Nonsyndromic cleft lip with or without cleft palate and cancer: Evaluation of a possible common genetic background through the analysis of GWAS data

Eva Dunkhase; Kerstin U. Ludwig; Michael Knapp; Christine F. Skibola; Jane C. Figueiredo; Fay Julie Hosking; Eva Ellinghaus; Maria Teresa Landi; Hongxia Ma; Hidewaki Nakagawa; Jong Won Kim; Jiali Han; Ping Yang; Anne C. Böhmer; Manuel Mattheisen; Markus M. Nöthen; Elisabeth Mangold

doi:10.1016/j.gdata.2016.08.017

Nonsyndromic cleft lip with or without cleft palate and cancer: Evaluation of a possible common genetic background through the analysis of GWAS data

Eva Dunkhase, Kerstin U. Ludwig, Michael Knapp, Christine F. Skibola, Jane C. Figueiredo, Fay Julie Hosking, Eva Ellinghaus, Maria Teresa Landi, Hongxia Ma, Hidewaki Nakagawa, Jong Won Kim, Jiali Han, Ping Yang, Anne C. Böhmer, Manuel Mattheisen, Markus M. Nöthen, Elisabeth Mangold

Quantitative Health Sciences

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Abstract

Previous research suggests a genetic overlap between nonsyndromic cleft lip with or without cleft palate (NSCL/P) and cancer. The aim of the present study was to identify common genetic risk loci for NSCL/P and cancer entities that have been reported to co-occur with orofacial clefting. This was achieved through the investigation of large genome-wide association study datasets. Investigations of 12 NSCL/P single nucleotide polymorphisms (SNPs) in 32 cancer datasets, and 204 cancer SNPs in two NSCL/P datasets, were performed. The SNPs rs13041247 (20q12) and rs6457327 (6p21.33) showed suggestive evidence for an association with both NSCL/P and a specific cancer entity. These loci harbor genes of biological relevance to oncogenesis (MAFB and OCT4, respectively). This study is the first to characterize possible pleiotropic risk loci for NSCL/P and cancer in a systematic manner. The data represent a starting point for future research by identifying a genetic link between NSCL/P and cancer.

Original language	English (US)
Pages (from-to)	22-29
Number of pages	8
Journal	Genomics Data
Volume	10
DOIs	https://doi.org/10.1016/j.gdata.2016.08.017
State	Published - Dec 1 2016

Keywords

Cancer
Cleft lip
Cleft palate
Genome-wide association study
Single nucleotide polymorphism

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Medicine
Genetics

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10.1016/j.gdata.2016.08.017

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Dunkhase, E., Ludwig, K. U., Knapp, M., Skibola, C. F., Figueiredo, J. C., Hosking, F. J., Ellinghaus, E., Landi, M. T., Ma, H., Nakagawa, H., Kim, J. W., Han, J., Yang, P., Böhmer, A. C., Mattheisen, M., Nöthen, M. M., & Mangold, E. (2016). Nonsyndromic cleft lip with or without cleft palate and cancer: Evaluation of a possible common genetic background through the analysis of GWAS data. Genomics Data, 10, 22-29. https://doi.org/10.1016/j.gdata.2016.08.017

Dunkhase, E, Ludwig, KU, Knapp, M, Skibola, CF, Figueiredo, JC, Hosking, FJ, Ellinghaus, E, Landi, MT, Ma, H, Nakagawa, H, Kim, JW, Han, J, Yang, P, Böhmer, AC, Mattheisen, M, Nöthen, MM & Mangold, E 2016, 'Nonsyndromic cleft lip with or without cleft palate and cancer: Evaluation of a possible common genetic background through the analysis of GWAS data', Genomics Data, vol. 10, pp. 22-29. https://doi.org/10.1016/j.gdata.2016.08.017

