UCSF Informatics Day 2014 - Robert Nussbaum, "The Genomic Medicine Initiative at UCSF"


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UCSF Informatics Day 2014 - Robert Nussbaum, "The Genomic Medicine Initiative at UCSF"

  1. 1. Genomic Medicine Initiative Bob Nussbaum
  2. 2. SUMMARY • UCSF-wide interdepartmental, and interdisciplinary effort established and funded by the EVC and SOM Dean, with support of the Chancellor • Create the infrastructure to allow UCSF to use genomics in translational research, implementation science, clinical trials and clinical care • Enhance professional education in applied genomics • Harness campus-wide knowledge and experience to create efficient, knowledgeable teams that serve campus needs
  3. 3. BENEFITS • Patient Care: Improve diagnostic and therapeutic abilities • Clinical Research: Create infrastructure that enables our faculty to obtain extramural grant support • Education: Create a “Clinical Learning System” in which large numbers of faculty and staff can study how to use genomics creatively and effectively in oncology, clinical genetics, prenatal care and neonatology  UCSF Health System: Raise the profile of UCSF by advancing Precision Medicine through innovative use of genomics in clinical care
  4. 4. MAJOR COMPONENTS • Clinical Cancer Genetics Laboratory (Bastian CLIA Lab at MZ) – Targeted deep sequencing of driver oncogenes for solid and liquid tumors customized to the needs of the UCSF clinical oncology community - Transcriptome and cell-free DNA analysis • IHG Genomics Services Laboratory – CLIA approval pending – Whole exome and whole genome analysis for oncology, undiagnosed disease in NICU, and maternal and fetal medicine • Collaboration with UCLA Department of Pathology – CLIA-approved whole exome analysis for undiagnosed diseases – Sharing of sequence and variant data files for a joint video signout • Coursera Course
  5. 5. Confidential Genomic Medicine Initiative Clinical Cancer Genomics Laboratory (CLIA Lab at Mount Zion) Director: Boris Bastian Targeted Sequencing: Tumor/Normal Pairs Phase 1 Goal = Actionable Cancer Genome by Hybrid Capture Phase 2 Goal = RNASeq, Cell-Free DNA IHG Genomics Services Laboratory (CLIA-pending Lab at Parnassus) Director: Pui Kwok Whole Exome & Genome Sequencing Phase 1 Goal = Undiagnosed Diseases Phase 2 Goals = Prenatal and sick NICU children Genomic Medicine Initiative: Laboratory Structure - First Initiatives and Expansion 5 Phase 1
  6. 6. 6 • Sequence exons of ~300 oncogenes for mutations and copy number changes • Analyze for select structural rearrangements. • Plan on paired germline/somatic sequencing • Phase 1 assay does not assess epigenetic alterations or transcriptome Targeted Oncogene Panel Reporting Logistics • The test will be orderable in APeX. • Results will be available in APeX in approximately 3-4 weeks. • Patient’s insurance will be billed using CPT codes for targeted panel sequencing • Initial launch subsidized by the Genomic Medicine Initiative • Findings annotated and reported in APeX. • Annotation to include information on clinical trials or predicted drug responses • Molecular Pathologists interpret results at Tumor Boards. Clinical Cancer Genetics Laboratory Overview of the Phase 1 Pipeline
  7. 7. 7 Confidential CCGL: Reporting Molecular Oncology Results Sample of reporting format available from software vendor Syapse – will be viewable in APeX.
  8. 8. 8 Confidential CCGL: Software Support for Oncologists
  9. 9. Confidential Patient consents to data included in GMI database Patient Meets Criteria for Sequencing Sequencing ordered in APeX Sample acquired: surgery, or pre- existing sample Sample prepared by Pathology / Derm Path Oncology: Targeted Sequencing – Clinical Cancer Genetics Lab Inherited Diseases: IHG Genomics Services Lab Pipeline Processing: Automated preprocessing, variant calling, annotation Clinical Data Input: Tumor Size, Tissue Type, etc, manually input into Syapse Filtering: Reviewed by Lab Director - additional clinical annotation in Syapse Searchable Database in Syapse: all variants and phenotypes Molecular Case Review: Discussion in context of other findings Clinical Molecular Report: Case signed out by Primary Lab Director Delivery to Tumor Board & Ordering MD: Molecular Pathologists Final Clinical Findings: APeX – searchable format – phenotype and outcome data Billing Biobanking Genomic Medicine Initiative: Workflow Updated: 04/28/2014
  10. 10. THIS MONTH’S EXOME SIGNOUT WITH UCLA 10 Nussbaum – 2 patients Portale – 1 patient Slavotinek – 1 patient Alsadeh – 1 patient Shieh – 2 patients Fastq and VCF files requested and sent in advance from UCLA
  11. 11. COURSERA COURSE 11
  12. 12. Collaborations Collaborations Pathology • Abul Abbas • JP Grenert Clinical Laboratories/Laboratory Medicine • Tim Hamill • Michael Skehan • Laura van’t Veer • Betty Yalich Institute for Human Genetics • Steven Brenner • Brad Dispensa • Mark Kvale • Pui Kwok • Neil Risch • Brandon Zerbe Helen Diller Family Cancer Center • Sorena Nadaf • Eric Small • Barry Taylor UCLA • Wayne Grody, Stan Nelson, Sam Strom et al. Teams “On the Ground” • Boris Bastian • Michael Korn • Heather Pua • Jessica van Ziffle • Iweh Yei • Jon Hirsch (Syapse) Exome Clinic • Gilberto de Gente • Marta Sabbadini • Elliott Sherr • Joseph Shieh • Anne Slavotinek Prenatal/Neonatal Applications • Mary Norton Coursera • Jeanette McCarthy • Bryce Mendelssohn Administration • Kristen McCaleb • Karen Ely