MAY 08, 2019 1:30 PM PDT

Highly Accurate Long Sequence Reads for Comprehensive Genomic Analysis

Sponsored by: PacBio
C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Chief Scientific Officer, Pacific Biosciences
    Biography
      Jonas Korlach was appointed Chief Scientific Officer of Pacific Biosciences in July 2012. He was previously a Scientific Fellow, supporting commercial development of the PacBio RS II system and performing research aimed at developing new applications for SMRT technologies. He co-invented the SMRT technology with Stephen Turner, Ph.D., Pacific Biosciences Founder and Chief Technology Officer, when the two were graduate students at Cornell University.

      Dr. Korlach joined Pacific Biosciences as the company's eighth employee in 2004. Previously, he was a Postdoctoral Researcher at Cornell University. Dr. Korlach is the recipient of multiple grants, an inventor on 70 issued U.S. patents and 61 international patents, and an author of over 100 scientific studies on the principles and applications of SMRT technology, including publications in Nature, Science, and PNAS. In 2013, Dr. Korlach was honored by the Obama White House as an Immigrant Innovator "Champion of Change." He received both his Ph.D. and his M.S. degrees in Biochemistry, Molecular and Cell Biology from Cornell, and received M.S. and B.A. degrees in Biological Sciences from Humboldt University in Berlin, Germany.

    Abstract

    Recent improvements in sequencing chemistry and instrument performance combine to create a new PacBio data type of highly accurate (HiFi), long insert reads. Increased read length and improvement in library construction enables average read lengths of 10-20 kb with average sequence identity greater than 99% from raw single molecule reads. The resulting reads have the accuracy comparable to short read NGS but with 50-100 times longer read length. These highly accurate long reads allow for comprehensive variation detection from single nucleotide polymorphism to large structural variation with a single data type at 15- to 30-fold coverage. Using existing variation detection pipelines (e.g. GATK) to call variants and construct phase blocks, we achieve state of the art sensitivity and specificity for small nucleotide polymorphisms while preserving high sensitivity to detect larger structural variation (>50 bp) at single base resolution and delineate haplotype linkages. Additionally, the lack of sequence context bias and the unambiguous mappability of the longer HiFi reads allow a more complete survey of the human genome, expanding the detection of variants outside of the GIAB high confidence regions. We demonstrate the utility of this data type by sequencing to 15- to 30-fold coverage and calling all variants in the well-characterized HG002 genome. In addition to human resequencing analysis, HiFi reads may be used to assemble and call variants in plant or animal genomes, with assembly results rivaling the current long read sequencing approaches. The highly accurate raw data is directly compatible with many existing bioinformatics tools.

    Learning Objectives: 

    1. Understand the generation of HiFi sequence reads, and the uniqueness of this data type among sequencing technologies
    2. Learn about the different use cases uniquely enabled by the new HiFi sequence data type


    Show Resources
    You May Also Like
    OCT 08, 2020 7:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    C.E. CREDITS
    OCT 08, 2020 7:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    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...
    APR 07, 2020 8:00 AM PDT
    C.E. CREDITS
    APR 07, 2020 8:00 AM PDT
    DATE: April 7, 2020 TIME: 8:00am PT, 11:00am ET This webinar sets out to establish why quality control is key to robust, reliable, reproducible science. We will look at best practice criteri...
    MAY 08, 2020 10:00 AM PDT
    C.E. CREDITS
    MAY 08, 2020 10:00 AM PDT
    DATE: May 8, 2020 TIME: 10:00am PT, 11:00am MT, 1:00pm ET The application of next generation sequencing to interrogate immune repertoires and methods in which these highly complex dataset...
    FEB 25, 2020 9:00 AM PST
    C.E. CREDITS
    FEB 25, 2020 9:00 AM PST
    Learn about how to generate a small scale CAR-T workflow using ThermoFisher products See detailed characterization tools that can be utilized and applied in a CAR-T workflow...
    MAR 03, 2020 9:00 AM JST
    C.E. CREDITS
    MAR 03, 2020 9:00 AM JST
    DATE: March 3, 2020 TIME: 9:00am JST A major limitation in the ex vivo expansion of harvested human hematopoietic stem-progenitor cells (HSPCs) is the rapid differentiation of HSPCs at the e...
    FEB 26, 2020 9:00 AM PST
    C.E. CREDITS
    FEB 26, 2020 9:00 AM PST
    DATE: February 26, 2020 TIME: 9:00am PST 3D cell culture and analysis and the study of organoids and spheroids are becoming more prevalent as a research method in publications as traditional...
    Loading Comments...
    Show Resources