@article{281a9f2e8b004490ac322e65c5ce3b6c,

title = "Nonsyndromic cleft lip with or without cleft palate and cancer: Evaluation of a possible common genetic background through the analysis of GWAS data",

abstract = "Previous research suggests a genetic overlap between nonsyndromic cleft lip with or without cleft palate (NSCL/P) and cancer. The aim of the present study was to identify common genetic risk loci for NSCL/P and cancer entities that have been reported to co-occur with orofacial clefting. This was achieved through the investigation of large genome-wide association study datasets. Investigations of 12 NSCL/P single nucleotide polymorphisms (SNPs) in 32 cancer datasets, and 204 cancer SNPs in two NSCL/P datasets, were performed. The SNPs rs13041247 (20q12) and rs6457327 (6p21.33) showed suggestive evidence for an association with both NSCL/P and a specific cancer entity. These loci harbor genes of biological relevance to oncogenesis (MAFB and OCT4, respectively). This study is the first to characterize possible pleiotropic risk loci for NSCL/P and cancer in a systematic manner. The data represent a starting point for future research by identifying a genetic link between NSCL/P and cancer.",

keywords = "Cancer, Cleft lip, Cleft palate, Genome-wide association study, Single nucleotide polymorphism",

author = "Eva Dunkhase and Ludwig, {Kerstin U.} and Michael Knapp and Skibola, {Christine F.} and Figueiredo, {Jane C.} and Hosking, {Fay Julie} and Eva Ellinghaus and Landi, {Maria Teresa} and Hongxia Ma and Hidewaki Nakagawa and Kim, {Jong Won} and Jiali Han and Ping Yang and B{\"o}hmer, {Anne C.} and Manuel Mattheisen and N{\"o}then, {Markus M.} and Elisabeth Mangold",

