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Concordance of copy number abnormality detection using SNP arrays and Multiplex Ligation-dependent Probe Amplification (MLPA) in acute lymphoblastic leukaemia

Lookup NU author(s): Dr Matthew Bashton, Robin Hollis, Dr Sarra Ryan, Claire Schwab, Professor Christine Harrison FRCPath FMedSci, Professor Anthony MoormanORCiD, Dr Amir EnshaeiORCiD



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


In acute lymphoblastic leukaemia, MLPA has been used in research studies to identify clinically relevant copy number abnormality (CNA) profiles. However, in diagnostic settings other techniques are often employed. We assess whether equivalent CNA profiles are called using SNP arrays, ensuring platform independence. We demonstrate concordance between SNP6.0 and MLPA CNA calling on 143 leukaemia samples from two UK trials; comparing 1,287 calls within eight genes and a region. The techniques are 99% concordant using manually augmented calling, and 98% concordant using an automated pipeline. We classify these discordant calls and examine reasons for discordance. In nine cases the circular binary segmentation (CBS) algorithm failed to detect focal abnormalities or those flanking gaps in IKZF1 probe coverage. Eight cases were discordant due to probe design differences, with focal abnormalities detectable using one technique not observable by the other. Risk classification using manually augmented array calling resulted in four out of 143 patients being assigned to a different CNA risk group and eight patients using the automated pipeline. We conclude that MLPA defined CNA profiles can be accurately mirrored by SNP6.0 or similar array platforms. Automated calling using the CBS algorithm proved successful, except for IKZF1 which should be manually inspected.

Publication metadata

Author(s): Bashton M, Hollis R, Ryan S, Schwab CJ, Moppett J, Harrison CJ, Moorman AV, Enshaei A

Publication type: Article

Publication status: Published

Journal: Scientific Reports

Year: 2020

Volume: 10

Print publication date: 08/01/2020

Acceptance date: 19/12/2019

Date deposited: 20/01/2020

ISSN (electronic): 2045-2322

Publisher: Nature


DOI: 10.1038/s41598-019-56972-0


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Funder referenceFunder name
16002Bloodwise (Formerly Leukaemia and Lymphoma Research)