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 language | English (US) |
|---|---|
| Pages (from-to) | 4884-4894 |
| Number of pages | 11 |
| Journal | Cancer Research |
| Volume | 75 |
| Issue number | 22 |
| DOIs | |
| State | Published - Nov 15 2015 |
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ASJC Scopus subject areas
- Cancer Research
- Oncology
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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 journal › Article
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TY - JOUR
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.
UR - http://www.scopus.com/inward/record.url?scp=84955275619&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84955275619&partnerID=8YFLogxK
U2 - 10.1158/0008-5472.CAN-15-1105
DO - 10.1158/0008-5472.CAN-15-1105
M3 - Article
C2 - 26527286
AN - SCOPUS:84955275619
VL - 75
SP - 4884
EP - 4894
JO - Journal of Cancer Research
JF - Journal of Cancer Research
SN - 0099-7013
IS - 22
ER -