Low-pass whole-genome sequencing as a method of determining copy number variations in uveal melanoma tissue samples

Document Type

Journal Article

Publication Title

Journal of Molecular Diagnostics


Elsevier BV


School of Medical and Health Sciences




Edith Cowan University,

ECU Ophthalmic Research Institute of Australia,

ORIA Raine Medical Research Foundation Cancer Council Western Australia


Beasley, A. B., Bentel, J., Allcock, R. J., Vermeulen, T., Calapre, L., Isaacs, T., ... & Gray, E. S. (2020). Low-Pass Whole-Genome Sequencing as a Method of Determining Copy Number Variations in Uveal Melanoma Tissue Samples. The Journal of Molecular Diagnostics, 22(3) 429 - 434. https://doi.org/10.1016/j.jmoldx.2019.12.005


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. © 2020 American Society for Investigative Pathology and the Association for Molecular Pathology



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