Abstract

Recent genomic profiling of childhood acute lymphoblastic leukemia (ALL) identified a high-risk subtype with an expression signature resembling that of Philadelphia chromosome–positive ALL and poor prognosis (Ph-like ALL). However, the role of inherited genetic variation in Ph-like ALL pathogenesis remains unknown. In a genome-wide association study (GWAS) of 511 ALL cases and 6,661 non-ALL controls, we identified a susceptibility locus for Ph-like ALL (GATA3, rs3824662; P = 2.17 × 10−14, odds ratio (OR) = 3.85 for Ph-like ALL versus non-ALL; P = 1.05 × 10−8, OR = 3.25 for Ph-like ALL versus non-Ph-like ALL), with independent validation. The rs3824662 risk allele was associated with somatic lesions underlying Ph-like ALL (CRLF2 rearrangement, JAK gene mutation and IKZF1 deletion) and with variation in GATA3 expression. Finally, genotype at the GATA3 SNP was also associated with early treatment response and risk of ALL relapse. Our results provide insights into interactions between inherited and somatic variants and their role in ALL pathogenesis and prognosis.

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References

  1. 1.

    & Treatment of acute lymphoblastic leukemia. N. Engl. J. Med. 354, 166–178 (2006).

  2. 2.

    , , & Pediatric acute lymphoblastic leukemia: where are we going and how do we get there? Blood 120, 1165–1174 (2012).

  3. 3.

    et al. Improved survival for children and adolescents with acute lymphoblastic leukemia between 1990 and 2005: a report from the Children's Oncology Group. J. Clin. Oncol. 30, 1663–1669 (2012).

  4. 4.

    et al. Integrating molecular information into treatment of childhood acute lymphoblastic leukemia—a perspective from the BFM Study Group. Blood Cells Mol. Dis. 39, 160–163 (2007).

  5. 5.

    et al. Imatinib after induction for treatment of children and adolescents with Philadelphia-chromosome-positive acute lymphoblastic leukaemia (EsPhALL): a randomised, open-label, intergroup study. Lancet Oncol. 13, 936–945 (2012).

  6. 6.

    et al. A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. Lancet Oncol. 10, 125–134 (2009).

  7. 7.

    et al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell 22, 153–166 (2012).

  8. 8.

    et al. Identification of novel cluster groups in pediatric high-risk B-precursor acute lymphoblastic leukemia with gene expression profiling: correlation with genome-wide DNA copy number alterations, clinical characteristics, and outcome. Blood 116, 4874–4884 (2010).

  9. 9.

    et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N. Engl. J. Med. 360, 470–480 (2009).

  10. 10.

    et al. Rearrangement of CRLF2 is associated with mutation of JAK kinases, alteration of IKZF1, Hispanic/Latino ethnicity, and a poor outcome in pediatric B-progenitor acute lymphoblastic leukemia. Blood 115, 5312–5321 (2010).

  11. 11.

    et al. Tyrosine kinome sequencing of pediatric acute lymphoblastic leukemia: a report from the Children's Oncology Group TARGET Project. Blood 121, 485–488 (2013).

  12. 12.

    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).

  13. 13.

    et al. Variation in CDKN2A at 9p21.3 influences childhood acute lymphoblastic leukemia risk. Nat. Genet. 42, 492–494 (2010).

  14. 14.

    et al. Germline genomic variants associated with childhood acute lymphoblastic leukemia. Nat. Genet. 41, 1001–1005 (2009).

  15. 15.

    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).

  16. 16.

    et al. ARID5B genetic polymorphisms contribute to racial disparities in the incidence and treatment outcome of childhood acute lymphoblastic leukemia. J. Clin. Oncol. 30, 751–757 (2012).

  17. 17.

    et al. Genetic landscape of high hyperdiploid childhood acute lymphoblastic leukemia. Proc. Natl. Acad. Sci. USA 107, 21719–21724 (2010).

  18. 18.

    et al. JAK2 haplotype is a major risk factor for the development of myeloproliferative neoplasms. Nat. Genet. 41, 446–449 (2009).

  19. 19.

    et al. A common JAK2 haplotype confers susceptibility to myeloproliferative neoplasms. Nat. Genet. 41, 450–454 (2009).

  20. 20.

    et al. A germline JAK2 SNP is associated with predisposition to the development of JAK2V617F-positive myeloproliferative neoplasms. Nat. Genet. 41, 455–459 (2009).

  21. 21.

    et al. Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia. Nat. Genet. 43, 237–241 (2011).