note = "Funding Information: We thank all affected individuals and their families for their participation in this study, as well as the German support group for persons with cleft lip and/or palate (Deutsche Selbsthilfevereinigung f{\"u}r Lippen-Gaumen-Fehlbildungen e.V.).The study was supported by the Deutsche Forschungsgemeinschaft (FOR 423 and individual grants MA 2546/3-1 , KR 1912/7-1 , NO 246/6-1 and WI 1555/5-1 ). In particular, we thank the following researchers for the provision of data: deCODE Genetics (Reykjavik, Iceland); Victor Enciso (The Institute of Cancer Research, Sutton, Surrey, UK); Susan L. Slager (Mayo Clinic, Rochester, MN, USA); and Peter Kraft (Harvard School of Public Health, Boston, MA, USA). The study was also supported by Richard S. Houlston (The Institute of Cancer Research , Sutton, Surrey, UK); Noralane M. Lindor ( Mayo Clinic , Department of Health Sciences Research, Mayo Clinic Arizona, USA); and Zhibin Hu and Hongbing Shen of Nanjing Medical University . Funding Information: PLCO: Intramural Research Program of the Division of Cancer Epidemiology and Genetics and supported by contracts from the Division of Cancer Prevention, National Cancer Institute, NIH, DHHS. Additionally, a subset of control samples were genotyped as part of the Cancer Genetic Markers of Susceptibility (CGEMS) Prostate Cancer GWAS (Yeager, M et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007 May;39(5):645-9), Colon CGEMS pancreatic cancer scan (PanScan) (Amundadottir, L et al. Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. Nat Genet. 2009 Sep;41(9):986-90, and Petersen, GM et al. A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. Nat Genet. 2010 Mar;42(3):224-8), and the Lung Cancer and Smoking study (Landi MT, et al. A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am J Hum Genet. 2009 Nov;85(5):679-91). The prostate and PanScan study datasets were accessed with appropriate approval through the dbGaP online resource ( http://cgems.cancer.gov/data/ ) accession numbers phs000207.v1.p1 and phs000206.v3.p2, respectively, and the lung datasets were accessed from the dbGaP website ( http://www.ncbi.nlm.nih.gov/gap ) through accession number phs000093.v2.p2. Funding for the Lung Cancer and Smoking study was provided by National Institutes of Health (NIH), Genes, Environment and Health Initiative (GEI) Z01 CP 010200, NIH U01 HG004446, and NIH GEI U01 HG 004438. For the lung study, the GENEVA Coordinating Center provided assistance with genotype cleaning and general study coordination, and the Johns Hopkins University Center for Inherited Disease Research conducted genotyping. Funding Information: The Colon CFR GWAS was supported by funding from the National Cancer Institute, National Institutes of Health (U01 CA122839 and R01 CA143237 to Graham Casey). The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the Colon Cancer Family Registry (CCFR), nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government or the CCFR. Funding Information: OFCCR: National Institutes of Health, through funding allocated to the Ontario Registry for Studies of Familial Colorectal Cancer (U01 CA074783); see CCFR section above. Additional funding toward genetic analyses of OFCCR includes the Ontario Research Fund, the Canadian Institutes of Health Research, and the Ontario Institute for Cancer Research, through generous support from the Ontario Ministry of Research and Innovation. Funding Information: HPFS is supported by the National Institutes of Health (P01 CA 055075, UM1 CA167552, R01 137178, R01 CA151993 and P50 CA127003), NHS by the National Institutes of Health (UM1 CA186107, R01 CA137178, P01 CA87969, R01 CA151993 and P50 CA127003,) and PHS by the National Institutes of Health (R01 CA042182). Funding Information: Hidewaki Nakagawa was supported by BioBank Japan. Funding Information: Christine F Skibola was supported by the National Institutes of Health RO1CA1046282 and RO1CA154643. Funding Information: WHI: The WHI program is funded by the National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services through contracts HHSN268201100046C, HHSN268201100001C, HHSN268201100002C, HHSN268201100003C, HHSN268201100004C, and HHSN271201100004C. Funding Information: ASTERISK: a Hospital Clinical Research Program (PHRC) and supported by the Regional Council of Pays de la Loire, the Groupement des Entreprises Fran{\c c}aises dans la Lutte contre le Cancer (GEFLUC), the Association Anne de Bretagne G{\'e}n{\'e}tique and the Ligue R{\'e}gionale Contre le Cancer (LRCC). Funding Information: Ping Yang received support from grants NCI-CA77118 and CA80127, and from the Mayo Foundation. Funding Information: The Environment and Genetics in Lung Cancer Etiology (EAGLE), Prostate, Lung, Colon, Ovary Screening Trial (PLCO), and Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) studies were supported by the Intramural Research Program of the National Institutes of Health, National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics. ATBC was also supported by U.S. Public Health Service contracts (N01-CN-45165, N01-RC-45035, and N01-RC-37004) from the NCI. PLCO was also supported by individual contracts from the NCI to the University of Colorado Denver (NO1-CN-25514), Georgetown University (NO1-CN-25522), the Pacific Health Research Institute (NO1-CN-25515), the Henry Ford Health System (NO1-CN-25512), the University of Minnesota, (NO1-CN-25513), Washington University (NO1-CN-25516), the University of Pittsburgh (NO1-CN-25511), the University of Utah (NO1-CN-25524), the Marshfield Clinic Research Foundation (NO1-CN-25518), the University of Alabama at Birmingham (NO1-CN-75022), Westat, Inc. (NO1-CN-25476), and the University of California, Los Angeles (NO1-CN-25404). The Cancer Prevention Study-II (CPS-II) Nutrition Cohort was supported by the American Cancer Society. The NIH Genes, Environment and Health Initiative (GEI) partly funded DNA extraction and statistical analyses (HG-06-033-NCI-01 and RO1HL091172-01), genotyping at the Johns Hopkins University Center for Inherited Disease Research (U01HG004438 and NIH HHSN268200782096C), and study coordination at the GENEVA Coordination Center (U01 HG004446) for the EAGLE study and part of the PLCO. Genotyping for the remaining part of PLCO and all ATBC and CPS-II samples were supported by the Intramural Research Program of the National Institutes of Health, NCI, Division of Cancer Epidemiology and Genetics. The “Texas” study was supported by NIH grants CA55769, CA127219, R01CA133996, and CA121197. The Central European study was supported by the Institut National du Cancer (INCa) in France and the U.S. NCI (RO1 CA092039). The CARET study was supported by NIH grants R01CA78812 and U01CA63673. LUCY was partly funded by the Deutsche Forschungsgemeinschaft (DFG, BI 576/2-1; BI 576/2-2), and genotyping was funded by the Helmholtz Association in Germany. The Heidelberg sample collection was partly supported by the Deutsche Krebshilfe. The Estonian study was supported by Targeted Financing from Estonian Government (SF0180142 and ESF 6465) European Union through the European Regional Development Fund in the frame of Centre of Excellence in Genomics and 7 FP Project ECOGENE. Funding Information: DACHS: German Research Council (Deutsche Forschungsgemeinschaft, BR 1704/6-1, BR 1704/6-3, BR 1704/6-4 and CH 117/1-1), and the German Federal Ministry of Education and Research (01KH0404 and 01ER0814). Publisher Copyright: {\textcopyright} 2016",

