Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype by Gabriele Migliorini, Bettina Fiege, Fay.

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Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype by Gabriele Migliorini, Bettina Fiege, Fay J. Hosking, Yussanne Ma, Rajiv Kumar, Amy L. Sherborne, Miguel Inacio da Silva Filho, Jayaram Vijayakrishnan, Rolf Koehler, Hauke Thomsen, Julie A. Irving, James M. Allan, Tracy Lightfoot, Eve Roman, Sally E. Kinsey, Eamonn Sheridan, Pamela Thompson, Per Hoffmann, Markus M. Nöthen, Thomas W. Mühleisen, Lewin Eisele, Martin Zimmermann, Claus R. Bartram, Martin Schrappe, Mel Greaves, Martin Stanulla, Kari Hemminki, and Richard S. Houlston Blood Volume 122(19):3298-3307 November 7, 2013 ©2013 by American Society of Hematology

Forest plots of ORs for ALL associated with rs10828317 (PIP4K2A) and rs3824662 (GATA3) genotype. Forest plots of ORs for ALL associated with rs10828317 (PIP4K2A) and rs3824662 (GATA3) genotype. ORs for all BCP-ALL (A-B), TEL-AML ALL (C-D), HD ALL (E-F), non–HD/TEL-AML ALL (G-H). Gabriele Migliorini et al. Blood 2013;122:3298-3307 ©2013 by American Society of Hematology

Regional plots of association results, recombination rates, and chromatin state segmentation track for (A) 10p12.2 and (B) 10p14 susceptibility loci. Regional plots of association results, recombination rates, and chromatin state segmentation track for (A) 10p12.2 and (B) 10p14 susceptibility loci. The top panel shows the association results of both genotyped (triangles) and imputed (circles) SNPs in the GWAS samples and recombination rates for rates within the two loci. For each plot, −log10P values (y-axis) of the SNPs are shown according to their chromosomal positions (x-axis). The top genotyped SNP in each combined analysis is a large triangle and is labeled by its reference SNP ID. The color intensity of each symbol reflects the extent of LD with the top genotyped SNP: white (r2 = 0) through to dark red (r2 = 1.0). Genetic recombination rates (cM/Mb), estimated using HapMap CEU samples, are shown with a light blue line. Physical positions are based on National Centre for Biotechnology Information build 36 of the human genome. Also shown are the relative positions of genes and transcripts mapping to each region of association. Genes have been redrawn to show the relative positions; therefore, maps are not to physical scale. The lower panel shows the gene of interest together with all transcripts of the gene showing exons and introns; observed SNP and any imputed SNPs showing a stronger association with ALL risk, chromatin state segmentation track (ChromHMM), and phastCons score values corresponding to the posterior probability associated with a phylogenetic hidden Markov model (HMM) inferring the most conserved state at a given base position. Gabriele Migliorini et al. Blood 2013;122:3298-3307 ©2013 by American Society of Hematology

Cumulative effects of the 6 BCP-ALL risk alleles (rs4132601, IKZF1; rs7089424, ARID5B; rs2239633, CEBPE; rs3731217, CDKN2A/CDKN2B; rs10828317, PIP4K2A, and rs3824662, GATA3). Cumulative effects of the 6 BCP-ALL risk alleles (rs4132601, IKZF1; rs7089424, ARID5B; rs2239633, CEBPE; rs3731217, CDKN2A/CDKN2B; rs10828317, PIP4K2A, and rs3824662, GATA3). (A) Distribution of risk alleles in controls (black) and ALL cases (grey). (B) Plot of the increasing ORs for BCP-ALL with increasing number of risk alleles. The ORs are relative to the median number of 6 risk alleles; vertical bars correspond to 95% confidence intervals. The distribution of risk alleles follows a normal distribution in both cases and controls, with a shift toward a higher number of risk alleles in cases. Horizontal line denotes the null value (OR = 1.0). Gabriele Migliorini et al. Blood 2013;122:3298-3307 ©2013 by American Society of Hematology

Kaplan-Meir curves of event-free survivorship in BCP-ALL patients. Kaplan-Meir curves of event-free survivorship in BCP-ALL patients. (A-C) Stratified by rs3824662 (10p14) genotype: (A) German GWAS, (B) replication, and (C) combined. (D-F) Stratified by rs10828317 (10p12.2) genotype: (D) German GWAS, (E) replication, and (F) combined. Gabriele Migliorini et al. Blood 2013;122:3298-3307 ©2013 by American Society of Hematology