Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Polašek, Ozren ^a,b   Hayward, Caroline ^c   Bellenguez, Celine ^d,e   Vitart, Veronique ^c   Kolčić, Ivana ^b   McQuillan, Ruth ^a   Saftić, Vanja ^f   Gyllensten, Ulf ^g   Wilson, James F ^a   Rudan, Igor ^a,h,i   Wright, Alan F ^c   Campbell, Harry ^a   Leutenegger, Anne Louise ^d,e  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF ZAGREB   (Croatia)

^c MEDICAL RESEARCH COUNCIL   (United Kingdom)

^d INSERM   (France)

^e UNIVERSITÉ PARIS SACLAY   (France)

^f SESTRE MILOSRDNICE UNIVERSITY HOSPITAL   (Croatia)

^g UPPSALA UNIVERSITY   (Sweden)

^h ACTdoo   (Croatia)

ⁱ UNIVERSITY OF SPLIT   (Croatia)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; BIRTHPLACE; COMPARATIVE STUDY; GENE LINKAGE DISEQUILIBRIUM; GENEALOGY; GENOTYPE; GRANDPARENT; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; INBREEDING; PROGENY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; COMPUTER SIMULATION; CONSANGUINITY; CROATIA; GENETIC ASSOCIATION; HOMOZYGOTE; HUMAN GENOME; INHERITANCE; METHODOLOGY; STATISTICAL MODEL;

COMPUTER SIMULATION; CONSANGUINITY; CROATIA; GENETIC ASSOCIATION STUDIES; GENOME, HUMAN; GENOTYPE; HOMOZYGOTE; HUMANS; INHERITANCE PATTERNS; LIKELIHOOD FUNCTIONS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77951229712     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-139     Document Type: Article

References (30)

