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BIFOLD Colloquium 04/07/2022

Algorithms for inferring cancer evolution from haplotype-specific somatic copy-number alterations

Speaker: Prof. Dr. Roland F. Schwarz, Center for Integrative Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), University Hospital and University of Cologne
Date & Time: July 4, 2022; 4:00 pm
Venue: TU Berlin, Stra├če des 17. Juni 135, 10623 Berlin, Main building, Room: H 1028

Abstract: Traditionally, phylogenetic inference methods have mostly focused on inferring evolutionary trees from single nucleotide variants (SNVs). In cancer, in addition to SNVs, genomic rearrangements and somatic copy number alterations (SCNAs) play an important role in the development and progression of the disease, and SCNAs can provide a rich source of genetic variation suitable for reconstructing cancer evolution. SCNAs thereby pose specific algorithmic challenges owing to the non-independence of adjacent genomic loci and their overlapping and cascading nature. Additionally, accurate phylogenetic inference from SCNAs requires identifying the parental chromosome of origin of each evolutionary event, a non-trivial task in many short-read sequencing datasets.
Roland Schwarz will introduce two key algorithms for inferring cancer evolution from SCNA profiles derived from multi-region sequencing data: refphase, which identifies the parental chromosome of origin of SCNAs by leveraging heterozygous germline variants shared between multiple samples from the same patient, and MEDICC2, a complete phylogenetic inference algorithm for SCNA profiles. He will describe how his group overcomes the problem of phasing of SCNAs, leverage finite-state transducers to compute exact minimum event distances between pairs of SCNA profiles, and detect, order and place individual evolutionary SCNA events including whole-genome doublings on the phylogenetic tree. Finally, he is going to demonstrate how in the future, the event histories inferred by MEDICC2 might be leveraged by machine learning algorithms to derive copy-number signatures which can identify the mutational processes underlying individual cancer types.

Speaker: Dr. Roland F. Schwarz is Professor for Computational Cancer Biology at the Center for Integrative Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), University of Cologne, Germany. He is a renowned expert in machine learning, theoretical computer science and clinical oncology. He uses machine learning and statistical algorithms to explore the causes and functional consequences of differences in tumors and cancer evolution. 2016 Schwarz was awarded the Prize of the Berlin-Brandenburg Academy of Sciences for excellence in cancer research for his work on cancer genome evolution.

Prof. Dr. Roland Schwarz
C: private