Novel common copy number variation for early onset extreme obesity on chromosome 11q11 identified by a genome-wide analysis

Human Molecular Genetics

Volumn 20, Issue 4, 2011, Pages 840-852

  Jarick, Ivonne ^a   Vogel, Carla I G ^b   Scherag, Susann ^b   Schäfer, Helmut ^a   Hebebrand, Johannes ^b   Hinney, Anke ^b   Scherag, André ^b  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

^b UNIVERSITY OF DUISBURG ESSEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BODY WEIGHT; CHILD; CHROMOSOME 10Q; CHROMOSOME 11Q; CHROMOSOME 11Q11; CONFIDENCE INTERVAL; COPY NUMBER VARIATION; FOLLOW UP; GENE DELETION; GENETIC ANALYSIS; HUMAN; OBESITY; OLFACTORY RECEPTOR; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ADOLESCENT; ADULT; AGE OF ONSET; ALGORITHMS; ALLELES; BODY MASS INDEX; CHILD; CHROMOSOMES, HUMAN, PAIR 11; DNA COPY NUMBER VARIATIONS; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MIDDLE AGED; OBESITY; POLYMORPHISM, SINGLE NUCLEOTIDE; YOUNG ADULT;

EID: 78751700313     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddq518     Document Type: Article

References (48)

