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BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia.
de Smith, Adam J; Walsh, Kyle M; Francis, Stephen S; Zhang, Chenan; Hansen, Helen M; Smirnov, Ivan; Morimoto, Libby; Whitehead, Todd P; Kang, Alice; Shao, Xiaorong; Barcellos, Lisa F; McKean-Cowdin, Roberta; Zhang, Luoping; Fu, Cecilia; Wang, Rong; Yu, Herbert; Hoh, Josephine; Dewan, Andrew T; Metayer, Catherine; Ma, Xiaomei; Wiemels, Joseph L.
Afiliación
  • de Smith AJ; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA.
  • Walsh KM; Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA.
  • Francis SS; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA.
  • Zhang C; Department of Neurosurgery, Duke University, Durham, NC.
  • Hansen HM; Department of Epidemiology, School of Community Health Sciences, University of Nevada Reno, Reno, NV.
  • Smirnov I; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA.
  • Morimoto L; Department of Neurological Surgery, University of California San Francisco, San Francisco, CA.
  • Whitehead TP; Department of Neurological Surgery, University of California San Francisco, San Francisco, CA.
  • Kang A; Department of Neurological Surgery, University of California San Francisco, San Francisco, CA.
  • Shao X; School of Public Health, University of California Berkeley, Berkeley, CA.
  • Barcellos LF; School of Public Health, University of California Berkeley, Berkeley, CA.
  • McKean-Cowdin R; School of Public Health, University of California Berkeley, Berkeley, CA.
  • Zhang L; School of Public Health, University of California Berkeley, Berkeley, CA.
  • Fu C; School of Public Health, University of California Berkeley, Berkeley, CA.
  • Wang R; Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA.
  • Yu H; School of Public Health, University of California Berkeley, Berkeley, CA.
  • Hoh J; Children's Hospital of Los Angeles, Los Angeles, CA.
  • Dewan AT; Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT.
  • Metayer C; University of Hawaii Cancer Center, Honolulu, HI.
  • Ma X; Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT.
  • Wiemels JL; Department of Chronic Diseases Epidemiology, School of Public Health, Yale University, New Haven, CT.
Int J Cancer ; 143(11): 2647-2658, 2018 12 01.
Article en En | MEDLINE | ID: mdl-29923177
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 (pmeta < 10-10 ), 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 (pmeta = 2.1 x 10-10 ) 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 10-5 ) and p300 (p = 1.55 x 10-3 ) transcription factors using binomial tests on ChIP-Seq data from a SNP heterozygote. At PIP4K2A, we identified rs4748812 (pmeta = 1.3 x 10-15 ), 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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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Cromosomas Humanos Par 10 / Fosfotransferasas (Aceptor de Grupo Alcohol) / Polimorfismo de Nucleótido Simple / Leucemia-Linfoma Linfoblástico de Células Precursoras / Estudio de Asociación del Genoma Completo / Complejo Represivo Polycomb 1 Tipo de estudio: Prognostic_studies / Risk_factors_studies Límite: Adolescent / Adult / Child / Female / Humans / Male País/Región como asunto: America do norte Idioma: En Revista: Int J Cancer Año: 2018 Tipo del documento: Article

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Cromosomas Humanos Par 10 / Fosfotransferasas (Aceptor de Grupo Alcohol) / Polimorfismo de Nucleótido Simple / Leucemia-Linfoma Linfoblástico de Células Precursoras / Estudio de Asociación del Genoma Completo / Complejo Represivo Polycomb 1 Tipo de estudio: Prognostic_studies / Risk_factors_studies Límite: Adolescent / Adult / Child / Female / Humans / Male País/Región como asunto: America do norte Idioma: En Revista: Int J Cancer Año: 2018 Tipo del documento: Article