An expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM): Insights into population allelic architecture and its mutational history

Human Mutation

Volumn 31, Issue 4, 2010, Pages 414-420

  Gaunt, Tom R ^a   Rodriguez, Santiago ^a   Guthrie, Philip A I ^a   Day, Ian N M ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Amylase; CCL3L1; CNV; Copy number variation; Expectation maximization; SULT1A1

Indexed keywords

AMYLASE; CC CHEMOKINE LIGAND 3 LIKE 1 PROTEIN; PROTEIN; SULFOTRANSFERASE 1A1; UNCLASSIFIED DRUG;

ARTICLE; COPY NUMBER VARIATION; GENE FREQUENCY; GENE LOCUS; GENE MUTATION; GENETIC ALGORITHM; GENOTYPE; HARDY WEINBERG DISTRIBUTION LAW; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; PRIORITY JOURNAL;

ALGORITHMS; ALLELES; ARYLSULFOTRANSFERASE; COMPUTATIONAL BIOLOGY; DNA COPY NUMBER VARIATIONS; GENETICS, POPULATION; HUMANS; MUTATION; SALIVARY ALPHA-AMYLASES;

EID: 77950400632     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.21199     Document Type: Article

References (30)

1. Carrington M, Kissner T, Gerrard B, Ivanov S, O'Brien SJ, Dean M. 1997. Novel alleles of the chemokine-receptor gene CCR5. Am J Hum Genet 61:1261-1267.
2. Clark AG. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 7:111-122.
3. Daines B, Wang H, Li Y, Han Y, Gibbs R, Chen R. 2009. High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics 182:935-941.
4. Dempster AP, Laird NM, Rubin DB. 1977. Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Series B 39:1-38.
5. Excoffier L, Slatkin M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927.
6. Gaunt TR, Rodríguez S, Day IN. 2007. Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool "CubeX." BMC Bioinformatics 8:428.
7. Gaunt TR, Rodriguez S, Zapata C, Day IN. 2006. MIDAS: software for analysis and visualization of interallelic disequilibrium between multiallelic markers. BMC Bioinformatics 7:227.
8. Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Rovin BH, Bradley W, Clark RA, Anderson SA, O'Connell RJ, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ, Ahuja SK. 2005. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307:1434-1440.
9. Hardy GH. 1908. Mendelian proportions in a mixed population. Science 28:49-50.
10. Hastings PJ, Lupski JR, Rosenberg SM, Ira G. 2009. Mechanisms of change in gene copy number. Nat Rev Genet 10:551-564.
11. Hawley ME, Kidd KK. 1995. HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 86:409-411.
12. Hebbring SJ, Adjei AA, Baer JL, Jenkins GD, Zhang J, Cunningham JM, Schaid DJ, Weinshilboum RM, Thibodeau SN. 2007. Human SULT1A1 gene: copy number differences and functional implications. Hum Mol Genet 16:463-470.
13. Hill WG. 1974. Estimation of linkage disequilibrium in randomly mating populations. Heredity 33:229-239.
14. Kirk KM, Cardon LR. 2002. The impact of genotyping error on haplotype reconstruction and frequency estimation. Eur J Hum Genet 10:616-622.
15. Lin S, Cutler DJ, Zwick ME, Chakravarti A. 2002. Haplotype inference in random population samples. Am J Hum Genet 71:1129-1137.
16. Long JC, Williams RC, Urbanek M. 1995. An E-M algorithm and testing strategy for multiple-locus haplotypes. Am J Hum Genet 56:799-810.
17. Lucotte G. 2001. Distribution of the CCR5 gene 32-basepair deletion in West Europe. A hypothesis about the possible dispersion of the mutation by the vikings in historical times. Hum Immunol 62:933-936.
18. Mamtani M, Rovin B, Brey R, Camargo JF, Kulkarni H, Herrera M, Correa P, Holliday S, Anaya J, Ahuja SK. 2008. CCL3L1 gene-containing segmental duplications and polymorphisms in CCR5 affect risk of systemic lupus erythaematosus. Ann Rheum Dis 67:1076-1083.
19. McKinney C, Merriman ME, Chapman PT, Gow PJ, Harrison AA, Highton J, Jones PBB, McLean L, O'Donnell JL, Pokorny V, Spellerberg M, Stamp LK, Willis J, Steer S, Merriman TR. 2008. Evidence for an influence of chemokine ligand 3-like 1 (CCL3L1) gene copy number on susceptibility to rheumatoid arthritis. Ann Rheum Dis 67:409-413.
20. Nguyen D, Webber C, Ponting CP. 2006. Bias of selection on human copy-number variants. PLoS Genet 2:e20.
21. Nibbs RJ, Yang J, Landau NR, Mao JH, Graham GJ. 1999. LD78beta, a non-allelic variant of human MIP-1alpha (LD78alpha), has enhanced receptor interactions and potent HIV suppressive activity. J Biol Chem 274:17478-17483.
22. Niu T, Qin ZS, Xu X, Liu JS. 2002. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 70:157-169.
23. Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC. 2007. Diet and the evolution of human amylase gene copy number variation. Nat Genet 39:1256-1260.
24. Polańska J. 2003. The EM algorithm and its implementation for the estimation of frequencies of SNP-haplotypes. Int J Appl Math Comput Sci 13:419-429.
25. Stephens M, Donnelly P. 2003. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73:1162-1169.
26. Stephens M, Smith NJ, Donnelly P. 2001. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978-989.
27. Tishkoff SA, Pakstis AJ, Ruano G, Kidd KK. 2000. The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus. Am J Hum Genet 67:518-522.
28. United Nations. 1973. Determinants and consequences of population trends: new summary of findings on interaction of demographic, economic and social factors. Vol.1. New York: United Nations.
29. Weinshilboum RM, Otterness DM, Aksoy IA, Wood TC, Her C, Raftogianis RB. 1997. Sulfation and sulfotransferases 1: sulfotransferase molecular biology: cDNAs and genes. FASEB J 11:3-14.
30. Xie C, Tammi MT. 2009. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10:80.