Qxpak.5: Old mixed model solutions for new genomics problems

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Pérez Enciso, Miguel ^a   Misztal, Ignacy ^b  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION ANALYSIS; GENETIC ANALYSIS; GENETIC EFFECTS; MOLECULAR INFORMATION; POPULATION STRUCTURES; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODELING; UNIFIED APPROACH;

BIT ERROR RATE;

ALGORITHM; ANIMAL; ARTICLE; COMPUTER PROGRAM; GENETIC DATABASE; GENOMICS; HUMAN; METHODOLOGY; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; DATABASES, GENETIC; GENOMICS; HUMANS; MODELS, STATISTICAL; QUANTITATIVE TRAIT LOCI; SOFTWARE;

EID: 80052883231     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-202     Document Type: Article

References (17)

1. Henderson CR. Applications of Linear Models in Animal Breeding. 1984, University of Guelph.
2. Zhang Z, Ersoz E, Lai C-Q, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES. Mixed linear model approach adapted for genome-wide association studies. Nat Genet 2010, 42(4):355-360. 10.1038/ng.546, 2931336, 20208535.
3. Kang HM, Sul JH, Service SK, Zaitlen NA, Kong S, Freimer NB, Sabatti C, Eskin E. Variance component model to account for sample structure in genome-wide association studies. Nat Genet 2010, 42(4):348-354. 10.1038/ng.548, 3092069, 20208533.
4. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW, Goddard ME, Visscher PM. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 2010, 42(7):565-569. 10.1038/ng.608, 20562875.
5. Pérez-Enciso M, Misztal I. Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics 2004, 20(16):2792-2798. 10.1093/bioinformatics/bth331, 15166025.
6. Broman KW, Wu H, Sen S, Churchill GA. R/qtl: QTL mapping in experimental crosses. Bioinformatics 2003, 19(7):889-890. 10.1093/bioinformatics/btg112, 12724300.
7. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am J Hum Genet 2007, 81(3):559-575. 10.1086/519795, 1950838, 17701901.
8. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. GenABEL: an R library for genome-wide association analysis. Bioinformatics 2007, 23(10):1294-1296. 10.1093/bioinformatics/btm108, 17384015.
9. Ma CX, Wu R, Casella G. FunMap: functional mapping of complex traits. Bioinformatics 2004, 20(11):1808-1811. 10.1093/bioinformatics/bth156, 14988108.
10. Pérez-Enciso M, Varona L. Quantitative trait loci mapping in F2 crosses between outbred lines. Genetics 2000, 155(1):391-405. 1461080, 10790412.
11. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, Smink LJ, Lam AC, Ovington NR, Stevens HE, Nutland S, Howson JM, Faham M, Moorhead M, Jones HB, Falkowski M, Hardenbol P, Willis TD, Todd JA. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 2005, 37(11):1243-1246. 10.1038/ng1653, 16228001.
12. Yu J, Pressoir G, Briggs WH, Vroh I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 2006, 38(2):203-208. 10.1038/ng1702, 16380716.
13. Price AL, Zaitlen NA, Reich D, Patterson N. New approaches to population stratification in genome-wide association studies. Nat Rev Genet 2010, 11(7):459-463. 2975875, 20548291.
14. Legarra A, Aguilar I, Misztal I. A relationship matrix including full pedigree and genomic information. J Dairy Sci 2009, 92(9):4656-4663. 10.3168/jds.2009-2061, 19700729.
15. Ovilo C, Oliver A, Noguera JL, Clop A, Barragan C, Varona L, Rodriguez C, Toro M, Sanchez A, Perez-Enciso M, Silio L. Test for positional candidate genes for body composition on pig chromosome 6. Genet Sel Evol 2002, 34(4):465-479. 10.1186/1297-9686-34-4-465, 2705456, 12270105.
16. Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Haley CS, Buys N, Tally M, Andersson G, Georges M, Andersson L. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 2003, 425(6960):832-836. 10.1038/nature02064, 14574411.
17. Mercade A, Estelle J, Noguera JL, Folch JM, Varona L, Silio L, Sanchez A, Perez-Enciso M. On growth, fatness, and form: a further look at porcine chromosome 4 in an Iberian × Landrace cross. Mamm Genome 2005, 16(5):374-382. 10.1007/s00335-004-2447-4, 16104385.