‘Reveal Hidden Genetic Variation’
On-Demand Webinar Now Available
Tuesday, November 15, 2016
We recently co-sponsored a webinar with Springer Nature, and if you missed it live, you can now register to watch the recording. Moderated by Nature Publishing Group’s Jayshan Carpen, the webinar is entitled “Reveal hidden genetic variation by combining long-read target capture with SMRT Sequencing” and features several terrific speakers. We’d like to thank Tetsuo Ashizawa from Houston Methodist Research Institute, Melissa Laird Smith from the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai, and our own Meredith Ashby for taking the time to present fascinating data and answer audience questions.
The webinar kicks off with a talk from Ashby, a scientist at PacBio, who discusses the use of targeted capture approaches with long-read SMRT Sequencing. Noting that these read lengths are necessary for spanning large genomic elements such as insertions and deletions, she shares two case studies to illustrate the process and findings. In one, scientists in Australia used long-read sequencing with Roche NimbleGen capture probes to study transcripts of relaxin genes in samples from both cell lines and prostate cancer patients. They discovered new isoforms, including two fusion genes that could easily be missed with other methods. In the second project, scientists at Baylor College of Medicine developed a large-insert targeted sequencing protocol (called PacBio-LITS) to study Potocki-Lupski syndrome, a rare disorder caused by a duplication event on chromosome 17. Their work uncovered possible rearrangement mechanisms that suggest opportunity for even more long-read-powered discoveries in this area.
Next, Laird Smith, the Icahn Institute’s assistant director of technology development, presents data from long-read studies of the IGH locus, a remarkably complex region that encodes the VDJ gene segments which are recombined during the adaptive immune response. Nearly half of the IGH region falls in a segmental duplication, making it quite difficult to sequence. Her team is using long-read sequencing to generate fully resolved haplotypes of the IGH locus from ethnically diverse individuals. They have also developed an oligo-based enrichment and long-read sequencing approach that should make it more straightforward to interrogate this challenging genomic region and generate results that include large structural variants.
Finally, Ashizawa, who is Director of the Neuroscience Research Program at Houston Methodist, speaks about ATTCT repeat expansions in SCA10, which cause a form of spinocerebellar ataxia. He describes a novel enrichment method that uses CRISPR-Cas9 to target the repeat expansion, without the need for amplification. Paired with long-read sequencing, this approach has allowed his team to span extremely long repeat regions while identifying interruption sequence motifs associated with distinct, epilepsy-linked clinical phenotypes. Based on detailed work with family samples, Ashizawa was also able to trace the likely origin of the initial SCA10 mutation, which seems to have occurred first in Asia.
The speakers also respond to audience questions about sequencing GC-rich regions, sample preparation details, read length statistics, and more. This Q&A session nicely expanded on the earlier examples to show how SMRT Sequencing can be combined with capture techniques for an economical means of querying specific regions in the human genome.