AGBT13 – Thu 2/21 Afternoon session

Missed out on a talk and parts of others (and internet was so poor!):

Plenary Session: Clinical Genomics II
Sharon Plon, Baylor College of Medicine, Chair

2:45 p.m. – 3:15 p.m.
Stephen Kingsmore, Children’s Mercy Hospital
“Two Year Experience of Pediatric Genomic Medicine at a Large Children’s Hospital”
– In genetic diseases, genome sequence is uniquely deterministic – single gene diseases are proving ground for genomic medicine
– Bioinformatics whole genome analysis GSNAP -> GATK -> RUNES in ~17hr -> VIKING analysis for reporting
– 24hr STAT-seq test in 2013 – 18hr hiSeq sequencing, ~4hr bioinformatics
– Causal gene is known in 3677 / 7334 genetic diseases – treatment for ~500
– Diagnostic Odyssey – a surprising new term I came across – defined as the weird concert of multiple doctor visits, sanger gene tests, etc. to understand the genetic disorder – takes ~5 years!!
– Highlights inconsistent results from Sanger-seq
– 3 tests to pediatricians:

  • STAT-seq – 2 day time-to-result genome seq test
  • TaGSCAN – CLIA targeted panel for 514 disease genes – 800x coverage – ~$1350, 99% precision
  • WES

3:15 p.m. – 3:45 p.m.
Jonathan Berg, The University of North Carolina at Chapel Hill
“Binning” the Genome: Practical Management of Genomic Incidental Findings in a Clinical Context”

– Incidental findings – on vast majority of genome, and with not much clinical significance; Incidentalome best considered in the context of predictive value
– 3 bins of incidental variants – clinical mgmt implications (benefit > harm), clinically valid but uncertain, no clinical utility
– Define a priori, the actionability of gene-phenotype pairs – mindful of

  • medical ethics (duty to warn and autonomy)
  • reproducible & transparent
  • scalable & flexible

– talks about crowd-sourcing this task for consistency/variability of scores

4:15 p.m. – 4:45 p.m.
Zivana Tezak, FDA
“Translating Ultra High Throughput Sequencing into Clinical Applications-Regulatory Considerations”

4:45 p.m. – 5:15 p.m.
* Michael Talkowski, Harvard Medical School
“Rapid Prenatal Diagnosis by Whole-genome Clinical Sequencing of Jumping Libraries”

– WGS pipeline for detection of balanced chromosomal abnormalities (BCA) – FISH is the standard but low-resolution method
– Using customized large-insert jumping libraries – ~200-300x coverage (single HiSeq lane)
– 13-day sequence and analytic protocol for prenatal delineation of BCAs
– The challenge of interpreting morbid genome; imbalance in some regions is tolerated

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