Custom Resolving the “dark matter” of the exome:

Using linked reads and exome bait capture to map NGS short reads differentially to genes versus their paralogous segments.

Date: This event took place on June 2, 2016

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Mapping the repetitive regions of the genome remains challenging with current sequencing methods due to the reliance on short reads of ~200-400bp.  About 10% (1,998 genes) of the exome have highly homologous paralogs located elsewhere in the genome and are therefore difficult to resolve. 286 such genes belong to the medical exome.

In this webcast a methodology to systematically resolve these genes using the 10x Genomics Chromium platform coupled with Agilent’s SureSelect target enrichment and optimized baits will be presented. This optimised exome contains “bridging baits” spaced within intronic and intergenic regions to preserve long-range information following capture.  We show that 184/219 of the genes are resolvable (MAPQ≥30) when pre-processed via Chromium + optimized baits, thereby unveiling how linked-reads can be used for de-convoluting dark matter regions of the genome.

In this webcast you will learn:

  • New methodology to systematically resolve the medical exome using the 10x Genomics Chromium platform coupled with Agilent’s SureSelect target enrichment and optimised baits.
  • How “bridging baits” spaced within intronic and intergenic regions optimize exome capture.
  • How bridging-baits combined with linked-reads preserve long-range information in exome data.
  • How linked-reads can be used to resolve dark matter regions of the exome.

Speakers

  • Dr Hakon Hakonarson

    Dr Hakon Hakonarson

    Dr Hakon Hakonarson is the Director of the Center for Applied Genomics at the Children’s Hospital of Philadelphia (CHOP) and also an associate professor of pediatrics at The University of Pennsylvania School of Medicine.

    Originally from Iceland, Hakon completed his medical training and postgraduate studies at the University of Iceland before moving into the biopharmaceutical industry. He now investigates the genetic factors that underlie complex medical disorders such as autism.

    He leads a $40 million commitment from CHOP to genotype approximately 100,000 children, an initiative that has gained international attention.

  • Dr. Jayshan Carpen, Springer Nature

    Moderator: Dr. Jayshan Carpen, Springer Nature

    Jayshan is a Senior Publishing Manager for Springer Nature and oversees the custom multimedia unit. Previously he ran science events at the Royal Institution of Great Britain. He received his PhD from the University of Surrey, UK in Neurogenetics. His doctoral thesis focused on identifying polymorphisms associated with diurnal preference and circadian sleep disorders.