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

Aaron B Beasley; Jacqueline Bentel; Richard J N Allcock; Tersia Vermeulen; Leslie Calapre; Timothy Isaacs; Melanie R Ziman; Fred K Chen; Elin S Gray

doi:10.1016/j.jmoldx.2019.12.005

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

J Mol Diagn. 2020 Mar;22(3):429-434. doi: 10.1016/j.jmoldx.2019.12.005. Epub 2020 Jan 22.

Authors

Aaron B Beasley¹, Jacqueline Bentel², Richard J N Allcock³, Tersia Vermeulen², Leslie Calapre¹, Timothy Isaacs⁴, Melanie R Ziman⁵, Fred K Chen⁶, Elin S Gray⁷

Affiliations

¹ School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia.
² Department of Anatomical Pathology, PathWest Laboratory Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia.
³ School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia, Australia.
⁴ Perth Retina, Subiaco, Western Australia, Australia; Lions Eye Institute, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia; Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia.
⁵ School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia, Australia.
⁶ Lions Eye Institute, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia; Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia.
⁷ School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia; Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia. Electronic address: e.gray@ecu.edu.au.

PMID: 31978561
DOI: 10.1016/j.jmoldx.2019.12.005

Abstract

Analysis of specific somatic copy number alterations (SCNAs) using multiplex ligation-dependent probe amplification (MLPA) is used routinely as a prognostic test for uveal melanoma (UM). This technique requires relatively large amounts of input DNA, unattainable from many small fine-needle aspirate biopsy specimens. 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 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 (bias-corrected and accelerated 95% CI, 0.770-0.934). Only 13 of 147 (8.8%) chromosomal arms investigated 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 tissue or DNA yields.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
Aged
Aged, 80 and over
Biomarkers, Tumor
DNA Copy Number Variations*
Female
Genetic Association Studies* / methods
Genetic Predisposition to Disease*
Humans
Male
Melanoma / diagnosis*
Melanoma / genetics*
Middle Aged
Nucleic Acid Amplification Techniques
Uveal Neoplasms / diagnosis*
Uveal Neoplasms / genetics*
Whole Genome Sequencing*

Substances

Biomarkers, Tumor

Supplementary concepts

Uveal melanoma