1. Crnokrak P, Roff DA. Inbreeding depression in the wild. Heredity 1999, 83:260-270. 10.1038/sj.hdy.6885530, 10504423.
2. Keller LF, Waller DM. Inbreeding effects in wild populations. Trends in Ecology & Evolution 2002, 17:230-241.
3. Kristensen TN, Sorensen AC. Inbreeding - lessons from animal breeding, evolutionary biology and conservation genetics. Animal Science 2005, 80:121-133.
4. Balloux F, Amos W, Coulson T. Does heterozygosity estimate inbreeding in real populations?. Molecular Ecology 2004, 13:3021-3031. 10.1111/j.1365-294X.2004.02318.x, 15367117.
5. David P. Heterozygosity-fitness correlations: new perspectives on old problems. Heredity 1998, 80:531-537. 10.1046/j.1365-2540.1998.00393.x, 9650277.
6. Coltman DW, Slate J. Microsatellite measures of inbreeding: A meta-analysis. Evolution 2003, 57:971-983.
7. Penrose LS. Evidence of heterosis in man. Proceedings of the Royal Society B-Biological Sciences 1955, 144:203-213.
8. Rudan I, Campbell H. Five reasons why inbreeding may have considerable effect on post-reproductive human health. Collegium Antropologicum 2004, 28:943-950.
9. Bittles AH. Endogamy, consanguinity and community genetics. Journal of Genetics 2002, 81:91-98. 10.1007/BF02715905, 12717037.
10. Bittles AH. Endogamy, consanguinity and community disease profiles. Community Genetics 2005, 8:17-20. 10.1159/000083332, 15767749.
11. Bellis MA, Hughes K, Hughes S, Ashton JR. Measuring paternal discrepancy and its public health consequences. Journal of Epidemiology and Community Health 2005, 59:749-754. 10.1136/jech.2005.036517, 1733152, 16100312.
12. Spielman RS, Neel JV, Li FH. Inbreeding estimation from population data - models, procedures and implications. Genetics 1977, 85:355-371. 1213639, 863234.
13. Leutenegger AL, Prum B, Genin E, et al. Estimation of the inbreeding coefficient through use of genomic data. Am J Hum Genet 2003, 73:516-523. 10.1086/378207, 1180677, 12900793.
14. Carothers AD, Rudan I, Kolcic I, et al. Estimating human inbreeding coefficients: Comparison of genealogical and marker heterozygosity approaches. Annals of Human Genetics 2006, 70:666-676. 10.1111/j.1469-1809.2006.00263.x, 16907711.
15. Elston RC. Markers. Biostatistical genetics and genetic epidemiology 2003, West Sussex, England: John Wiley & Sons Ltd, Elston RC, Olson JM, Palmer L.
16. Slate J, Pemberton JM. Comparing molecular measures for detecting inbreeding depression. Journal of Evolutionary Biology 2002, 15:20-31.
17. Rudan I, Rudan D, Campbell H, et al. Inbreeding and risk of late onset complex disease. Journal of Medical Genetics 2003, 40:925-932. 10.1136/jmg.40.12.925, 1735350, 14684692.
18. Leutenegger AL, Labalme A, Genin E, et al. Using genomic inbreeding coefficient estimates for homozygosity mapping of rare recessive traits: Application to Taybi-Linder syndrome. Am J Hum Genet 2006, 79:62-66. 10.1086/504640, 1474127, 16773566.
19. Rudan I, Carothers AD, Polasek O, et al. Quantifying the increase in average human heterozygosity due to urbanization. European Journal of Human Genetics 2008, 16:1097-1102. 10.1038/ejhg.2008.48, 18322453.
20. Campbell H, Carothers AD, Rudan I, et al. Effects of genome-wide heterozygosity on a range of biomedically relevant human quantitative traits. Human Molecular Genetics 2007, 16:233-241. 10.1093/hmg/ddl473, 17220173.
21. Purcell S, Neale B, Todd-Brown K, et al. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 2007, 81:559-575. 10.1086/519795, 1950838, 17701901.
22. Rudan I, Campbell H, Rudan P. Genetic epidemiological studies of Eastern Adriatic island isolates, Croatia: Objectives and strategies. Collegium Antropologicum 1999, 23:531-546.
23. Vitart V, Biloglav Z, Hayward C, et al. 3000 years of solitude: extreme differentiation in the island isolates of Dalmatia, Croatia. European Journal of Human Genetics 2006, 14:478-487. 10.1038/sj.ejhg.5201589, 16493443.
24. Polasek O, Kolcic I, Smoljanovic A, Stojanovic D, Grgic M, Ebling B, Klaric M, Milas J, Puntaric D. Demonstrating reduced environmental and genetic diversity in human isolates by analysis of blood lipid levels. Croat Med J 2006, 47:649-55. 2080451, 16909463.
25. Pulanic D, Polasek O, Petrovecki M, Vorko-Jovic A, Pericic M, Barac Lauc L, et al. Effects of isolation and inbreeding on human quantitative traits: An example of biochemical markers of hemostasis and inflammation. Human Biology 2008, 80:513-33.
26. Polasek O, Kolcic I, Vorko-Jovic A, Kern J, Rudan I. Seasonality of births in Croatia. Collegium Antropologicum 2005, 29:249-255.
27. Coltman DW, Pilkington JG, Smith JA, Pemberton J. Parasite-mediated selection against inbred Soay sheep in a free-living, island population. Evolution 1999, 53:1259-1267.
28. Bellenguez C, Ober C, Bourgain C. Linkage Analysis with Dense SNP Maps in Isolated Populations. Human Heredity 2009, 68:87-97. 10.1159/000212501, 19365135.
29. Pemberton J. Measuring inbreeding depression in the wild: the old ways are the best. Trends in Ecology & Evolution 2004, 19:613-615.
30. Amos W, Wilmer JW, Fullard K, et al. The influence of parental relatedness on reproductive success. Proceedings of the Royal Society of London Series B-Biological Sciences 2001, 268:2021-2027.