Journal article
Evaluating Multiple Next-Generation Sequencing–Derived Tumor Features to Accurately Predict DNA Mismatch Repair Status
R Walker, P Georgeson, K Mahmood, JE Joo, E Makalic, M Clendenning, J Como, S Preston, S Joseland, BJ Pope, RA Hutchinson, K Kasem, MD Walsh, FA Macrae, AK Win, JL Hopper, D Mouradov, P Gibbs, OM Sieber, DE O'Sullivan Show all
Journal of Molecular Diagnostics | ELSEVIER SCIENCE INC | Published : 2023
Abstract
Identifying tumor DNA mismatch repair deficiency (dMMR) is important for precision medicine. Tumor features, individually and in combination, derived from whole-exome sequenced (WES) colorectal cancers (CRCs) and panel-sequenced CRCs, endometrial cancers (ECs), and sebaceous skin tumors (SSTs) were assessed for their accuracy in detecting dMMR. CRCs (n = 300) with WES, where mismatch repair status was determined by immunohistochemistry, were assessed for microsatellite instability (MSMuTect, MANTIS, MSIseq, and MSISensor), Catalogue of Somatic Mutations in Cancer tumor mutational signatures, and somatic mutation counts. A 10-fold cross-validation approach (100 repeats) evaluated the dMMR pre..
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Awarded by Australian Genome Research Facility
Funding Acknowledgements
Supported by a National Health and Medical Research Council of Australia (NHMRC) project grant GNT1125269 (principal investigator D.D.B.) , which supported the design, analysis, and interpretation of data; the Margaret and Irene Stewardson Fund Scholarship (R.W.) ; the Melbourne Research Scholarship (R.W.) ; NHMRC Investigator grants GNT1194896 (D.D.B.) , GNT1195099 (M.A.J.) , and GNT1194392 (A.K.W.) ; University of Melbourne Dame Kate Campbell Fellowship (D.D.B. and J.L.H.) ; the University of Melbourne Research Scholarship (P.G.) ; an NHMRC Senior Research Fellowship GNT1136119 (O.M.S.) ; a Canadian Institutes of Health Research Post-doctoral Fellowship (D.E.O.) ; and a Victorian Health and Medical Research Fellowship from the Victorian Government (B.J.P.) .