Estimating autozygosity from high-throughput information: Effects of SNP density and genotyping errors

Genetics Selection Evolution

Volumn 45, Issue 1, 2013, Pages

  Ferenčaković, Maja ^a   Sölkner, Johann ^b   Curik, Ino ^a  

^a UNIVERSITY OF ZAGREB   (Croatia)

^b UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SET; ERROR ANALYSIS; ESTIMATION METHOD; GENETIC MARKER; GENOTYPE; INBREEDING; POLYMORPHISM; POPULATION STRUCTURE; PREDICTION;

BOS;

ANIMAL; ARTICLE; CATTLE; CHROMOSOME; GENETIC VARIABILITY; GENETICS; GENOME; GENOTYPE; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; HOMOZYGOTE; HUMAN; INBREEDING; MALE; REGRESSION ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CATTLE; CHROMOSOMES; GENETIC VARIATION; GENOME; GENOTYPE; HETEROZYGOTE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOMOZYGOTE; HUMANS; INBREEDING; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; REGRESSION ANALYSIS;

EID: 84886403456     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/1297-9686-45-42     Document Type: Article

References (24)

1. Extended tracts of homozygosity in outbred human populations. Gibson J, Morton NE, Collins A, Hum Mol Genet 2006 15 789 795 10.1093/hmg/ddi493 16436455 (Pubitemid 43264703)
2. Long homozygous chromosomal segments in reference families from the centre d'étude du polymorphisme humain. Broman KW, Weber JL, Am J Hum Genet 1999 65 1493 1500 10.1086/302661 10577902 (Pubitemid 30468661)
3. Genomic runs of homozygosity record population history and consanguinity. Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF, PLoS One 2010 5 13996 10.1371/journal.pone.0013996 21085596
4. Quantification of inbreeding due to distant ancestors and its detection using dense SNP data. Keller MC, Visscher PM, Goddard ME, Genetics 2011 189 237 249 10.1534/genetics.111.130922 21705750
5. Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Kucherlapati R, Malhotra AK, Proc Natl Acad Sci USA 2007 104 19942 19947 10.1073/pnas.0710021104 18077426
6. Runs of homozygosity and population history in cattle. Purfield DC, Berry DP, McParland S, Bradley DG, BMC Genet 2012 13 70 10.1186/1471-2156-13-70 22888858
7. Runs of homozygosity reveal genome-wideautozygosity in the Austrian fleckvieh cattle. Ferenčaković M, Hamzic E, Gredler B, Curik I, Sölkner J, Agric Conspec Sci 2011 76 325 328
8. Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. Ferenčaković M, Hamzić E, Gredler B, Solberg TR, Klemetsdal G, Curik I, Sölkner J, J Anim Breed Genet 2013 130 286 293 10.1111/jbg.12012 23855630
9. Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Bjelland DW, Weigel KA, Vukasinovic N, Nkrumah JD, J Dairy Sci 2013 96 4697 4706 10.3168/jds.2012-6435 23684028
10. Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. Silió L, Rodríguez MC, Fernández A, Barragán C, Benítez R, Óvilo C, Fernández AI, J Anim Breed Genet 2013 130 349 360 24074172
11. Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms. Howrigan DP, Simonson MA, Keller MC, BMC Genomics 2011 12 460 10.1186/1471-2164-12-460 21943305
12. Ascertainment biases in SNP chips affect measures of population divergence. Albrechtsen A, Nielsen FC, Nielsen R, Mol Biol Evol 2010 27 2534 2547 10.1093/molbev/msq148 20558595
13. A note on exact tests of Hardy-Weinberg equilibrium. Wigginton JE, Cutler DJ, Abecasis GR, Am J Hum Genet 2005 76 887 893 10.1086/429864 15789306 (Pubitemid 40563110)
14. A genotype calling algorithm for affymetrix SNP arrays. Rabbee N, Speed TP, Bioinformatics 2006 22 7 12 10.1093/bioinformatics/bti741 16267090 (Pubitemid 43057002)
15. Genetic variability of populations and similarity of subpopulations in Austria cattle breeds determined by analysis of pedigrees. Sölkner J, Filipcic L, Hampshire N, Anim Sci 1998 67 249 256 10.1017/S1357729800010006
16. PLINK: a toolset for whole-genome association and population-based linkage analysis. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC, Am J Hum Genet 2007 81 559 575 10.1086/519795 17701901 (Pubitemid 47330214)
17. Reconciling the analysis of IBD and IBS in complex trait studies. Powell JE, Visscher PM, Goddard ME, Nat Rev Genet 2010 11 800 805 10.1038/nrg2865 20877324
18. Estimation of the inbreeding coefficient through use of genomic data. Leutenegger AL, Prum B, Genin E, Verny C, Lemainque A, Clerget-Darpoux F, Thompson EA, Am J Hum Genet 2003 73 516 523 10.1086/378207 12900793 (Pubitemid 37076266)
19. SAS Institute Inc, SAS/STAT Software Cary NC: SAS Institute Inc: Version 9.3 2011
20. A simple sequentially rejective multiple test procedure. Holm S, Scand J Stat 1979 6 65 70
21. Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity. Esko T, Mezzavilla M, Nelis M, Borel C, Debniak T, Jakkula E, Julia A, Karachanak S, Khrunin A, Kisfali P, Krulisova V, Aušrelé Kučinskiené Z, Rehnström K, Traglia M, Nikitina-Zake L, Zimprich F, Antonarakis SE, Estivill X, Glavač D, Gut I, Klovins J, Krawczak M, Kučinskas V, Lathrop M, Macek M, Marsal S, Meitinger T, Melegh B, Limborska S, Lubinski J, et al. Eur J Hum Genet 2013 21 659 665 10.1038/ejhg.2012.229 23249956
22. cgaTOH: extended approach for identifying tracts of homozygosity. Zhang L, Orloff MS, Reber S, Li S, Zhao Y, Eng C, PLoS One 2013 8 57772 10.1371/journal.pone.0057772 23469237
23. Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans. Nothnagel M, Lu TT, Kayser M, Krawczak M, Hum Mol Genet 2010 19 2927 2935 10.1093/hmg/ddq198 20462934
24. Genomic patterns of homozygosity in worldwide human populations. Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ, Am J Hum Genet 2012 91 275 292 10.1016/j.ajhg.2012.06.014 22883143.