  22. 22.

    et al. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol. Cell 36, 667–681 (2009).

  23. 23.

    et al. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity 35, 299–311 (2011).

  24. 24.

    , & An updated view on transcription factor GATA3-mediated regulation of Th1 and Th2 cell differentiation. Int. Immunol. 23, 415–420 (2011).

  25. 25.

    et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481, 157–163 (2012).

  26. 26.

    et al. A genome-wide association study of Hodgkin's lymphoma identifies new susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3). Nat. Genet. 42, 1126–1130 (2010).

  27. 27.

    et al. High frequency of GATA2 mutations in patients with mild chronic neutropenia evolving to MonoMac syndrome, myelodysplasia, and acute myeloid leukemia. Blood 121, 822–829 (2013).

  28. 28.

    et al. Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia. Nat. Genet. 43, 1012–1017 (2011).

  29. 29.

    et al. Pharmacogenetics of minimal residual disease response in children with B-precursor acute lymphoblastic leukemia: a report from the Children's Oncology Group. Blood 111, 2984–2990 (2008).

  30. 30.

    et al. A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc. Natl. Acad. Sci. USA 104, 9758–9763 (2007).

  31. 31.

    et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482, 390–394 (2012).

  32. 32.

    et al. Clinical significance of minimal residual disease in childhood acute lymphoblastic leukemia and its relationship to other prognostic factors: a Children's Oncology Group study. Blood 111, 5477–5485 (2008).

  33. 33.

    et al. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature 460, 753–757 (2009).

  34. 34.

    et al. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460, 748–752 (2009).

  35. 35.

    et al. Genome-wide association study implicates PARD3B-based AIDS restriction. J. Infect. Dis. 203, 1491–1502 (2011).

  36. 36.

    et al. Lower bronchodilator responsiveness in Puerto Rican than in Mexican subjects with asthma. Am. J. Respir. Crit. Care Med. 169, 386–392 (2004).

  37. 37.

    et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet. 40, 1253–1260 (2008).

  38. 38.

    , & Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

  39. 39.

    et al. A genomewide admixture mapping panel for Hispanic/Latino populations. Am. J. Hum. Genet. 80, 1171–1178 (2007).

  40. 40.

    , , & Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl. Acad. Sci. USA 99, 6567–6572 (2002).

  41. 41.

    , , & MaCH-admix: genotype imputation for admixed populations. Genet. Epidemiol. 37, 25–37 (2013).

  42. 42.

    et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics 26, 2336–2337 (2010).

  43. 43.

    et al. Outcome modeling with CRLF2, IKZF1, JAK, and minimal residual disease in pediatric acute lymphoblastic leukemia: a Children's Oncology Group study. Blood 119, 3512–3522 (2012).

  44. 44.

    & Pseudo-observations in survival analysis. Stat. Methods Med. Res. 19, 71–99 (2010).

  45. 45.

    et al. Genetic architecture of transcript-level variation in humans. Am. J. Hum. Genet. 82, 1101–1113 (2008).

  46. 46.

    et al. Common genetic variants account for differences in gene expression among ethnic groups. Nat. Genet. 39, 226–231 (2007).

  47. 47.

    et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43–49 (2011).

  48. 48.

    et al. The Human Epigenome Browser at Washington University. Nat. Methods 8, 989–990 (2011).

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Acknowledgements

We thank the patients and parents who participated in the COG protocols included in this study, the clinicians and research staff at COG institutions and J. Pullen (University of Mississippi at Jackson) for assistance in the classification of patients with ALL. Genome-wide genotyping of COG P9905 samples was performed by the Center for Molecular Medicine with generous financial support from the Jeffrey Pride Foundation and the National Childhood Cancer Foundation. V.P.-A. is supported by a Spanish Ministry of Education Fellowship Grant and by a St. Jude Children's Research Hospital Academic Programs Special Fellowship. J.J.Y. is supported by an American Society of Hematology Scholar Award, an Alex Lemonade Stand Foundation for Childhood Cancer Young Investigator Grant and by the Order of St. Francis Foundation. K.G.R. is supported by a National Health and Medical Research Council (Australia) Overseas Training Fellowship and by a Haematology Society of Australia and New Zealand Novartis New Investigator Scholarship. C.G.M. is a Pew Scholar in the Biomedical Sciences and a St. Baldrick's Scholar. We thank M. Shriver (Pennsylvania State University) for sharing SNP genotype data for the Native American references, J. Pritchard and J. Degner (University of Chicago) for sharing DNase I hypersensitivity data for HapMap YRI cell lines, R.C. Ribeiro (St. Jude Children's Research Hospital) and P. De Alarcon (University of Illinois College of Medicine at Peoria) for coordinating collaborations in Guatemala and S. Naron for her editorial assistance. This work was supported by the US National Institutes of Health (grant numbers CA156449, CA21765, CA36401, CA98543, CA114766, CA98413, CA140729 and GM92666), in part by the intramural Program of the National Cancer Institute and by the American Lebanese Syrian Associated Charities (ALSAC). Study sponsors were not directly involved in the design of the study, the collection, analysis and interpretation of data, the writing of the manuscript or the decision to submit the manuscript. Detailed acknowledgments for the dbGaP data sets are provided in the Supplementary Note.

