MAY 09, 2018 6:00 AM PDT

Genome in a Bottle: Developing Benchmark Sets for Structural Variants

Speaker

Abstract

The Genome in a Bottle Consortium (GIAB) has characterized an Ashkenazi trio from the Personal Genome Project (NIST Reference Material 8392) with 12 short, long, and linked read sequencing and mapping methods.  Datasets are public without embargo for analysis and methods development by the community. We have characterized ~3.7 million small variants as well as reference calls for ~90% of the genome with estimated errors of ~2 FPs and 2 FNs per million variants. To extend this characterization to larger indels and structural variants, we collected analyses of variants >=20 bp from 33 bioinformatics methods and five technologies. Nineteen discovery and refinement methods produced sequence-resolved calls using local or global assembly or split reads, giving a precise prediction of deletion breakpoints, inserted sequences, and complex changes.  We designed an integration approach to address challenges in comparing and evaluating large variants, which are frequently in tandem repeats (>50% of all calls) and not precisely characterized. We have iteratively refined our integration process based on feedback received for publicly released draft “straw man” callsets.   Current work includes developing 2-tiered high-confidence variant calls and a high-confidence bed file for benchmarking SVs, as well as a web app for crowd-sourced manual curation of SVs.  These results represent a significant step in GIAB work towards improved benchmarking of large variants in research and clinical settings.


Show Resources
You May Also Like
OCT 08, 2020 7:00 AM PDT
C.E. CREDITS
OCT 08, 2020 7:00 AM PDT
DATE: October 8, 2020 TIME: 7:00am PDT, 10:00am EDT, 4:00pm CEST How often do you pipette in your cell culture lab every day? Usually, we do it so often that we tend stop thinking about ho...
DEC 02, 2020 8:00 AM PST
Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
C.E. CREDITS
DEC 02, 2020 8:00 AM PST
Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
DATE: December 2nd, 2020 TIME: 08:00am PDT, 11:00pm EDT Bioreactors and shakers are used to cultivate microorganisms, plant, insect, and mammalian cells in different volumes. Upscaling of pr...
SEP 10, 2020 9:00 AM PDT
C.E. CREDITS
SEP 10, 2020 9:00 AM PDT
Date: September 10, 2020 Time: 9:00am (PDT), 12:00pm (EDT) Osmolality testing is relevant throughout the entire bioprocessing workflow. As customers look to refine mAb and gene therapy workf...
AUG 25, 2020 8:00 AM PDT
C.E. CREDITS
AUG 25, 2020 8:00 AM PDT
DATE: August 25, 2020 TIME: 8:00am PDT, 10:00am CDT, 11:00am EDT Recombinant lentivirus (LV) and adeno-associated virus (AAV) are critical components of cell and gene therapies, which show g...
NOV 16, 2020 8:00 AM PST
C.E. CREDITS
NOV 16, 2020 8:00 AM PST
Date: November 16, 2020 Time: 8:00am (PST), 11:00am (EST) CRISPR screening has become the prime discovery tool in modern biomedical research and drug discovery. At the same time, most screen...
OCT 29, 2020 6:00 AM PDT
C.E. CREDITS
OCT 29, 2020 6:00 AM PDT
Date: October 29, 2020 Time: 6:00am (PDT), 9:00am (EDT), Chronic inflammation can occur as a result of a combination of genetic predispositions and environmental factors. Epigenetic modifica...
Loading Comments...
Show Resources
Attendees
  • See more