Dr Karin Kassahn

SA Pathology

Dr Kassahn holds a PhD in genomics and genetics, awarded 2007, and has 6 years of postdoctoral research experience in bioinformatics and cancer genomics, obtained from her roles at the University of Queensland. She transitioned from environmental genomics to bioinformatics and cancer research in 2009. She has been an active member of the International Cancer Genome Consortium and has contributed to establishing next-generation sequencing for pancreatic cancer genomics in Australia. She has developed several pipelines for somatic mutation calling in low purity tumours and has been invited to present at multiple national and international cancer genomics and bioinformatics meetings, and more recently on the clinical applications of NGS. In early 2013, she took up the role of Head of Technology Advancement at SA Pathology to introduce NGS into clinical translational research and diagnostics. In her new role, she is contributing to national efforts to implement these technologies in routine clinical care and to develop standards for their application in clinical diagnostics.

Introduction to NGS and variant calling

Next-generation sequencing (NGS) is providing the ability to sequence genomes at an unprecedented rate and has been driving a new understanding and application of genetics in both human disease and general biology. The applications of this technology range from Mendelian gene discovery, cancer, genome assembly and de novo sequencing, to gene expression and functional genomic studies. In recent years, NGS has been increasingly applied to clinical translational research and diagnostics where it is helping to improve our ability to diagnose genetic disorders and to stratify cancer patients for therapy based on the somatic mutations in their tumours. Underlying these enormous advances in the application of this technology are the successful generation and bioinformatic processing of the resulting short read data. This talk will give a brief overview of the steps involved in an NGS experiment and will provide the foundation for the talks and exercises that follow later in the day. The talk will briefly introduce template enrichment, library preparation, sequencing, and read alignment and then discuss common strategies for variant calling from short read data.