MAY 09, 2018 09:00 AM PDT

Size Matters: Accurate Detection and Phasing of Structural Variations

C.E. CREDITS: CEU | P.A.C.E. CE | Florida CE
Speakers
  • Lead Scientific Programmer, Baylor College of Medicine
    Biography
      Dr. Fritz Sedlazeck completed his PhD in 2012 in the group of Dr. Arndt von Haeseler at the Max F. Perutz Laboratory in Vienna. After a two year postdoc, he transitioned to the lab of Dr. Michael Schatz at Cold Spring Harbor Laboratory and later to Johns Hopkins University. Since 2017 he leads his own group at the Human Genome Sequencing Centre at Baylor College of Medicine. His research focuses on developing computational methods to detect and analyse genomic variations with a focus on Structural Variations. Structural Variations are genomic events that manipulate multiple positions in a genome, which impact evolution, genomic disorders, regulation as well as play an important role in explaining multiple phenotypes.

    Abstract:

    In this presentation I will describe our latest work to obtain comprehensive genomes leveraging long and linked reads. The vast majority of NGS whole-genome data covers hundreds of thousands of samples with short illumina reads, which are unable to capture the full spectrum of genetic variation and genomic complexity. Such comprehensive variation is critical to understanding the full heritability and genetic foundations of human disease. In this seminar I will present our novel alignment strategy (NGMLR) for long read data (Oxford Nanopore and PacBio) and our novel Structural Variations (SVs) caller Sniffles. These two methods improved the accuracy for both technologies enabling the accurate and easy detection of SVs. This includes also nested events that we have previously been blind to or linked events connecting genes over multiple regions.  We will discuss problems, characteristics and limitations of short reads. In addition, I will discuss the impact of these novel found SVs in cancer and other genomes with respect to RNA seq. In the end, I will highlight our current findings where we combine these long read technologies with linked reads to be able to phase SNV and SVs together to obtain a diploid genome per sample. These phased genomes are the most comprehensive representation of genomes up to date and we can now finally generate them within days. 


    Show Resources
    You May Also Like
    SEP 05, 2019 04:00 PM CEST
    C.E. CREDITS
    SEP 05, 2019 04:00 PM CEST
    DATE: September 5, 2019TIME: 7:00am PT, 10:00am ET, 4:00pm CEST PCR (Polymerase Chain Reaction) has gone through a massive evolution since its development in 1983. Besides it...
    MAY 16, 2019 04:00 PM CEST
    C.E. CREDITS
    MAY 16, 2019 04:00 PM CEST
    DATE: May 16, 2019TIME: 7:00am PDT, 10:00am EDT, 4:00pm CEST The emergence of NGS is revolutionizing the microbiological sciences and transforming medicine. Deep sequencing has...
    JUN 05, 2019 05:00 PM CEST
    C.E. CREDITS
    JUN 05, 2019 05:00 PM CEST
    DATE: June 5, 2019TIME: 8:00am PDT, 11:00am EDT, 5:00pm CEST Eukaryotic cell cultures respond to the most subtle influence. Apart from the risk of contamination, minimal chan...
    NOV 18, 2019 08:00 AM PST
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    C.E. CREDITS
    NOV 18, 2019 08:00 AM PST
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    DATE: November 18, 2019TIME: 8:00am PST, 11:00am EST, 4:00pm CEWT How often do you pipette in your cell culture lab every day? Usually, we do it so often that we tend stop th...
    AUG 27, 2019 09:00 AM PDT
    C.E. CREDITS
    AUG 27, 2019 09:00 AM PDT
    DATE: August 27, 2019 TIME: 9:00am PDT, 12:00pm EDT Immunotherapies targeting PD-1 or PD-L1 have proven remarkably effective for treating cancer in some patients, with considerabl...
    OCT 02, 2019 11:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    OCT 02, 2019 11:00 AM PDT
    Add to Calendar Select one of the following: iCal Google Calendar Outlook Calendar Yahoo Calendar
    DATE: October 2, 2019TIME: 11:00am PDT, 2:00pm EDT Ditch the Excel spreadsheets and manage your molecular workflows entirely in your LIMS Achieve configuration of molecular workf...
    Loading Comments...
    Show Resources