Author information

Affiliations

  1. Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Virginia Perez-Andreu
    • , Wenjian Yang
    • , Heng Xu
    • , Shuyu E
    • , Joshua Yew-Suang Lim
    • , Colton Smith
    • , William E Evans
    • , Mary V Relling
    •  & Jun J Yang
  2. Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Kathryn G Roberts
    •  & Charles G Mullighan
  3. Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA.

    • Richard C Harvey
    • , I-Ming Chen
    •  & Cheryl L Willman
  4. Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Cheng Cheng
    •  & Deqing Pei
  5. Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.

    • Julie Gastier-Foster
  6. Department of Pediatrics, Ohio State University School of Medicine, Columbus, Ohio, USA.

    • Julie Gastier-Foster
  7. Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.

    • Joshua Yew-Suang Lim
  8. Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Yiping Fan
  9. Department of Epidemiology and Health Policy Research, University of Florida, Gainesville, Florida, USA.

    • Meenakshi Devidas
  10. Johns Hopkins Medical Institute, Baltimore, Maryland, USA.

    • Michael J Borowitz
  11. Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Geoffrey Neale
  12. Department of Bioengineering & Therapeutic Science and Medicine, University of California, San Francisco, San Francisco, California, USA.

    • Esteban G Burchard
    •  & Dara G Torgerson
  13. Unidad Nacional de Oncología Pediátrica, Guatemala City, Guatemala.

    • Federico Antillon Klussmann
    •  & Cesar Rolando Najera Villagran
  14. Department of Pediatric Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

    • Naomi J Winick
  15. Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.

    • Bruce M Camitta
  16. New York University Cancer Institute, New York, New York, USA.

    • Elizabeth Raetz
    •  & William L Carroll
  17. Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.

    • Brent Wood
  18. Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.

    • Feng Yue
  19. Maine Children's Cancer Program, Scarborough, Maine, USA.

    • Eric Larsen
  20. Department of Hematology and Oncology, Cook Children's Medical Center, Fort Worth, Texas, USA.

    • W Paul Bowman
  21. Department of Pediatrics, University of California, San Francisco, San Francisco, California, USA.

    • Mignon L Loh
  22. Laboratory of Experimental Immunology, National Cancer Institute, Frederick, Maryland, USA.

    • Michael Dean
  23. Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Deepa Bhojwani
    •  & Ching-Hon Pui
  24. Department of Hematology and Oncology, Children's Hospital Colorado, University of Colorado, Aurora, Colorado, USA.

    • Stephen P Hunger

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Contributions

J.J.Y. supervised the research. V.P.-A., S.P.H., C.L.W., C.G.M. and J.J.Y. conceived and designed the experiments. V.P.-A., K.G.R., R.C.H., J.G.-F., S.E., I.-M.C., G.N., E.G.B., D.G.T. and C.R.N.V. performed the experiments. V.P.-A., J.J.Y., R.C.H., W.Y., C.C., D.P., Y.F., M. Devidas, C.S. and G.N. performed statistical analysis. V.P.-A., K.G.R., R.C.H., W.Y., H.X., S.E., J.Y.-S.L., I.-M.C., Y.F., M.J.B., C.S., G.N., E.G.B., D.G.T., F.A.K., C.R.N.V., M.L.L., M. Devidas, D.B., C.-H.P., W.E.E., M.V.R., S.P.H., C.L.W. and C.G.M. analyzed the data. R.C.H., J.G.-F., J.Y.-S.L., Y.F., E.G.B., F.A.K., C.R.N.V., N.J.W., B.M.C., E.R., B.W., F.Y., W.L.C., E.L., W.P.B., M.L.L., M. Dean, S.P.H., C.L.W. and C.G.M. contributed reagents, materials and/or analysis tools. V.P.-A. and J.J.Y. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jun J Yang.

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https://doi.org/10.1038/ng.2803

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