year = "2016",

month = dec,

day = "1",

doi = "10.1016/j.gdata.2016.08.017",

language = "English (US)",

volume = "10",

pages = "22--29",

journal = "Genomics Data",

issn = "2213-5960",

publisher = "Elsevier Inc.",

}

TY - JOUR

T1 - Nonsyndromic cleft lip with or without cleft palate and cancer

T2 - Evaluation of a possible common genetic background through the analysis of GWAS data

AU - Dunkhase, Eva

AU - Ludwig, Kerstin U.

AU - Knapp, Michael

AU - Skibola, Christine F.

AU - Figueiredo, Jane C.

AU - Hosking, Fay Julie

AU - Ellinghaus, Eva

AU - Landi, Maria Teresa

AU - Ma, Hongxia

AU - Nakagawa, Hidewaki

AU - Kim, Jong Won

AU - Han, Jiali

AU - Yang, Ping

AU - Böhmer, Anne C.

AU - Mattheisen, Manuel

AU - Nöthen, Markus M.

AU - Mangold, Elisabeth

N1 - Funding Information: We thank all affected individuals and their families for their participation in this study, as well as the German support group for persons with cleft lip and/or palate (Deutsche Selbsthilfevereinigung für Lippen-Gaumen-Fehlbildungen e.V.).The study was supported by the Deutsche Forschungsgemeinschaft (FOR 423 and individual grants MA 2546/3-1 , KR 1912/7-1 , NO 246/6-1 and WI 1555/5-1 ). In particular, we thank the following researchers for the provision of data: deCODE Genetics (Reykjavik, Iceland); Victor Enciso (The Institute of Cancer Research, Sutton, Surrey, UK); Susan L. Slager (Mayo Clinic, Rochester, MN, USA); and Peter Kraft (Harvard School of Public Health, Boston, MA, USA). The study was also supported by Richard S. Houlston (The Institute of Cancer Research , Sutton, Surrey, UK); Noralane M. Lindor ( Mayo Clinic , Department of Health Sciences Research, Mayo Clinic Arizona, USA); and Zhibin Hu and Hongbing Shen of Nanjing Medical University . Funding Information: PLCO: Intramural Research Program of the Division of Cancer Epidemiology and Genetics and supported by contracts from the Division of Cancer Prevention, National Cancer Institute, NIH, DHHS. Additionally, a subset of control samples were genotyped as part of the Cancer Genetic Markers of Susceptibility (CGEMS) Prostate Cancer GWAS (Yeager, M et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 2007 May;39(5):645-9), Colon CGEMS pancreatic cancer scan (PanScan) (Amundadottir, L et al. Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. Nat Genet. 2009 Sep;41(9):986-90, and Petersen, GM et al. A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. Nat Genet. 2010 Mar;42(3):224-8), and the Lung Cancer and Smoking study (Landi MT, et al. A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. Am J Hum Genet. 2009 Nov;85(5):679-91). The prostate and PanScan study datasets were accessed with appropriate approval through the dbGaP online resource ( http://cgems.cancer.gov/data/ ) accession numbers phs000207.v1.p1 and phs000206.v3.p2, respectively, and the lung datasets were accessed from the dbGaP website ( http://www.ncbi.nlm.nih.gov/gap ) through accession number phs000093.v2.p2. Funding for the Lung Cancer and Smoking study was provided by National Institutes of Health (NIH), Genes, Environment and Health Initiative (GEI) Z01 CP 010200, NIH U01 HG004446, and NIH GEI U01 HG 004438. For the lung study, the GENEVA Coordinating Center provided assistance with genotype cleaning and general study coordination, and the Johns Hopkins University Center for Inherited Disease Research conducted genotyping. Funding Information: The Colon CFR GWAS was supported by funding from the National Cancer Institute, National Institutes of Health (U01 CA122839 and R01 CA143237 to Graham Casey). The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the Colon Cancer Family Registry (CCFR), nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government or the CCFR. Funding Information: OFCCR: National Institutes of Health, through funding allocated to the Ontario Registry for Studies of Familial Colorectal Cancer (U01 CA074783); see CCFR section above. Additional funding toward genetic analyses of OFCCR includes the Ontario Research Fund, the Canadian Institutes of Health Research, and the Ontario Institute for Cancer Research, through