Copy-Number Alterations and Copy-Neutral Loss of Heterozygosity in Adult T-ALL: A Descriptive Study in Relation to Day +70 MRD

Chromosomal microarray analysis (CMA) detects copy-number alterations and copy-neutral loss of heterozygosity (cnLOH), but the CMA landscape of adult T-ALL has been described in few cohorts. Day +70 measurable residual disease (MRD) is a surrogate marker of early treatment response, available only after induction. Thirty-nine adults with Ph-negative T-ALL on a single protocol underwent diagnostic CMA. Mosaic events were catalogued per chromosome and against a 57-gene panel and described in relation to day +70 MRD status (13 MRD-positive, 25 MRD-negative). The analysis is presented as descriptive without formal inference. Mosaic alterations were present in almost all patients, so groups differed in the amount rather than the presence of genomic change. Complex profiles (≥3 affected chromosomes) were seen in 46.2% of MRD-positive and 20.0% of MRD-negative patients. Biallelic 9p21.3 deletion occurred in both groups, whereas 9p cnLOH without deletion occurred predominantly in MRD-negative patients. Total cnLOH burden did not track with copy-number burden. Copy-number and copy-neutral events are mechanistically distinct and were not interchangeable here: 9p deletion and 9p cnLOH are separable by SNP array and should be reported separately rather than pooled. No association reached significance, although the cohort was too small to detect all but very large effects.