Genome-Wide 500K SNP Array Analyses Reveal High Frequencies of Cryptic Genetic Abnormalities and Identify Recurrent Microdeletions Targeting Novel Genes in Adult Acute Lymphoblastic Leukemia.
Authors: Paulsson Kajsa , Cazier Jean-Baptiste , Stevens Jane , Chaplin Tracy , MacDougall Finlay , Lillington Debra , Lister T. Andrew , Young Bryan D. 
Published: November 2019

Abstract
The long-term disease-free survival rate of adult acute lymphoblastic leukemia (ALL) patients remains less than 40%, in contrast to pediatric cases where it approaches 80%. Furthermore, whereas genetic abnormalities are widely used in childhood ALL for assigning patients to prognostic risk groups, their use in adult ALL is generally restricted to the presence or absence of the t(9;22)/[BCR-ABL1]. Novel prognostic markers, allowing better treatment stratification, and new treatment targets are therefore much needed. We have investigated diagnostic samples from 45 adult ALL cases using genome-wide, high-resolution single nucleotide polymorphism (SNP) array analysis with the Affymetrix 10K, 250K Nsp, and 250K Sty chips, in total including more than 500,000 SNPs with a median inter-marker distance of <2.5 kb. This method, which has not previously been applied to adult ALL, enables the detection of genetic copy number abnormalities as well as uniparental disomies (UPDs) with a much higher resolution than cytogenetic and molecular genetic techniques. We detected 367 genetic abnormalities not corresponding to known copy number polymorphisms among the 45 cases. These comprised 94 copy number gains, 211 hemizygous deletions, 47 homozygous deletions, and 15 UPDs. All but three of the patients (93%) displayed one or more anomaly not detectable with standard genetic analyses. Most notably, we found high frequencies of deletions targeting the genes CDKN2A (P16) (21 cases; 47%), PAX5 (15 cases; 33%), IKZF1 (IKAROS) (8 cases; 18%), ETV6 (7 cases; 16%), RB1 (5 cases; 11%), and EBF1 (2 cases; 4.4%). Thirty-two cases (71%) harbored a deletion of at least one of these genes. CDKN2A deletions were homozygous in 17 cases and associated with partial UPDs in 5 cases. PAX5 deletions were always hemizygous and frequently large, including also CDKN2A in all but three patients. Notably, loss of IKZF1 was found in 5 of 10 (50%) t(9;22)/[BCR-ABL1]-positive ALL cases. Reverse transcriptase-PCR for this gene showed that some t(9;22)-positive cases without this deletion expressed a dominant-negative isoform of IKZF1, suggesting that different mechanisms for downregulation of IKZF1 occur and that this gene is frequently targeted in t(9;22)+ ALL. Furthermore, the SNP array analysis revealed novel recurrent deletions targeting the genes DLG2 (4 cases; 8.9%), LDOC1 (3 cases; 6.7%), ERBB4, and CDH13 (2 cases each; 4.4%). In conclusion, using high-resolution SNP arrays we detect a very high frequency of hidden genetic changes in adult ALL cases. Deletions, frequently cryptic, comprised 70% of the found abnormalities, suggesting that microdeletions are a characteristic feature of adult ALL. Most importantly, the analyses revealed recurrent genetic abnormalities in adult ALL targeting novel genes, not previously implicated in leukemogenesis. In addition to giving new insights into the leukemogenic process, these findings are likely to be clinically important, with the possibility of identifying new prognostic markers as well as future treatment targets in adult ALL.