generous support from the Ontario Ministry of Research and Innovation. Funding Information: HPFS is supported by the National Institutes of Health (P01 CA 055075, UM1 CA167552, R01 137178, R01 CA151993 and P50 CA127003), NHS by the National Institutes of Health (UM1 CA186107, R01 CA137178, P01 CA87969, R01 CA151993 and P50 CA127003,) and PHS by the National Institutes of Health (R01 CA042182). Funding Information: Hidewaki Nakagawa was supported by BioBank Japan. Funding Information: Christine F Skibola was supported by the National Institutes of Health RO1CA1046282 and RO1CA154643. Funding Information: WHI: The WHI program is funded by the National Heart, Lung, and Blood Institute, National Institutes of Health, U.S. Department of Health and Human Services through contracts HHSN268201100046C, HHSN268201100001C, HHSN268201100002C, HHSN268201100003C, HHSN268201100004C, and HHSN271201100004C. Funding Information: ASTERISK: a Hospital Clinical Research Program (PHRC) and supported by the Regional Council of Pays de la Loire, the Groupement des Entreprises Françaises dans la Lutte contre le Cancer (GEFLUC), the Association Anne de Bretagne Génétique and the Ligue Régionale Contre le Cancer (LRCC). Funding Information: Ping Yang received support from grants NCI-CA77118 and CA80127, and from the Mayo Foundation. Funding Information: The Environment and Genetics in Lung Cancer Etiology (EAGLE), Prostate, Lung, Colon, Ovary Screening Trial (PLCO), and Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) studies were supported by the Intramural Research Program of the National Institutes of Health, National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics. ATBC was also supported by U.S. Public Health Service contracts (N01-CN-45165, N01-RC-45035, and N01-RC-37004) from the NCI. PLCO was also supported by individual contracts from the NCI to the University of Colorado Denver (NO1-CN-25514), Georgetown University (NO1-CN-25522), the Pacific Health Research Institute (NO1-CN-25515), the Henry Ford Health System (NO1-CN-25512), the University of Minnesota, (NO1-CN-25513), Washington University (NO1-CN-25516), the University of Pittsburgh (NO1-CN-25511), the University of Utah (NO1-CN-25524), the Marshfield Clinic Research Foundation (NO1-CN-25518), the University of Alabama at Birmingham (NO1-CN-75022), Westat, Inc. (NO1-CN-25476), and the University of California, Los Angeles (NO1-CN-25404). The Cancer Prevention Study-II (CPS-II) Nutrition Cohort was supported by the American Cancer Society. The NIH Genes, Environment and Health Initiative (GEI) partly funded DNA extraction and statistical analyses (HG-06-033-NCI-01 and RO1HL091172-01), genotyping at the Johns Hopkins University Center for Inherited Disease Research (U01HG004438 and NIH HHSN268200782096C), and study coordination at the GENEVA Coordination Center (U01 HG004446) for the EAGLE study and part of the PLCO. Genotyping for the remaining part of PLCO and all ATBC and CPS-II samples were supported by the Intramural Research Program of the National Institutes of Health, NCI, Division of Cancer Epidemiology and Genetics. The “Texas” study was supported by NIH grants CA55769, CA127219, R01CA133996, and CA121197. The Central European study was supported by the Institut National du Cancer (INCa) in France and the U.S. NCI (RO1 CA092039). The CARET study was supported by NIH grants R01CA78812 and U01CA63673. LUCY was partly funded by the Deutsche Forschungsgemeinschaft (DFG, BI 576/2-1; BI 576/2-2), and genotyping was funded by the Helmholtz Association in Germany. The Heidelberg sample collection was partly supported by the Deutsche Krebshilfe. The Estonian study was supported by Targeted Financing from Estonian Government (SF0180142 and ESF 6465) European Union through the European Regional Development Fund in the frame of Centre of Excellence in Genomics and 7 FP Project ECOGENE. Funding Information: DACHS: German Research Council (Deutsche Forschungsgemeinschaft, BR 1704/6-1, BR 1704/6-3, BR 1704/6-4 and CH 117/1-1), and the German Federal Ministry of Education and Research (01KH0404 and 01ER0814). Publisher Copyright: © 2016