1. Friedman, J.M. (2000) Obesity in the new millennium. Nature, 404, 632-634.
2. Walley, A.J., Asher, J.E. and Froguel, P. (2009) The genetic contribution to non-syndromic human obesity. Nat. Rev. Genet., 10, 431-442.
3. Herbert, A., Gerry, N.P., McQueen, M.B., Heid, I.M., Pfeufer, A., Illig, T., Wichmann, H.E., Meitinger, T., Hunter, D., Hu, F.B. et al. (2006) A common genetic variant is associated with adult and childhood obesity. Science, 312, 279-283.
4. Hinney, A., Nguyen, T.T., Scherag, A., Friedel, S., Brönner, G., Müller, T.D., Grallert, H., Illig, T., Wichmann, H.E., Rief, W. et al. (2007) Genome wide association (GWA) study for early onset extreme obesity supports the role of fat mass and obesity associated gene (FTO) variants. PLoS One, 2, e1361.
5. Loos, R.J., Lindgren, C.M., Li, S., Wheeler, E., Zhao, J.H., Prokopenko, I., Inouye, M., Freathy, R.M., Attwood, A.P., Beckmann, J.S. et al. (2008) Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat. Genet., 40, 768-775.
6. Meyre, D., Delplanque, J., Chévre, J.C., Lecoeur, C., Lobbens, S., Gallina, S., Durand, E., Vatin, V., Degraeve, F., Proença, C. et al. (2009) Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations. Nat. Genet., 41, 157-159.
7. Thorleifsson, G., Walters, G.B., Gudbjartsson, D.F., Steinthorsdottir, V., Sulem, P., Helgadottir, A., Styrkarsdottir, U., Gretarsdottir, S., Thorlacius, S., Jonsdottir, I. et al. (2009) Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. Nat. Genet., 41, 18-24.
8. Willer, C.J., Speliotes, E.K., Loos, R.J., Li, S., Lindgren, C.M., Heid, I.M., Berndt, S.I., Elliott, A.L., Jackson, A.U., Lamina, C. et al. (2009) Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat. Genet., 41, 25-34.
9. Hinney, A., Vogel, C.I. and Hebebrand, J. (2010) From monogenic to polygenic obesity, recent advances. Eur. Child. Adolesc. Psychiatry, 19, 297-310.
10. Manolio, T.A., Collins, F.S., Cox, N.J., Goldstein, D.B., Hindorff, L.A., Hunter, D.J., McCarthy, M.I., Ramos, E.M., Cardon, L.R., Chakravarti, A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
11. Conrad, D.F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T.D., Barnes, C., Campbell, P. et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature, 464, 704-712.
12. Ionita-Laza, I., Rogers, A.J., Lange, C., Raby, B.A. and Lee, C. (2009) Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis. Genomics, 93, 22-26.
13. McCarroll, S.A., Kuruvilla, F.G., Korn, J.M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M.H., deBakker, P.I., Maller, J.B., Kirby, A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., 40, 1166-1174.
14. McCarroll, S.A. (2008) Copy-number analysis goes more than skin deep. Nat. Genet., 40, 5-6.
15. Stefansson, H., Rujescu, D., Cichon, S., Pietiläinen, O.P., Ingason, A., Steinberg, S., Fossdal, R., Sigurdsson, E., Sigmundsson, T., Buizer-Voskamp, J.E. et al. (2008) Large recurrent microdeletions associated with schizophrenia. Nature, 455, 232-236.
16. Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J. et al. (2007) Strong association of de novo copy number mutations with autism. Science, 316, 445-449.
17. Lee, J.A. and Lupski, J.R. (2006) Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders. Neuron, 52, 103-121.
18. Gonzalez, E., Kulkarni, H., Bolivar, H., Mangano, A., Sanchez, R., Catano, G., Nibbs, R.J., Freedman, B.I., Quinones, M.P., Bamshad, M.J. et al. (2005) The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science, 307, 1434-1440.
19. Sha, B.Y., Yang, T.L., Zhao, L.J., Chen, X.D., Guo, Y., Chen, Y., Pan, F., Zhang, Z.X., Dong, S.S., Xu, X.H. and Deng, H.W. (2009) Genome-wide association study suggested copy number variation may be associated with body mass index in the Chinese population. J. Hum. Genet., 54, 199-202.
20. Bochukova, E.G., Huang, N., Keogh, J., Henning, E., Purmann, C., Blaszczyk, K., Saeed, S., Hamilton-Shield, J., Clayton-Smith, J., O'Rahilly, S. et al. (2010) Large, rare chromosomal deletions associated with severe early-onset obesity. Nature, 463, 666-670.
21. Walters, R.G., Jacquemont, S., Valsesia, A., deSmith, A.J., Martinet, D., Andersson, J., Falchi, M., Chen, F., Andrieux, J., Lobbens, S. et al. (2010) A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature, 463, 671-675.
22. Wang, K., Li, W.D., Glessner, J.T., Grant, S.F., Hakonarson, H. and Price, R.A. (2010) Large copy number variations are enriched in cases with moderate to extreme obesity. Diabetes, 59, 2960-2964.
23. Weiss, L.A., Shen, Y., Korn, J.M., Arking, D.E., Miller, D.T., Fossdal, R., Saemundsen, E., Stefansson, H., Ferreira, M.A., Green, T. et al. (2008) Association between microdeletion and microduplication at 16p11.2 and autism. N. Engl. J. Med., 358, 667-675.
24. Park, J.H., Wacholder, S., Gail, M.H., Peters, U., Jacobs, K.B., Chanock, S.J. and Chatterjee, N. (2010) Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat. Genet., 42, 570-575.
25. Yang, J., Benyamin, B., McEvoy, B.P., Gordon, S., Henders, A.K., Nyholt, D.R., Madden, P.A., Heath, A.C., Martin, N.G., Montgomery, G.W. et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat. Genet., 42, 565-569.
