GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes

Nature Communications

Volumn 9, Issue 1, 2018, Pages

  Wiemels, Joseph L ^a,b,c   Walsh, Kyle M ^a   De Smith, Adam J ^a   Metayer, Catherine ^d   Gonseth, Semira ^a,c   Hansen, Helen M ^a   Francis, Stephen S ^a,e   Ojha, Juhi ^a   Smirnov, Ivan ^a   Barcellos, Lisa ^d   Xiao, Xiaorong ^d   Morimoto, Libby ^d   McKean Cowdin, Roberta ^c   Wang, Rong ^f   Yu, Herbert ^g   Hoh, Josephine ^f   Dewan, Andrew T ^f   Ma, Xiaomei ^f  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF NEVADA   (United States)

^f YALE UNIVERSITY   (United States)

^g UNIVERSITY OF HAWAII CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CANCER; CHILD HEALTH; CHROMOSOME; COHORT ANALYSIS; EPIDEMIOLOGY; GENE EXPRESSION; GENETIC ANALYSIS;

ACUTE LYMPHOBLASTIC LEUKEMIA; ARTICLE; CASE CONTROL STUDY; CELL MATURATION; CHILD; CHILDHOOD LEUKEMIA; CHROMOSOME 17Q; CHROMOSOME 8Q; CONTROLLED STUDY; FEMALE; FUNCTIONAL ASSESSMENT; GENE; GENE EXPRESSION; GENE INTERACTION; GENE LOCUS; GENETIC ASSOCIATION; GENOME-WIDE ASSOCIATION STUDY; GROWTH REGULATION; GSDMB GENE; HEMATOPOIESIS; HUMAN; IKZF3 GENE; LYMPHOCYTE; MAJOR CLINICAL STUDY; MALE; NEWBORN; ONCOGENE MYC; ORMDL3 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; ZPBP2 GENE; ADOLESCENT; CALIFORNIA; CHROMOSOME 17; CHROMOSOME 8; ETHNOLOGY; GENE FREQUENCY; GENETIC PREDISPOSITION; GENETICS; HISPANIC; INFANT; PRESCHOOL CHILD; RISK FACTOR;

CALIFORNIA; UNITED STATES;

ADOLESCENT; CALIFORNIA; CHILD, PRESCHOOL; CHROMOSOMES, HUMAN, PAIR 17; CHROMOSOMES, HUMAN, PAIR 8; FEMALE; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HISPANIC AMERICANS; HUMANS; INFANT; INFANT, NEWBORN; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; RISK FACTORS;

EID: 85040778292     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-017-02596-9     Document Type: Article

References (51)

