13 Apr In-person UBC Seminar (16:00Jul3)@MIN 2.01, UU. “Identifying the system wide impact of genomic alterations”
On Monday, July 3 at 16:00, Prof. dr. Sanne Abeln from AI Technology for Life, UU will share her most recent bioinformatics related research.
Just come without registration. Don’t miss this opportunity to learn more about how bioinformaticians and computer scientists can work together and to catch up with other UBCers with drinks!
Identifying the system wide impact of genomic alteration
Background: Genomic alterations can significantly affect cellular biology, however identifying which alterations have a system-wide impact is a challenging task. Cancer samples typically contain many alterations. Identifying those with an impact is essential for biomarkers development. Here we present a novel computation tool, CIBRA, to detect genomic alterations with a system-wide impact.
Method: CIBRA integrates two omics data types to determine the system-wide impact: one indicates genomic alterations, and another defines the system-wide expression response, e.g. RNAseq data. CIBRA is both able to identify the system-wide response of genomic alterations and evaluate the degree of similarity in expression responses between alterations.
Results: Applying CIBRA to a genome-wide screen of SNVs in several cancer types, we could identify the system-wide impact on expression for most known drivers, validating CIBRA’s ability to detect biologically relevant impact. Surprisingly, when applying CIBRA to structural variants, we found a similarly large proportion of genomic alterations with a system-wide impact, suggesting that the biological impact of structural variants has been largely underreported.
Relevance: CIBRA is an essential new tool to identify the impact of genomic alterations by combining multi-omics data types and can refine our current definitions of alterations, in order to derive more accurate biomarkers.
There will be a 35-min presentation followed by a 15-min in-depth discussion.
Speaker overview
Prof. dr. Sanne Abeln has recently been appointed as the Professor of AI Technology for Life at Utrecht University. Abeln and her research group focus on developing technology in the field of artificial intelligence (AI) with the aim of gaining more insight into complex biological systems, such as cells, organisms and ecosystems. In this way, Abeln and her colleagues form a bridge between the university’s Department of Biology and Department of Information and Computing Science. Abeln herself studied mathematics and computing science, received her PhD in bioinformatics at Oxford and then did a postdoc in biophysics.
Location: Minneart Building 2.01
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