Genomics · 2022
Methylation microarray-based detection of clinical copy-number aberrations in CLL benchmarked to standard FISH analysis.
СтатьяПоддержка исследования: вне правительства СШАНазвание и аннотация: Перевод пока не подготовлен
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Hussmann Dianna, Starnawska Anna, Kristensen Louise, Daugaard Iben, Cédile Oriane, Nguyen Vivi Quoc, Kjeldsen Tina E, Hansen Christine Søholm, Bybjerg-Grauholm Jonas, Kristensen Thomas, Larsen Thomas Stauffer, Møller Michael Boe, Nyvold Charlotte Guldborg, Hansen Lise Lotte, Wojdacz Tomasz K
Аннотация
Copy-number aberrations (CNAs) are assessed using FISH analysis in diagnostics of chronic lymphocytic leukemia (CLL), but CNAs can also be extrapolated from Illumina BeadChips developed for genome-wide methylation microarray screening. Increasing numbers of microarray data-sets are available from diagnostic samples, making it useful to assess the potential in CNA diagnostics. We benchmarked the limitations of CNA testing from two Illumina BeadChips (EPIC and 450k) and using two common packages for analysis (conumee and ChAMP) to FISH-based assessment of 11q, 13q, and 17p deletions in 202 CLL samples. Overall, the two packages predicted CNAs with similar accuracy regardless of the microarray type, but lower than FISH-based assessment. We showed that the bioinformatics analysis needs to be adjusted to the specific CNA, as no general settings were identified. Altogether, we were able to predict CNAs using methylation microarray data, however, with limited accuracy, making FISH-based assessment of deletions the superior diagnostic choice.