Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction

Artem Baranovskii; Irem B Gündüz; Vedran Franke; Bora Uyar; Altuna Akalin

doi:10.3390/cancers14225604

Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction

Cancers (Basel). 2022 Nov 15;14(22):5604. doi: 10.3390/cancers14225604.

Authors

Artem Baranovskii¹, Irem B Gündüz², Vedran Franke³, Bora Uyar³, Altuna Akalin³

Affiliations

¹ Non-Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation Lab, Berlin Institute for Medical Systems Biology, Max Delbrück Center (MDC) for Molecular Medicine, Hannoversche Str. 28, 10115 Berlin, Germany.
² Integrative Cellular Biology & Bioinformatics Lab, Saarland University, 66123 Saarbrücken, Germany.
³ Max Delbrück Center (MDC) for Molecular Medicine, Bioinformatics and Omics Data Science Platform, The Berlin Institute for Medical Systems Biology, Hannoversche Str. 28, 10115 Berlin, Germany.

Abstract

Comprehensive genomic profiling using cancer gene panels has been shown to improve treatment options for a variety of cancer types. However, genomic aberrations detected via such gene panels do not necessarily serve as strong predictors of drug sensitivity. In this study, using pharmacogenomics datasets of cell lines, patient-derived xenografts, and ex vivo treated fresh tumor specimens, we demonstrate that utilizing the transcriptome on top of gene panel features substantially improves drug response prediction performance in cancer.

Keywords: cancer; drug response prediction; multi-omics; panel sequencing; pharmacogenomics.

Grants and funding

This research partly funded by Berlin Institute of Health, Digital Health Accelerator grant number and The APC was funded by Helmholtz Association.