We use whole-genome and whole-transcriptome sequencing data from primary cancer samples to elucidate genetic subgroups of potential clinical relevance. Our next step will be to identify mutational signatures on the single-nucleotide, copy number and structural variant levels. To do so, multiple variant callers will be used, their output consolidated into a consensus list of variants per case, and then signature profilers will extract and annotate relevant mutational signatures. The project would entail setting up a pipeline that can generate variant call format (vcf) files from ready-mapped whole-genome sequencing data, match the output of multiple variant callers within each category of mutations and then apply signature extraction tools.
Contacts:
Karolin Hansén Nord PhD, karolin.hansen_nord@med.lu.se
Associate Professor, Senior Lecturer
Karim H. Saba PhD
Associate Researcher
Division of Clinical Genetics
Department of Laboratory Medicine
Faculty of Medicine
Lund University
Web page Complex Genomes in Cancer