Inference of identity by descent in population isolates and optimal sequencing studies

European Journal of Human Genetics

Volumn 21, Issue 10, 2013, Pages 1140-1145

  Glodzik, Dominik ^a   Navarro, Pau ^a   Vitart, Veronique ^a   Hayward, Caroline ^a   Mcquillan, Ruth ^b   Wild, Sarah H ^b   Dunlop, Malcolm G ^a   Rudan, Igor ^a   Campbell, Harry ^a   Haley, Chris ^a   Wright, Alan F ^a   Wilson, James F ^b   Mckeigue, Paul ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

IBD; isolates; resequencing

Indexed keywords

ACCURACY; ADULT; AGED; ARTICLE; CONTROLLED STUDY; GENE LOCUS; GENE SEQUENCE; GENETIC PROCEDURES; GENOME; GENOTYPE; HAPLOTYPE; HUMAN; IDENTITY BY DESCENT; ISOLATION PROCEDURE; MAJOR CLINICAL STUDY; PARENT; PRIORITY JOURNAL; PROGENY; SENSITIVITY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; ALGORITHMS; CASE-CONTROL STUDIES; GENETIC LOCI; GENETICS, MEDICAL; HAPLOTYPES; HUMANS; ISLANDS; MIDDLE AGED; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION; REPRODUCTIVE ISOLATION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 84884587140     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2012.307     Document Type: Article

References (25)

1. Powell JE, Visscher PM, Goddard ME: Reconciling the analysis of IBD and IBS in complex trait studies. Nat Rev Genet 2010; 11: 800-805
2. Gusev A, Kenny EE, Lowe JK et al: Dash: A method for identical-by-descent haplotype mapping uncovers association with recent variation. Am J Hum Genet 2011; 88: 706-717
3. Browning SR, Thompson EA: Detecting rare variant associations by identity-by-descent mapping in case-control studies. Genetics 2012; 190: 1521-1531
4. Zeggini E: Next-generation association studies for complex traits. Nat Genet 2011; 43: 287-288
5. Terwilliger JD, Weiss KM: Linkage disequilibrium mapping of complex disease: Fantasy or reality? Curr Opin Biotechnol 1998; 9: 578-594
6. Johnson G, Esposito L, Barratt BJ et al: Haplotype tagging for the identification of common disease genes. Nat Genet 2001; 29: 233-237
7. Morris AP, Whittaker JC, Balding DJ: Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies. Am J Hum Genet 2002; 70: 686-707
8. Browning SR, Browning BL: Haplotype phasing: Existing methods and new developments. Nat Rev Genet 2011; 12: 703-714
9. Kong A, Masson G, Frigge ML et al: Detection of sharing by descent, long-range phasing and haplotype imputation. Nat Genet 2008; 40: 1068-1075
10. Kong A, Steinthorsdottir V, Masson G et al: Parental origin of sequence variants associated with complex diseases. Nature 2009; 462: 868-874
11. Hickey JM, Kinghorn P, Tier B et al: A combined long-range phasing and long haplotype imputation method to impute phase for snp genotypes. Genet Sel Evol 2011; 43: 12
12. Palin K, Campbell H, Wright AF, Wilson JF, Durbin R: Identity-by-descent- based phasing and imputation in founder populations using graphical models. Genet Epidemiol 2011; 8: 853-860
13. Browning BL, Browning SR: A fast, powerful method for detecting identity by descent. Am J Hum Genet 2011; 88: 173-182
14. McQuillan R, Leutenegger AL, Abdel-Rahman R et al: Runs of homozygosity in european populations. Am J Hum Genet 2008; 83: 359-372
15. Wilson JF, Weiss DA, Richards M et al: Genetic evidence for different male and female roles during cultural transitions in the British isles. Proc Natl Acad Sci USA 2001; 98: 5078-5083
16. Vitart V, Biloglav Z, Hayward C et al: 3000 years of solitude: Extreme differentiation in the island isolates of Dalmatia, Croatia. Eur J Hum Genet 2006; 14: 478-4876
17. Polasek O, Marusic A, Rotim K et al: Genome-wide association study of anthropometric traits in Korcula Island, Croatia. Croat Med J 2009; 50: 7-16
18. Browning SR, Browning BL: High-resolution detection of identity by descent in unrelated individuals. Am J Hum Genet 2010; 86: 526-539
19. Duret L: Mutation patterns in the human genome: More variable than expected. PLoS Biol 2009; 7: E1000028
20. Nachman MW, Crowell SL: Estimate of the mutation rate per nucleotide in humans. Genetics 2000; 156: 297-304
21. Genovese G, Leibon G, Pollak MR, Rockmore DN: Improved IBD detection using incomplete haplotype information. BMC Genet 2010; 11: 58
22. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P: A fine-scale map of recombination rates and hotspots across the human genome. Science 2005; 310: 321-324
23. International HapMap ConsortiumFrazer KA, Ballinger DG, Cox DR et al: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851-861
24. Albrechtsen A, Moltke I, Nielsen R: Natural selection and the distribution of identityby- descent in the human genome. Genetics 2010; 186: 295-308
25. Gusev A, Kenny EE, Lowe JK et al: Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population. Genetics 2012; 190: 679-689