1. Zhang, J. et al. Germline mutations in predisposition genes in pediatric cancer. N. Engl. J. Med. 373, 2336-2346 (2015).
2. Papaemmanuil, E. et al. Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia. Nat. Genet. 41, 1006-1010 (2009).
3. Perez-Andreu, V. et al. Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse. Nat. Genet. 45, 1494-1498 (2013).
4. Trevino, L. R. et al. Germline genomic variants associated with childhood acute lymphoblastic leukemia. Nat. Genet. 41, 1001-1005 (2009).
5. Xu, H. et al. Novel susceptibility variants at 10p12.31-12.2 for childhood acute lymphoblastic leukemia in ethnically diverse populations. J. Natl. Cancer Inst. 105, 733-742 (2013).
6. Vijayakrishnan, J. et al. A genome-wide association study identifies risk loci for childhood acute lymphoblastic leukemia at 10q26.13 and 12q23.1. Leukemia 31, 573-579 (2017).
7. Xu, H. et al. Inherited coding variants at the CDKN2A locus influence susceptibility to acute lymphoblastic leukaemia in children. Nat. Commun. 6, 7553 (2015).
8. Vijayakrishnan, J. et al. The 9p21.3 risk of childhood acute lymphoblastic leukaemia is explained by a rare high-impact variant in CDKN2A. Sci. Rep. 5, 15065 (2015).
9. Walsh, K. M. et al. A heritable missense polymorphism in CDKN2A confers strong risk of childhood acute lymphoblastic leukemia and is preferentially selected during clonal evolution. Cancer Res. 75, 4884-4894 (2015).
10. Wiemels, J. L. et al. A functional polymorphism in the CEBPE gene promoter influences acute lymphoblastic leukemia risk through interaction with the hematopoietic transcription factor Ikaros. Leukemia 30, 1194-1197 (2016).
11. Studd, J. B. et al. Genetic and regulatory mechanism of susceptibility to high-hyperdiploid acute lymphoblastic leukaemia at 10p21.2. Nat. Commun. 8, 14616 (2017).
12. Steliarova-Foucher, E. et al. International incidence of childhood cancer, 2001-10: a population-based registry study. Lancet Oncol. 18, 719-731 (2017).
13. 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68-74 (2015).
14. Ludwig, K. U. et al. Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci. Nat. Genet. 44, 968-971 (2012).
15. Geller, F. et al. Genome-wide association analyses identify variants in developmental genes associated with hypospadias. Nat. Genet. 46, 957-963 (2014).
16. van der Valk, R. J. et al. A novel common variant in DCST2 is associated with length in early life and height in adulthood. Hum. Mol. Genet. 24, 1155-1168 (2015).
17. Stadler, Z. K. et al. Genome-wide association studies of cancer. J. Clin. Oncol. 28, 4255-4267 (2010).
18. Ayabe, T. et al. Variants associated with autoimmune Type 1 diabetes in Japanese children: implications for age-specific effects of cis-regulatory haplotypes at 17q12-q21. Diabet. Med. 33, 1717-1722 (2016).
19. Moffatt, M. F. et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448, 470-473 (2007).
20. Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014).
21. Liu, X. et al. Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis. Nat. Genet. 42, 658-660 (2010).
22. Martin, J. E. et al. A systemic sclerosis and systemic lupus erythematosus pan-meta-GWAS reveals new shared susceptibility loci. Hum. Mol. Genet. 22, 4021-4029 (2013).
23. Barrett, J. C. et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat. Genet. 40, 955-962 (2008).
24. McGovern, D. P. et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat. Genet. 42, 332-337 (2010).
25. Swafford, A. D. et al. An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes. Diabetes 60, 1041-1044 (2011).
26. Chang, J. S., Tsai, C. R., Tsai, Y. W. & Wiemels, J. L. Medically diagnosed infections and risk of childhood leukaemia: a population-based case-control study. Int. J. Epidemiol. 41, 1050-1059 (2012).
27. Crouch, S. et al. Infectious illness in children subsequently diagnosed with acute lymphoblastic leukemia: modeling the trends from birth to diagnosis. Am. J. Epidemiol. 176, 402-408 (2012).
28. Urayama, K., Buffler, P., Gallagher, E., Ayoob, J. & Ma, X. A meta-analysis of the association between day-care attendance and childhood acute lymphoblastic leukemia. Int. J. Epidemiol. 39, 718-732 (2010).
29. Berlivet, S. et al. Interaction between genetic and epigenetic variation defines gene expression patterns at the asthma-associated locus 17q12-q21 in lymphoblastoid cell lines. Hum. Genet. 131, 1161-1171 (2012).
30. Verlaan, D. J. et al. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Am. J. Hum. Genet. 85, 377-393 (2009).
31. Holmfeldt, L. et al. The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat. Genet. 45, 242-252 (2013).
32. Boi, M., Zucca, E., Inghirami, G. & Bertoni, F. PRDM1/BLIMP1: a tumor suppressor gene in B and T cell lymphomas. Leuk. Lymphoma 56, 1223-1228 (2015).
33. Aglietti, R. A. & Dueber, E. C. Recent insights into the molecular mechanisms underlying pyroptosis and gasdermin family functions. Trends Immunol. 38, 261-271 (2017).
34. Cole, M. D. MYC association with cancer risk and a new model of MYC-mediated repression. Cold Spring Harb. Perspect. Med. 4, a014316 (2014).
35. Hoffmann, T. J. et al. Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm. Genomics 98, 422-430 (2011).
36. Dilthey, A. et al. Multi-population classical HLA type imputation. PLoS Comput. Biol. 9, e1002877 (2013).
37. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
38. Lee, P., Bhansali, R., Izraeli, S., Hijiya, N. & Crispino, J. D. The biology, pathogenesis and clinical aspects of acute lymphoblastic leukemia in children with Down syndrome. Leukemia 30, 1816-1823 (2016).
39. Pe'er, I., Yelensky, R., Altshuler, D. & Daly, M. J. Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet. Epidemiol. 32, 381-385 (2008).
40. Yang, J. J. et al. Genome-wide association study identifies germline polymorphisms associated with relapse of childhood acute lymphoblastic leukemia. Blood 120, 4197-4204 (2012).
41. Wellcome Trust Case-Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature 447, 661-678 (2007).
42. Howie, B. N., Donnelly, P. & Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529 (2009).
43. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
44. Marchini, J. & Howie, B. Genotype imputation for genome-wide association studies. Nat. Rev. Genet. 11, 499-511 (2010).
45. Liu, J. Z. et al. Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nat. Genet. 42, 436-440 (2010).
46. Higgins, J. P., Thompson, S. G., Deeks, J. J. & Altman, D. G. Measuring inconsistency in meta-analyses. BMJ 327, 557-560 (2003).
47. GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580-585 (2013).
48. Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506-511 (2013).
49. Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99-101 (2016).
50. Boyle, A. P. et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 22, 1790-1797 (2012).
51. Ward, L. D. & Kellis, M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 40, D930-D934 (2012).