Germline variants in IKZF1, ARID5B, and CEBPE as risk factors for adult-onset acute lymphoblastic leukemia: an analysis from the GMALL study group

Germline variants in IKZF1, ARID5B, and CEBPE as risk factors for adult-onset acute lymphoblastic leukemia: an analysis from the GMALL study groupA number of single nucleotide polymorphisms (SNPs) in the genes IKZF1, ARID5B, CEBPE and CDKN2A have been implicated in the propensity to develop acute lymphoblastic leukemia (ALL) in childhood (< 15 years of age) 1-4 but since the genetic background of adult and childhood ALL is different, it is not clear if these are also risk factors for adult-onset ALL.We analyzed seven SNPs (two in IKZF1: rs11978267, rs4132601; three in ARID5B: rs10821936, rs10994982, rs7089424; and one each in CEBPE: rs2239633 and CDKN2A: rs3731217) which were reported to confer an increased risk for childhood ALL in 322 immunologically and genetically well-characterized adult or adolescent ALL patient samples.All samples were obtained from BCR-ABL-negative patients at time points when they were in molecular remission, thus excluding mutations acquired during onset of disease and randomly selected from a large collection of archived samples obtained during diagnostic procedures in the framework of the German Multicenter ALL Study Group (GMALL) trial 07/2003 (Clinicaltrials.govidentifier:00198991).This trial has been approved by various local and central ethics committees and our study complied with the principles set forth in the Declaration of Helsinki.The median age of the patient cohort was 38 years (range 16-76 years), and 58.4% of the patients were male.Flow cytometry immunophenotyping and molecular genetic analyses for BCR-ABL, MLL-AF4, MLL-ENL, TCF3-PBX1, and ETV6-RUNX1 were performed at primary diagnosis as described previously.5,6 Assessment of minimal residual disease was made as described.7,8 BCR-ABL-positive samples and mature B-ALL (sIg + , or MYC-IGH + ) samples were excluded.Twenty-six patients were MLL-AF4-positive, 5 MLL-ENL-positive, 2 TCF3-PBX1-positive, and 2 ETV6-RUNX1-positive. Patient samples were selected in such a way as to match the distribution of immunophenotypes observed in the last ten years in the GMALL study group, thereby taking into consideration that BCR-ABL-positive patients had been excluded (Table 1).The control group comprised a total of 1516 healthy individuals of German origin collected through 2004 at the Institute of Transfusion Medicine in Mannheim, Germany (genotyped for rs4132601, rs7089424, rs2239633, rs3731217).4,9 Since no German control data were available for ARID5B rs10994982, this SNP was compared to a cohort comprising 14,311 individuals of European descent without ALL, collected by the Wellcome Trust Case Control Consortium (WTCCC); these results are only reported for completeness and are not listed in Table 2. 10 Details of the control groups have been described previously.2,4 The SNP Genotyping Assays (Applied Biosystems, Darmstadt/Germany, Cat # 4351379) were used with the TaqMan Genotyping Master Mix (Applied Biosystems, Cat # 4371355) on a RotorGene cycler (QIAGEN, Hilden/Germany) using basically the conditions recommended by the supplier.Some SNPs in the same gene were very closely correlated suggesting that they belonged to gene haplotypes.Linkage disequilibrium (LD) analysis revealed the following correlations: IKZF1 rs4132601-rs11978267: D'=0.9931, r 2 =0.9794;ARID5B rs7089424-rs10821936: D'=0.9731, r 2 =0.9407,ARID5B rs10821936-rs10994982: