Copy Number Changes and Allele Distribution Patterns of Chromosome 21 in B Cell Precursor Acute Lymphoblastic Leukemia

SIMPLE SUMMARY: Array analysis is an efficient method for defining in a single experiment all genome-wide large and fine-scale copy number abnormalities, as well as their corresponding allele patterns. Based on the results of the analysis that we performed in 578 children with acute lymphoblastic leukemia, we provide a comprehensive overview of the genetic subgroup-specific incidence and distribution of all the various types of chromosome 21 copy number alterations in this cohort, most of which are of eminent diagnostic and clinical relevance. By doing so, we also uncovered some unusual and difficult to explain discrepancies between copy number and allele distribution patterns that we investigated and eventually succeeded to resolve with polymorphic short tandem repeat analyses. ABSTRACT: Chromosome 21 is the most affected chromosome in childhood acute lymphoblastic leukemia. Many of its numerical and structural abnormalities define diagnostically and clinically important subgroups. To obtain an overview about their types and their approximate genetic subgroup-specific incidence and distribution, we performed cytogenetic, FISH and array analyses in a total of 578 ALL patients (including 26 with a constitutional trisomy 21). The latter is the preferred method to assess genome-wide large and fine-scale copy number abnormalities (CNA) together with their corresponding allele distribution patterns. We identified a total of 258 cases (49%) with chromosome 21-associated CNA, a number that is perhaps lower-than-expected because ETV6-RUNX1-positive cases (11%) were significantly underrepresented in this array-analyzed cohort. Our most interesting observations relate to hyperdiploid leukemias with tetra- and pentasomies of chromosome 21 that develop in constitutionally trisomic patients. Utilizing comparative short tandem repeat analyses, we were able to prove that switches in the array-derived allele patterns are in fact meiotic recombination sites, which only become evident in patients with inborn trisomies that result from a meiosis 1 error. The detailed analysis of such cases may eventually provide important clues about the respective maldistribution mechanisms and the operative relevance of chromosome 21-specific regions in hyperdiploid leukemias.