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Size matters: accurate detection and phasing of Structural Variations

Friday 26 July 2019, 1.00PM

Speaker(s): Dr Fritz Sedlazeck, Baylor College of Medicine

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 and in general biology. 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 efforts to combine phased SNP, SVs and methylation from only one inexpensive sequencing run. Thus, representing the most comprehensive representation of genomes up to date, which we can now finally generate within days.

Location: Dianna Bowles Lecture Theatre (K018)

Email: daniel.jeffares@york.ac.uk