Abstract
Previous cytogenetic studies of myeloid and acute lymphoblastic leukemias in children with Down syndrome (ML‐DS and DS‐ALL) have revealed significant differences in abnormality patterns between such cases and acute leukemias in general. Also, certain molecular genetic aberrations characterize DS‐related leukemias, such as GATA1 mutations in ML‐DS and deregulation of the CRLF2 gene in DS‐ALL. Whether microdeletions/microduplications also vary between DS and non‐DS cases is presently unclear. To address this issue, we performed single nucleotide polymorphism array analyses of eight pediatric ML‐DS and 17 B‐cell precursor DS‐ALL. In the ML‐DS cases, a total of 29 imbalances (20 gains and nine losses) and two partial uniparental isodisomies (pUPDs) were detected. None of the 11 small (defined as <10 Mb) imbalances were recurrent, nor were the pUPDs, whereas of the 18 large aberrations, three were recurrent—dup(1q), +8 and +21. In contrast, several frequent changes were identified in the DS‐ALL cases, which harbored 82 imbalances (30 gains and 52 losses) and four pUPDs. Of the 40 large changes, 28 were gains and 12 losses, with +X, dup(Xq), dup(1q), del(7p), dup(8q), del(9p), dup(9p), del(12p), dup(17q), and +21 being recurrent. Of the 40 microdeletions identified, several targeted specific genes, with the following being repeatedly deleted: BTG1 and CDKN2A/B (29% of cases), ETV6, IKZF1, PAX5 and SERP2 (18%), and BTLA, INPP4B, P2RY8, and RB1 (12%). Loss of the SERP2 and INPP4B genes, encoding the stress‐associated endoplasmic reticulum protein family member 2 and the inositol polyphosphate 4‐phosphatase‐II, respectively, has previously never been implicated in leukemia. Although deletions of the other genes have been associated with ALL, the high frequency of BTG1 loss is a novel finding. Such deletions may characterize a clinical subgroup of DS‐ALL, comprising mainly boys with a high median age. In conclusion, ML‐DS and DS‐ALL are genetically distinct, with mainly gains in ML‐DS and deletions in DS‐ALL. Furthermore, DS‐ALL is characterized by several recurrent gene deletions, with BTG1 loss being particularly frequent. © 2011 Wiley Periodicals, Inc.