Dr. Tobias Rausch
„DNA variant detection and its caveats“
Abstract:
Most cancers harbor many somatic point mutations and have numerous chromosomal abnormalities, both in number and in structure. Predisposing germline variants can influence the somatic mutation landscape and varying degrees of tumor purity, heterogeneity and ploidy complicate the discovery and genotyping of DNA variants. Large catalogues of both germline variants (1000 Genomes Project) and somatic variants (TCGA, ICGC) have been accumulated enabling researchers to study the interplay between germline and somatic variants, possibly in a haplotype-aware manner using novel haplotyping approaches and long read single molecule sequencing. After a brief introduction to crucial parameters in cancer genomics (purity, ploidy, heterogeneity) we will focus on recent progress we made in the discovery, genotyping and visualization of somatic & germline variants, in particular for small insertions & deletions and larger structural variants. We will then discuss properties and limitations of current DNA variant calling pipelines and call sets. We will conclude with some hands-on experience of novel haplotyping approaches (10X Genomics) and long read single molecule sequencing (Pacific Biosciences) and outline how these ‘third-generation’ sequencing technologies can possibly alter our abilities to detect, phase & interpret germline and somatic variants.
Dr. Jonathon Blake
„Short Read Assembly Scaffolding with Oxford Nanopore Long Reads“
Abstract:
Dr. Jonathon Blake is a Senior Bioinformatican at EMBL’s Genomics Core Facility where he has specialized in bringing new sequencing technologies into mainstream use by developing novel applications and data analysis techniques that advance their adoption. With many years of experience working with different NGS technologies, Jonathon’s current focus is developing applications for the Oxford Nanopore MinION sequencer. As with all new technologies the application has to be adapted to the profile of the data produced and Jonathon will talk about his work here in the context of genomic assembly.