26. Craddock, N., Hurles, M.E., Cardin, N., Pearson, R.D., Plagnol, V., Robson, S., Vukcevic, D., Barnes, C., Conrad, D.F., Giannoulatou, E. et al. (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature, 464, 713-720.
27. Sainsbury, A., Baldock, P.A., Schwarzer, C., Ueno, N., Enriquez, R.F., Couzens, M., Inui, A., Herzog, H. and Gardiner, E.M. (2003) Synergistic effects of Y2 and Y4 receptors on adiposity and bone mass revealed in double knockout mice. Mol. Cell. Biol., 23, 5225-5233.
28. Wong, K.K., deLeeuw, R.J., Dosanjh, N.S., Kimm, L.R., Cheng, Z., Horsman, D.E., MacAulay, C., Ng, R.T., Brown, C.J., Eichler, E.E. and Lam, W.L. (2007) A comprehensive analysis of common copy-number variations in the human genome. Am. J. Hum. Genet., 80, 91-104.
29. Hasin, Y., Olender, T., Khen, M., Gonzaga-Jauregui, C., Kim, P.M., Urban, A.E., Snyder, M., Gerstein, M.B., Lancet, D. and Korbel, J.O. (2008) High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genet., 4, e1000249.
30. Young, J.M., Endicott, R.M., Parghi, S.S., Walker, M., Kidd, J.M. and Trask, B.J. (2008) Extensive copy-number variation of the human olfactory receptor gene family. Am. J. Hum. Genet., 83, 228-242.
31. Richardson, B.E., VanderWoude, E.A., Sudan, R., Thompson, J.S. and Leopold, D.A. (2004) Altered olfactory acuity in the morbidly obese. Obes. Surg., 14, 967-969.
32. Sainsbury, A., Shi, Y.C., Zhang, L., Aljanova, A., Lin, Z., Nguyen, A.D., Herzog, H. and Lin, S. (2010) Y4 receptors and pancreatic polypeptide regulate food intake via hypothalamic orexin and brain-derived neurotropic factor dependent pathways. Neuropeptides, 44, 261-268.
33. Speliotes, E.K., Willer, C.J., Berndt, S.I., Monda, K.L., Thorleifsson, G., Jackson, A.U., Allen, H.L., Lindgren, C.M., Luan, J., Mägi, R. et al. (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat. Genet., 42, 937-948.
34. Heid, I.M., Jackson, A.U., Randall, J.C., Winkler, T.W., Qi, L., Steinthorsdottir, V., Thorleifsson, G., Zillikens, M.C., Speliotes, E.K., Mägi, R. et al. (2010) Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat. Genet., 42, 949-960.
35. Hebebrand, J., Heseker, H., Himmelmann, G.W., Schäfer, H. and Remschmidt, H. (1994) Altersperzentilen für den Body Mass Index aus Daten der Nationalen Verzehrstudie einschließlich einer Übersicht zu relevanten Einflussfaktoren. Aktuel. Ernährungsmed., 19, 259-265.
36. McCarroll, S.A. and Altshuler, D.M. (2007) Copy-number variation and association studies of human disease. Nat. Genet., 39, 37-42.
37. Ionita-Laza, I., Perry, G.H., Raby, B.A., Klanderman, B., Lee, C., Laird, N.M., Weiss, S.T. and Lange, C. (2008) On the analysis of copy-number variations in genome-wide association studies, a translation of the family-based association test. Genet. Epidemiol., 32, 273-284.
38. Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
39. Fridlyand, J., Snijders, A.M., Pinkel, D., Albertson, D.G. and Jain, A.N. (2004) Hidden Markov models approach to the analysis of array CGH data. J. Multivar. Anal., 90, 132-153.
40. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., Fiegler, H., Shapero, M.H., Carson, A.R., Chen, W. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454.
41. Marioni, J.C., Thorne, N.P., Valsesia, A., Fitzgerald, T., Redon, R., Fiegler, H., Andrews, T.D., Stranger, B.E., Lynch, A.G., Dermitzakis, E.T. et al. (2007) Breaking the waves, improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol., 8, R228.
42. deSmith, A.J., Tsalenko, A., Sampas, N., Scheffer, A., Yamada, N.A., Tsang, P., Ben-Dor, A., Yakhini, Z., Ellis, R.J., Bruhn, L., et al. (2007) Array CGH analysis of copy number variation identifies 1284 new genes variant in healthy white males, implications for association studies of complex diseases. Hum. Mol. Genet., 16, 2783-2794.
43. deKovel, C.G., Trucks, H., Helbig, I., Mefford, H.C., Baker, C., Leu, C., Kluck, C., Muhle, H., vonSpiczak, S., Ostertag, P. et al. (2010) Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies. Brain, 133, 23-32.
44. Winchester, L., Yau, C. and Ragoussis, J. (2009) Comparing CNV detection methods for SNP arrays. Brief Funct. Genomic Proteomic, 8, 353-366.
45. Scherag, A., Dina, C., Hinney, A., Vatin, V., Scherag, S., Vogel, C.I., Müller, T.D., Grallert, H., Wichmann, H.E., Balkau, B. et al. (2010) Two new loci for body-weight regulation identified in a joint analysis of genome-wide association studies for early-onset extreme obesity in French and German study groups. PLoS Genet., 6, e1000916.
46. Schaid, D.J., Batzler, A.J., Jenkins, G.D. and Hildebrandt, M.A. (2006) Exact tests of Hardy-Weinberg equilibrium and homogeneity of disequilibrium across strata. Am. J. Hum. Genet., 79, 1071-1080.
47. Spielman, R.S., McGinnis, R.E. and Ewens, W.J. (1993) Transmission test for linkage disequilibrium, the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet., 52, 506-516.
48. Falk, C.T. and Rubinstein, P. (1987) Hyplotype relative risks, an easy reliable way to construct a proper control sample for risk calculations. Ann. Hum. Genet., 51, 227-233.