Following the footprints of polymorphic inversions on SNP data: From detection to association tests

Nucleic Acids Research

Volumn 43, Issue 8, 2015, Pages

  Cáceres, Alejandro ^a,b   González, Juan R ^a,b,c,d  

^a CENTRE FOR RESEARCH IN ENVIRONMENTAL EPIDEMIOLOGY CREAL   (Spain)

^b HOSPITAL DEL MAR   (Spain)

^c CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

^d UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AMERICAN; ARTICLE; BODY MASS; CHROMOSOME INVERSION; COHORT ANALYSIS; CONTROLLED STUDY; DNA FOOTPRINTING; FLUORESCENCE IN SITU HYBRIDIZATION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; PHENOTYPE; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; GENOTYPING TECHNIQUE; HAPLOTYPE MAP; PRESCHOOL CHILD; PROCEDURES; UNITED STATES;

ALGORITHMS; BODY MASS INDEX; CHILD, PRESCHOOL; CHROMOSOME INVERSION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPING TECHNIQUES; HAPLOTYPES; HAPMAP PROJECT; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; UNITED STATES;

EID: 84929481938     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv073     Document Type: Article

References (22)

1. Kirkpatrick, M. (2010) How and why chromosome inversions evolve. PLoS Biol., 8, e1000501.
2. Martínez-Fundichely, A., Casillas, S., Egea, R., Ràmia, M., Barbadilla, A., Pantano, L., Puig, M. and Cáceres, M. (2014) InvFEST, a database integrating information of polymorphic inversions in the human genome. Nucleic Acids Res., 42, D1027-D1032.
3. Cáceres, A., Sindi, S.S., Raphael, B.J., Cáceres, M. and González, J.R. (2012) Identification of polymorphic inversions from genotypes. BMC Bioinformatics, 13, 28.
4. Ma, J. and Amos, C.I. (2012) Investigation of inversion polymorphisms in the human genome using principal components analysis. PLOS ONE, 7, e40224.
5. Feuk, L. (2010) Inversion variants in the human genome: role in disease and genome architecture. Genome Med., 2, 11.
6. González, J.R., Cáceres, A., Esko, T., Cuscó, I., Puig, M., Esnaola, M., Reina, J., Siroux, V., Bouzigon, E., Nadif, R. et al. (2014) A common 16p11.2 inversion underlies the joint susceptibility to asthma and obesity. Am. J. Hum. Gen., 94, 361-372.
7. Salm, M.P., Horswell, S.D., Hutchison, C.E., Speedy, H.E., Yang, X., Liang, L., Schadt, E.E., Cookson, W.O., Wierzbicki, A.S., Naoumova, R.P. et al. (2012) The origin, global distribution, and functional impact of the human 8p23 inversion polymorphism. Genome Res., 22, 1144-1153.
8. Stefansson, H., Helgason, A., Thorleifsson, G., Steinthorsdottir, V., Masson, G., Barnard, J., Baker, A., Jonasdottir, A., Ingason, A., Gudnadottir, V.G. et al. (2005) A common inversion under selection in Europeans. Nat. Genet., 37, 129-137.
9. deJong, S., Chepelev, I., Janson, E., Strengman, E., van denBerg, L.H., Veldink, J.H. and Ophoff, R.A. (2012) Common inversion polymorphism at 17q21. 31 affects expression of multiple genes in tissue-specific manner. BMC Genomics, 13, 458.
10. Alves, J.M., Chikhi, L., Amorim, A. and Lopes, A.M. (2014) The 8p23 inversion polymorphism determines local recombination heterogeneity across human populations. Genome Biol. Evol., 6, 921-930.
11. Sindi, S.S. and Raphael, B.J. (2010) Identification and frequency estimation of inversion polymorphisms from haplotype data. J. Comp. Biol., 17, 517-531.
12. Bansal, V., Bashir, A. and Bafna, V. (2007) Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res., 17, 219-230.
13. Deng, L., Zhang, Y., Kang, J., Liu, T., Zhao, H., Gao, Y., Li, C., Pan, H., Tang, X., Wang, D. et al. (2008) An unusual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism. Hum. Mutat., 29, 1209-1216.
14. Teslovich, T.M., Musunuru, K., Smith, A.V., Edmondson, A.C., Stylianou, I.M., Koseki, M., Pirruccello, J.P., Ripatti, S., Chasman, D.I., Willer, C.J. et al. (2010) Biological, clinical and population relevance of 95 loci for blood lipids. Nature, 466, 707-713.
15. Global Lipids Genetics Consortium. (2013) Discovery and refinement of loci associated with lipid levels. Nat. Genet., 45, 1274-1283.
16. Comuzzie, A.G., Cole, S.A., Laston, S.L., Voruganti, V.S., Haack, K., Gibbs, R.A. and Butte, N.F. (2012) Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. PLOS ONE, 7, e51954.
17. González, J.R., Carrasco, J.L., Dudbridge, F., Armengol, L., Estivill, X. and Moreno, V. (2008)Maximizing association statistics over genetic models. Genet. Epidemiol., 32, 246-254.
18. O'Reilly, P.F., Coin, L.J. and Hoggart, C.J. (2010) invertFREGENE: software for simulating inversions in population genetic data. Bioinformatics, 26, 838-840.
19. Murray, T., Beaty, T.H., Mathias, R.A., Rafaels, N., Grant, A.V., Faruque, M.U., Watson, H.R., Ruczinski, I., Dunston, G.M. and Barnes, K.C. (2010) African and non-African admixture components in African Americans and an African Caribbean population. Genet. Epidemiol., 34, 561-568.
20. Galanter, J.M., Fernandez-Lopez, J.C., Gignoux, C.R., Barnholtz-Sloan, J., Fernandez-Rozadilla, C., Via, M., Hidalgo-Miranda, A., Contreras, A.V., Figueroa, L.U., Raska, P. et al. (2012) Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. PLoS Genet., 8, e1002554.
21. Steinberg, K.M., Antonacci, F., Sudmant, P.H., Kidd, J.M., Campbell, C.D., Vives, L., Malig, M., Scheinfeldt, L., Beggs, W., Ibrahim, M. et al. (2012) Structural diversity and African origin of the 17q21. 31 inversion polymorphism. Nat. Genet., 44, 872-880.
22. Kidd, J.M., Cooper, G.M., Donahue, W.F., Hayden, H.S., Sampas, N., Graves, T., Hansen, N., Teague, B., Alkan, C., Antonacci, F. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56-64.