MAY 09, 2018 09:00 AM PDT

Size Matters: Accurate Detection and Phasing of Structural Variations

C.E. CREDITS: CME | CEU | P.A.C.E. CE | Florida CE
  • Lead Scientific Programmer, Baylor College of Medicine
      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.


    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. 

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