A heritable missense polymorphism in CDKN2A confers strong risk of childhood acute lymphoblastic leukemia and is preferentially selected during clonal evolution

Kyle M. Walsh, Adam J. De Smith, Helen M. Hansen, Ivan V. Smirnov, Semira Gonseth, Alyson A. Endicott, Jianqiao Xiao, Terri Rice, Cecilia H. Fu, Lucie S. McCoy, Daniel H Lachance, Jeanette E Eckel-Passow, John K. Wiencke, Robert Brian Jenkins, Margaret R. Wrensch, Xiaomei Ma, Catherine Metayer, Joseph L. Wiemels

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Abstract

Genome-wide association studies (GWAS) have identified SNPs in six genes that are associated with childhood acute lymphoblastic leukemia (ALL). A lead SNP was found to occur on chromosome 9p21.3, a region that is deleted in 30% of childhood ALLs, suggesting the presence of causal polymorphisms linked to ALL risk. We used SNP genotyping and imputation-based fine-mapping of a multiethnic ALL case-control population (Ncases = 1,464, Ncontrols = 3,279) to identify variants of large effect within 9p21.3. We identified a CDKN2A missense variant (rs3731249) with 2% allele frequency in controls that confers three-fold increased risk of ALL in children of European ancestry (OR, 2.99; P = 1.51 × 10-9) and Hispanic children (OR, 2.77; P = 3.78 × 10-4). Moreover, of 17 patients whose tumors displayed allelic imbalance at CDKN2A, 14 preferentially retained the risk allele and lost the protective allele (PBinomial = 0.006), suggesting that the risk allele provides a selective advantage during tumor growth. Notably, the CDKN2A variant was not significantly associated with melanoma, glioblastoma, or pancreatic cancer risk, implying that this polymorphism specifically confers ALL risk but not general cancer risk. Taken together, our findings demonstrate that coding polymorphisms of large effect can underlie GWAS "hits" and that inherited polymorphisms may undergo directional selection during clonal expansion of tumors.

Original languageEnglish (US)
Pages (from-to)4884-4894
Number of pages11
JournalCancer Research
Volume75
Issue number22
DOIs
StatePublished - Nov 15 2015

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Clonal Evolution
Precursor Cell Lymphoblastic Leukemia-Lymphoma
Single Nucleotide Polymorphism
Genome-Wide Association Study
Alleles
Neoplasms
Allelic Imbalance
Glioblastoma
Pancreatic Neoplasms
Hispanic Americans
Gene Frequency
Melanoma
Chromosomes
Growth

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

A heritable missense polymorphism in CDKN2A confers strong risk of childhood acute lymphoblastic leukemia and is preferentially selected during clonal evolution. / Walsh, Kyle M.; De Smith, Adam J.; Hansen, Helen M.; Smirnov, Ivan V.; Gonseth, Semira; Endicott, Alyson A.; Xiao, Jianqiao; Rice, Terri; Fu, Cecilia H.; McCoy, Lucie S.; Lachance, Daniel H; Eckel-Passow, Jeanette E; Wiencke, John K.; Jenkins, Robert Brian; Wrensch, Margaret R.; Ma, Xiaomei; Metayer, Catherine; Wiemels, Joseph L.

In: Cancer Research, Vol. 75, No. 22, 15.11.2015, p. 4884-4894.

Research output: Contribution to journalArticle

Walsh, KM, De Smith, AJ, Hansen, HM, Smirnov, IV, Gonseth, S, Endicott, AA, Xiao, J, Rice, T, Fu, CH, McCoy, LS, Lachance, DH, Eckel-Passow, JE, Wiencke, JK, Jenkins, RB, Wrensch, MR, Ma, X, Metayer, C & Wiemels, JL 2015, 'A heritable missense polymorphism in CDKN2A confers strong risk of childhood acute lymphoblastic leukemia and is preferentially selected during clonal evolution', Cancer Research, vol. 75, no. 22, pp. 4884-4894. https://doi.org/10.1158/0008-5472.CAN-15-1105
Walsh, Kyle M. ; De Smith, Adam J. ; Hansen, Helen M. ; Smirnov, Ivan V. ; Gonseth, Semira ; Endicott, Alyson A. ; Xiao, Jianqiao ; Rice, Terri ; Fu, Cecilia H. ; McCoy, Lucie S. ; Lachance, Daniel H ; Eckel-Passow, Jeanette E ; Wiencke, John K. ; Jenkins, Robert Brian ; Wrensch, Margaret R. ; Ma, Xiaomei ; Metayer, Catherine ; Wiemels, Joseph L. / A heritable missense polymorphism in CDKN2A confers strong risk of childhood acute lymphoblastic leukemia and is preferentially selected during clonal evolution. In: Cancer Research. 2015 ; Vol. 75, No. 22. pp. 4884-4894.
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title = "A heritable missense polymorphism in CDKN2A confers strong risk of childhood acute lymphoblastic leukemia and is preferentially selected during clonal evolution",
abstract = "Genome-wide association studies (GWAS) have identified SNPs in six genes that are associated with childhood acute lymphoblastic leukemia (ALL). A lead SNP was found to occur on chromosome 9p21.3, a region that is deleted in 30{\%} of childhood ALLs, suggesting the presence of causal polymorphisms linked to ALL risk. We used SNP genotyping and imputation-based fine-mapping of a multiethnic ALL case-control population (Ncases = 1,464, Ncontrols = 3,279) to identify variants of large effect within 9p21.3. We identified a CDKN2A missense variant (rs3731249) with 2{\%} allele frequency in controls that confers three-fold increased risk of ALL in children of European ancestry (OR, 2.99; P = 1.51 × 10-9) and Hispanic children (OR, 2.77; P = 3.78 × 10-4). Moreover, of 17 patients whose tumors displayed allelic imbalance at CDKN2A, 14 preferentially retained the risk allele and lost the protective allele (PBinomial = 0.006), suggesting that the risk allele provides a selective advantage during tumor growth. Notably, the CDKN2A variant was not significantly associated with melanoma, glioblastoma, or pancreatic cancer risk, implying that this polymorphism specifically confers ALL risk but not general cancer risk. Taken together, our findings demonstrate that coding polymorphisms of large effect can underlie GWAS {"}hits{"} and that inherited polymorphisms may undergo directional selection during clonal expansion of tumors.",
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T1 - A heritable missense polymorphism in CDKN2A confers strong risk of childhood acute lymphoblastic leukemia and is preferentially selected during clonal evolution

