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Grant Details

Grant Number: 5R01CA155461-03 Interpret this number
Primary Investigator: Wiemels, Joseph
Organization: University Of California, San Francisco
Project Title: Genome-Wide Association Study of Childhood Leukemia By Hispanic Status
Fiscal Year: 2013
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Abstract

DESCRIPTION (provided by applicant): Although acute lymphoblastic leukemia (ALL) is the most common malignancy in children (0 - 14 years), there are few known risk factors. In the United States, Hispanic children have higher incidence of ALL than any other ethnic/racial groups; they have 1.3 times of the risk for ALL than non-Hispanic white children. Two small genome-wide association studies (GWAS) recently identified 2-3 genetic risk factors for childhood ALL, but only in European white populations with non-population based ascertainment. High birth weight and other markers of fetal growth have been consistently linked to an increased risk of childhood ALL in most studies, and Hispanics appear to have accelerated fetal growth early on during pregnancy. In the current application, we seek to significantly advance leukemia research by clarifying the roles of genetic susceptibility and fetal growth in the etiology of childhood ALL in a large population-based sample of Hispanics and non-Hispanic whites in California, using high dimension arrays specifically designed for the two ethnic groups. We will (1) link California birth records with California Cancer Registry data (1988 - 2008) to assemble a population-based case-control study with an unprecedented size (4,000 cases and 4,000 controls, about half of which will be Hispanics and half non-Hispanic whites); (2) obtain the archived neonatal dried blood spots of all cases and controls from the California Department of Public Health; (3) genotype the study population with custom Affymetrix whole genome arrays designed for the California population, with optimized designs for Hispanics and non-Hispanic whites separately; (4) use data from these cases and controls to identify distinct and shared genetic risk alleles for Hispanics and non-Hispanic whites; and (5) validate top GWAS hits in the California Childhood Leukemia Study (an ongoing NIH-funded case-control study with a separate and distinct subject ascertainment, >1000 cases, > 1000 controls, approximately half of which will be Hispanics and half non- Hispanic whites) and in a Brazilian childhood leukemia study with Latin American cases (n = 200) and controls (n = 400). In addition, we will utilize data on the characteristics of all births in California during 1988 - 2008 to develop an algorithm to predict birth weight based on factors such as gestational age, gender, birth order, parental race, parental Hispanic status, and parental ages, and calculate a proportion of expected birth weight (PEBW) for all cases and controls (n = 8000) by dividing their actual observed birth weight by the expected birth weight derived from the algorithm. Subsequently, we will determine whether the PEBW or birth weight is associated with (i) childhood ALL, (ii) the top GWAS hits, and (iii) the SNPs in genes potentially related to fetal growth, in Hispanics and non-Hispanic whites separately. Given the unprecedented sample size, especially the large number of Hispanics included, and ethnic-specific genotyping panels with great genome coverage, this study will clarify the role of genetic susceptibility in childhood ALL, the mechanism involving fetal growth, and in the process identify potential reasons for the puzzling ethnic difference in disease incidence.

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Publications

Genomic ancestry and somatic alterations correlate with age at diagnosis in Hispanic children with B-cell acute lymphoblastic leukemia.
Authors: Walsh KM, de Smith AJ, Welch TC, Smirnov I, Cunningham MJ, Ma X, Chokkalingam AP, Dahl GV, Roberts W, Barcellos LF, Buffler PA, Metayer C, Wiemels JL
Source: Am J Hematol, 2014 Jul;89(7), p. 721-5.
EPub date: 2014 Apr 18.
PMID: 24753091
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The role of KIR genes and their cognate HLA class I ligands in childhood acute lymphoblastic leukemia.
Authors: de Smith AJ, Walsh KM, Ladner MB, Zhang S, Xiao C, Cohen F, Moore TB, Chokkalingam AP, Metayer C, Buffler PA, Trachtenberg EA, Wiemels JL
Source: Blood, 2014 Apr 17;123(16), p. 2497-503.
EPub date: 2014 Feb 11.
PMID: 24518758
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PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia.
Authors: Xiao J, Lee ST, Xiao Y, Ma X, Houseman EA, Hsu LI, Roy R, Wrensch M, de Smith AJ, Chokkalingam A, Buffler P, Wiencke JK, Wiemels JL
Source: Int J Cancer, 2014 Sep 1;135(5), p. 1101-9.
EPub date: 2014 Feb 19.
PMID: 24496747
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Associations between genome-wide Native American ancestry, known risk alleles and B-cell ALL risk in Hispanic children.
Authors: Walsh KM, Chokkalingam AP, Hsu LI, Metayer C, de Smith AJ, Jacobs DI, Dahl GV, Loh ML, Smirnov IV, Bartley K, Ma X, Wiencke JK, Barcellos LF, Wiemels JL, Buffler PA
Source: Leukemia, 2013 Dec;27(12), p. 2416-9.
EPub date: 2013 Apr 25.
PMID: 23615557
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A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network.
Authors: Lee ST, Xiao Y, Muench MO, Xiao J, Fomin ME, Wiencke JK, Zheng S, Dou X, de Smith A, Chokkalingam A, Buffler P, Ma X, Wiemels JL
Source: Nucleic Acids Res, 2012 Dec;40(22), p. 11339-51.
EPub date: 2012 Oct 16.
PMID: 23074194
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Perspectives on the causes of childhood leukemia.
Authors: Wiemels J
Source: Chem Biol Interact, 2012 Apr 5;196(3), p. 59-67.
EPub date: 2012 Feb 2.
PMID: 22326931
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Profound deficit of IL10 at birth in children who develop childhood acute lymphoblastic leukemia.
Authors: Chang JS, Zhou M, Buffler PA, Chokkalingam AP, Metayer C, Wiemels JL
Source: Cancer Epidemiol Biomarkers Prev, 2011 Aug;20(8), p. 1736-40.
EPub date: 2011 Jun 8.
PMID: 21653647
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Unusual space-time patterning of the Fallon, Nevada leukemia cluster: Evidence of an infectious etiology.
Authors: Francis SS, Selvin S, Yang W, Buffler PA, Wiemels JL
Source: Chem Biol Interact, 2012 Apr 5;196(3), p. 102-9.
EPub date: 2011 Feb 23.
PMID: 21352818
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