline HybridEnvironment PHI Data Repository– HIPAA Compliant Environment to hold PII Data Metadata GeneratePDFs Final Reports PDFs, XMLs PII Remove Intake Portal PII Merge JSON to XML Approve/Sign-out Clinical Sites Requisitions LIMS Pre Reports Review Portal VIP Filter Samples HTML JSON Novel Variants Sample Intake & Sequencing Analysis & QC VIP DB

  10. JSON to GeneInsight XML Converter • Diffe ring JSON & XML Formats • BCM/GI change resolutions • DNAnexusexecutes JSON2XML • JSON2XML Technologies • Jackson Project ("best JSON parser for Java") • JSON to Java • Java™ Architecture for XML Binding (JAXB) • Java to XML

  11. BCM/Broad XML Changes • BCM extensions to XML • PGx • CNV • Sanger Confirmation • Gene Coverage • More Variant elements • Conform to existing structure as much as possible

  12. 1. Data Standardization – Future Direction • Need for National Standard • HL7 FHIR Standards for Clinical Genomics • FHIR (Fast Healthcare Interoperability Resource) • Best of HL7 V2, V3, CDA • Established Standard • Standard Ontologies • Established Architecture for Growth and Extensions • Dedicated HL7 WG for Clinical Genomics • HL7 FHIR fits eMERGE reporting

  13. 1. Data Standardization – Proposed Plan with FHIR FHIR integration plan over eMERGE years 4 & 5: • Understand the FHIR Genomics Specification • Create a FHIR Genomics Bundle for eMERGE • Map to BCM/LMM existing Report Structure/Content • Reconcile Differences with HL7 Clinical Genomics WG • Consolidate and Finalize eMERGE FHIR Genomics Bundle • Generate eMERGE FHIR reports * Y4 06/10/2018 – 05/31/2019; Y5 06/10/2019 – 05/31/2020

  14. 1. Data Standardization – Proposed Plan with FHIR • No impact to existing protocol • GI XMLs will continue to be generated • FHIR will be piloted for selected use cases • All reports will additionally be submitted as FHIR documents

  15. 1. Data Standardization – Proposed Project Timelines FHIR integration plan over eMERGE years 4 & 5:

  16. 2. Process Optimizations & Change Management • Improved high throughput reporting • Optimized batch processing • Report enhancements • Changes include: • PGx • CNV • LDL Risk Scores • Generation of updated reports • Increased reporting logistics and bookkeeping • Pipeline support for changes

  17. Goals Products 3. Tracking, Dashboard, Analytics • Tracking & Metrics Dashboard • Research Tool for Mining & Analysis • Access tool for reports and sequencing raw data • eDAP (eMERGE Dashboard & Analysis Portal) • eCAP (eMERGE Commons Access Portal)

  18. 4. Managing Variant Reclassification Process/System for managing Variant Reclassification Report Re-generation/Alerts

  19. 4. ReVU: Reclassification of Variants & Updates – Future Direction Auto ReV VIP 1.a. External Reclassification VIP History 4. Reclassification Alert Partial Automation Manual ReV NEPTUNE 2.a. Auto Update 5. VIP Update 3. Variant Reclassified Harmonization 6. Issue Updated Report & Send Alert 2.b. Manual Update 1.b.Expert Sourcing • eDAP • VIP • VIP History ReVU 1: Identifies internal and external updates, 2: Triggers pipeline for report updates 3: Manages alerts

  20. Acknowledgements Acknowledgements Richard Gibbs Eric Boerwinkle Will Salerno Donna Muzny Jianhong Hu Ritika Raj Christie Kovar ViktoriyaKorchina Jessica de la Cruz • Darren Ames • Andrew Carroll Eric Venner Sam Lu Jeremy Easton Marks Liwen Wang Piyush Panchal Victoria Yi FUNDING: NIH/NHGRI

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