Low Pass Whole Genome Sequencing as a Method of Determining Copy Number Variations in Uveal Melanoma Tissue Samples

Publication date: Available online 22 January 2020Source: The Journal of Molecular DiagnosticsAuthor(s): Aaron B. Beasley, Jacqueline Bentel, Richard J.N. Allcock, Tersia Vermeulen, Leslie Calapre, Timothy Isaacs, Melanie R. Ziman, Fred K. Chen, Elin S. GrayAbstractAnalysis of specific somatic copy number alterations (SCNAs) using multiplex ligation-dependent probe amplification (MLPA) is routinely used as prognostic test for uveal melanoma (UM). This technique requires relatively large amounts of input DNA, unattainable from many small fine needle aspirate biopsies. Herein we compared the use of MLPA with whole genome amplification (WGA) combined with low-pass whole genome sequencing (LP-WGS) for detection of SCNA profiles in UM biopsy specimens. DNA was extracted from 21 formalin-fixed paraffin-embedded FFPE UM samples and SCNAs were assessed using MLPA and WGA followed by LP-WGS. Cohen’s κ was used to assess the concordance of copy number calls of each individual chromosome arm for each patient. MLPA and WGA/LP-WGS detection of SCNAs in chromosomes 1p, 3, 6, and 8 were compared and found to be highly concordant with a Cohen’s κ of 0.856 (BCa 95% CI 0.770-0.934). Only 13 of 147 (8.8%) chromosomal arms interrogated resulted in discordant calls, predominantly SCNAs detected by WGA/LP-WGS but not MLPA. These results indicate that LP-WGS might be a suitable alternative or adjunct to MLPA for the detection of SCNAs associated with prognosis of UM, for cases with limiting t...
Source: The Journal of Molecular Diagnostics - Category: Pathology Source Type: research