AU - Walsh, Kyle M.

AU - De Smith, Adam J.

AU - Hansen, Helen M.

AU - Smirnov, Ivan V.

AU - Gonseth, Semira

AU - Endicott, Alyson A.

AU - Xiao, Jianqiao

AU - Rice, Terri

AU - Fu, Cecilia H.

AU - McCoy, Lucie S.

AU - Lachance, Daniel H

AU - Eckel-Passow, Jeanette E

AU - Wiencke, John K.

AU - Jenkins, Robert Brian

AU - Wrensch, Margaret R.

AU - Ma, Xiaomei

AU - Metayer, Catherine

AU - Wiemels, Joseph L.

PY - 2015/11/15

Y1 - 2015/11/15

N2 - Genome-wide association studies (GWAS) have identified SNPs in six genes that are associated with childhood acute lymphoblastic leukemia (ALL). A lead SNP was found to occur on chromosome 9p21.3, a region that is deleted in 30% of childhood ALLs, suggesting the presence of causal polymorphisms linked to ALL risk. We used SNP genotyping and imputation-based fine-mapping of a multiethnic ALL case-control population (Ncases = 1,464, Ncontrols = 3,279) to identify variants of large effect within 9p21.3. We identified a CDKN2A missense variant (rs3731249) with 2% allele frequency in controls that confers three-fold increased risk of ALL in children of European ancestry (OR, 2.99; P = 1.51 × 10-9) and Hispanic children (OR, 2.77; P = 3.78 × 10-4). Moreover, of 17 patients whose tumors displayed allelic imbalance at CDKN2A, 14 preferentially retained the risk allele and lost the protective allele (PBinomial = 0.006), suggesting that the risk allele provides a selective advantage during tumor growth. Notably, the CDKN2A variant was not significantly associated with melanoma, glioblastoma, or pancreatic cancer risk, implying that this polymorphism specifically confers ALL risk but not general cancer risk. Taken together, our findings demonstrate that coding polymorphisms of large effect can underlie GWAS "hits" and that inherited polymorphisms may undergo directional selection during clonal expansion of tumors.

AB - Genome-wide association studies (GWAS) have identified SNPs in six genes that are associated with childhood acute lymphoblastic leukemia (ALL). A lead SNP was found to occur on chromosome 9p21.3, a region that is deleted in 30% of childhood ALLs, suggesting the presence of causal polymorphisms linked to ALL risk. We used SNP genotyping and imputation-based fine-mapping of a multiethnic ALL case-control population (Ncases = 1,464, Ncontrols = 3,279) to identify variants of large effect within 9p21.3. We identified a CDKN2A missense variant (rs3731249) with 2% allele frequency in controls that confers three-fold increased risk of ALL in children of European ancestry (OR, 2.99; P = 1.51 × 10-9) and Hispanic children (OR, 2.77; P = 3.78 × 10-4). Moreover, of 17 patients whose tumors displayed allelic imbalance at CDKN2A, 14 preferentially retained the risk allele and lost the protective allele (PBinomial = 0.006), suggesting that the risk allele provides a selective advantage during tumor growth. Notably, the CDKN2A variant was not significantly associated with melanoma, glioblastoma, or pancreatic cancer risk, implying that this polymorphism specifically confers ALL risk but not general cancer risk. Taken together, our findings demonstrate that coding polymorphisms of large effect can underlie GWAS "hits" and that inherited polymorphisms may undergo directional selection during clonal expansion of tumors.

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