A germ-line deletion of APOBEC3B does not contribute to subtype-specific childhood acute lymphoblastic leukemia etiology

Wallace, Amelia D.; Francis, Stephen; Shao, Xiaorong; Smith, Adam J. de; Walsh, Kyle M.; McKean‐Cowdin, Roberta; Ma, Xiaomei; Dahl, Gary V.; Barcellos, Lisa F.; Metayer, Catherine

doi:10.3324/haematol.2017.179317

Cited by 1 publication

(2 citation statements)

References 17 publications

(15 reference statements)

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“…SNP genotype data was available for 927 ALL cases (589 Latino, 338 non-Latino white, Table S1) including 238 with high hyperdiploidy (HD) (156 Latino, 82 non-Latino white), as confirmed by FISH or G-banding 25 , and 750 controls (506 Latino, 244 non-Latino white). DNA was extracted from neonatal DBS, saliva, or buccal cells, and genotyped on Illumina HumanOmniExpress or HumanOmniExpressExome genome-wide SNP arrays 26 . SNP imputation was performed using Impute2, as described earlier for analysis in CCRLP.…”

Section: Methodsmentioning

confidence: 99%

“…DNA was extracted from neonatal DBS, saliva, or buccal cells and genotyped on Illumina HumanOmniExpress or HumanOmniExpressExome genomewide SNP arrays. 26 SNP imputation was performed using Impute2, as described earlier for analysis in CCRLP. Multidimensional scaling (MDS) components were calculated using PLINK1.9 27 to control for population stratification.…”

Section: Replication and Cytogenetic Subtype Analysis In The Cclsmentioning

confidence: 99%

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BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia

Smith

Walsh

Francis

et al. 2018

Intl Journal of Cancer

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Genome-wide association studies of childhood acute lymphoblastic leukemia (ALL) have identified regions of association at PIP4K2A and upstream of BMI1 at chromosome 10p12.31-12.2. The contribution of both loci to ALL risk and underlying functional variants remain to be elucidated. We carried out single nucleotide polymorphism (SNP) imputation across chromosome 10p12.31-12.2 in Latino and non-Latino white ALL cases and controls from two independent California childhood leukemia studies, and additional Genetic Epidemiology Research on Aging study controls. Ethnicity-stratified association analyses were performed using logistic regression, with meta-analysis including 3,133 cases (1,949 Latino, 1,184 non-Latino white) and 12,135 controls (8,584 Latino, 3,551 non-Latino white). SNP associations were identified at both BMI1 and PIP4K2A. After adjusting for the lead PIP4K2A SNP, genome-wide significant associations remained at BMI1, and vice-versa (p < 10 ), supporting independent effects. Lead SNPs differed by ethnicity at both peaks. We sought functional variants in tight linkage disequilibrium with both the lead Latino SNP among Admixed Americans and lead non-Latino white SNP among Europeans. This pinpointed rs11591377 (p = 2.1 x 10 ) upstream of BMI1, residing within a hematopoietic stem cell enhancer of BMI1, and which showed significant preferential binding of the risk allele to MYBL2 (p = 1.73 x 10 ) and p300 (p = 1.55 x 10 ) transcription factors using binomial tests on ChIP-Seq data from a SNP heterozygote. At PIP4K2A, we identified rs4748812 (p = 1.3 x 10 ), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.

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Section: Methodsmentioning

confidence: 99%

Section: Replication and Cytogenetic Subtype Analysis In The Cclsmentioning

confidence: 99%