PY - 2016/12/1

Y1 - 2016/12/1

N2 - Previous research suggests a genetic overlap between nonsyndromic cleft lip with or without cleft palate (NSCL/P) and cancer. The aim of the present study was to identify common genetic risk loci for NSCL/P and cancer entities that have been reported to co-occur with orofacial clefting. This was achieved through the investigation of large genome-wide association study datasets. Investigations of 12 NSCL/P single nucleotide polymorphisms (SNPs) in 32 cancer datasets, and 204 cancer SNPs in two NSCL/P datasets, were performed. The SNPs rs13041247 (20q12) and rs6457327 (6p21.33) showed suggestive evidence for an association with both NSCL/P and a specific cancer entity. These loci harbor genes of biological relevance to oncogenesis (MAFB and OCT4, respectively). This study is the first to characterize possible pleiotropic risk loci for NSCL/P and cancer in a systematic manner. The data represent a starting point for future research by identifying a genetic link between NSCL/P and cancer.

AB - Previous research suggests a genetic overlap between nonsyndromic cleft lip with or without cleft palate (NSCL/P) and cancer. The aim of the present study was to identify common genetic risk loci for NSCL/P and cancer entities that have been reported to co-occur with orofacial clefting. This was achieved through the investigation of large genome-wide association study datasets. Investigations of 12 NSCL/P single nucleotide polymorphisms (SNPs) in 32 cancer datasets, and 204 cancer SNPs in two NSCL/P datasets, were performed. The SNPs rs13041247 (20q12) and rs6457327 (6p21.33) showed suggestive evidence for an association with both NSCL/P and a specific cancer entity. These loci harbor genes of biological relevance to oncogenesis (MAFB and OCT4, respectively). This study is the first to characterize possible pleiotropic risk loci for NSCL/P and cancer in a systematic manner. The data represent a starting point for future research by identifying a genetic link between NSCL/P and cancer.

KW - Cancer

KW - Cleft lip

KW - Cleft palate

KW - Genome-wide association study

KW - Single nucleotide polymorphism

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UR - http://www.scopus.com/inward/citedby.url?scp=84985023582&partnerID=8YFLogxK

U2 - 10.1016/j.gdata.2016.08.017

DO - 10.1016/j.gdata.2016.08.017

M3 - Article

AN - SCOPUS:84985023582

VL - 10

SP - 22

EP - 29

JO - Genomics Data

JF - Genomics Data

SN - 2213-5960

ER -

Nonsyndromic cleft lip with or without cleft palate and cancer: Evaluation of a possible common genetic background through the analysis of GWAS data

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