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Sunday, October 25, 2020

ASM PacBio Workshop: Phasevarion – switching expression of multiple genes by methyltransferases in host-adapted pathogens

Epigenetics expert Michael Jennings from Griffith University first posited the phasevarion, or the phase variable regulon mechanism in host-adapted pathogens. This mechanism switches expression of multiple genes in a coordinated fashion and has significant implications on pathogen virulence. In his talk, Jennings describes the phasevarion and his use of whole methylome data to rapidly identify methylation targets.

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Sunday, October 25, 2020

Labroots Webinar: More comprehensive views of human genetic variation

In this BioConference Live webinar, PacBio CSO Jonas Korlach highlights how multi-kilobase reads from SMRT Sequencing can resolve many of the previously considered ‘difficult-to-sequence’ genomic regions. The long reads also allow phasing of the sequence information along the maternal and paternal alleles, demonstrated by full-length, fully phased HLA class I & II gene sequencing. In addition, characterizing the complex landscape of alternative gene products is currently very difficult with short-read sequencing technologies, and he describes how long-read, full-length mRNA sequencing can be used to describe the diversity of transcript isoforms, with no assembly required. Lastly, in the exciting area of…

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Sunday, October 25, 2020

ASHG PacBio Workshop: Personalized and allele specific long-read transcriptomes

At the PacBio ASHG workshop, Hagen Tilgner describes how he used long-read sequencing with Iso-Seq method to generate the first personal transcriptomes for three individuals. From these three family members, he and his collaborators were able to unambigously assign allele-specific RNA haplotypes, including HLA haplotypes, and demonstrated Mendelian inheritance of RNA molecules.

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Sunday, October 25, 2020

ASHG Virtual Poster: Long range phasing of cardiac disease genes using new long read sequencing technologies

Alex Dainis, a graduate student in Euan Ashley’s lab at Stanford University, presents her ASHG 2015 poster on haplotyping for genes linked to hypertrophic cardiomyopathy. Using the Iso-Seq method with SMRT Sequencing, she sequenced full transcripts of two genes of interest, generating data on 150 different isoforms. Rare variants, which could not be found with other technologies, were associated with haplotypes.

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Sunday, October 25, 2020

Webinar: Benefits of SMRT Sequencing for HLA typing at Anthony Nolan

Neema Mayor from Anthony Nolan Research Institute offers an introduction to the challenges of characterizing the HLA region, noting that improvements in resolution have allowed scientists to dramatically expand the number of classifications used to match donors to recipients. As sequencing resolution improves, Mayor says, scientists expect to find even more polymorphisms than what has been already catalogued.

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Sunday, October 25, 2020

Xtalks Webinar: Long genomic DNA fragment capture and SMRT Sequencing enables accurate phasing of cancer and HLA loci

In this webinar, the presenters describe a targeted sequencing workflow that combines Roche NimbleGen’s SeqCap EZ enrichment technology with PacBio’ SMRT Sequencing to provide a more comprehensive view of variants and haplotype information over multi-kilobase, contiguous regions. They demonstrate that 6 kb fragments can also be utilized to enrich for long fragments that extend beyond the targeted capture site and well into (and often across) the adjacent intronic regions. When combined with SMRT Sequencing, multi-kilobase genomic regions can be phased and variants, including complex structural variants, can be detected in exons, introns and intergenic regions.

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Sunday, October 25, 2020

AGBT Roche and PacBio Workshop: Towards precision medicine

Euan Ashley speaks about precision medicine and said clinical-grade analysis has been limited by complex regions in the human genome. His key theme,”Precision medicine needs to be accurate medicine,” was illustrated with several examples where short-read sequencing or traditional clinical sequencing methods failed to be accurate. Also included: targeted RNA sequencing and gene phasing with long-read sequencing.

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Sunday, October 25, 2020

PAG Conference: Diploid genome assembly and comprehensive haplotype sequence reconstruction

Jason Chin, senior director of bioinformatics at PacBio, talks about using long-read sequence data to generate diploid genome assemblies to produce comprehensive haplotype sequence reconstructions. In the presentation, Chin describes the FALCON Unzip process that combines SNP phasing with the assembly process and allows for determination of the haplotype sequences and identification of structural variants. He presents an example of diploid assembly from inbred Arabidopsis strains.

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