Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Didion, John P ^a,b   Yang, Hyuna ^c   Sheppard, Keith ^d   Fu, Chen Ping ^e   McMillan, Leonard ^e   De Villena, Fernando P M ^a,b   Churchill, Gary A ^d  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c DUKE UNIVERSITY MEDICAL CENTER   (United States)

^d JACKSON LABORATORY   (United States)

^e Brooks Computer Science Building   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; ANALYTICAL ERROR; ARTICLE; ASCERTAINMENT BIAS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA HYBRIDIZATION; EXPERIMENTAL MOUSE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE MAP; HETEROZYGOSITY; MICROARRAY ANALYSIS; MOUSE; MOUSE STRAIN; NONHUMAN; OLIGONUCLEOTIDE PROBE; PHYLOGENY; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; VARIABLE INTENSITY OLIGONUCLEOTIDE PROBE; ALGORITHM; ANIMAL; CATTLE; CHEMISTRY; CLUSTER ANALYSIS; DOG; GENETIC ASSOCIATION; HAPLOTYPE; HUMAN; NUCLEIC ACID HYBRIDIZATION;

BOS; CANIS FAMILIARIS;

ALGORITHMS; ANIMALS; CATTLE; CLUSTER ANALYSIS; DOGS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HAPLOTYPES; HUMANS; MICE; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84855886780     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-34     Document Type: Article

References (38)

1. Yang H, Ding Y, Hutchins LN, Szatkiewicz J, Bell TA, Paigen BJ, Graber JH, Pardo-Manuel de Villena F, Churchill GA. A customized and versatile high-density genotyping array for the mouse. Nat Methods 2009, 6:663-666. 10.1038/nmeth.1359, 2735580, 19668205.
2. Kennedy GC, Matsuzaki H, Dong S, Liu W, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, Liu W, Yang G, Di X, Ryder T, He Z, Surti U, Phillips MS, Boyce-Jacino MT, Fodor SPA, Jones KW. Large-scale genotyping of complex DNA. Nat Biotechnol 2003, 21:1233-1237. 10.1038/nbt869, 12960966.
3. Affymetrix Inc BRLMM-P: A Genotype Calling Method for the SNP 5.0 Array. Affymetrix Inc., http://www.affymetrix.com/support/technical/whitepapers/brlmmp_whitepaper.pdf
4. Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Hon-Tsen Yu A, Nachman MW, Pialek J, Tucker P, Boursot P, McMillan L, Churchill GA, Pardo-Manuel de Villena F. Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet 2011, 43:648-655. 10.1038/ng.847, 3125408, 21623374.
5. Keane TM, Goodstadt L, Danecek P, White M, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte N, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward C, Bala S, Stalker J, Mott R, et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 2011, 477:289-294. 10.1038/nature10413, 21921910.
6. Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R. Ascertainment bias in studies of human genome-wide polymorphism. Genome Res 2005, 15:1496-1502. 10.1101/gr.4107905, 1310637, 16251459.
7. Gibbs R, Taylor J, Van Tassell C, Barendse W, Eversole K, Gill C, Green R, Hamernik D, Kappes S, Lien S, Matukumalli L, McEwan J, Nazareth L, Schnabel R, Weinstock G, Wheeler D, Ajmone-Marsan P, Boettcher P, Caetano A, Garcia J, Hanotte O, Mariani P, Skow L, Sonstegard T, Williams J, Diallo B, Hailemariam L, Martinez M, Morris C, Silva L, et al. Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. Science 2009, 324:528-532. 2735092, 19390050.
8. Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Castelhano M, Mosher DS, Sutter NB, Johnson GS, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bustamante CD, Ostrander EA. A simple genetic architecture underlies morphological variation in dogs. PLoS Biology 2010, 8:e1000451. 10.1371/journal.pbio.1000451, 2919785, 20711490.
9. Callen DF, Thompson AD, Shen Y, Phillips HA, Richards RI, Mulley JC, Sutherland GR. Incidence and origin of "null" alleles in the (AC)n microsatellite markers. Am J Hum Genet 1993, 52:922-7. 1682051, 8488841.
10. Kelly AC, Mateus-Pinilla NE, Douglas M, Douglas M, Shelton P, Novakofski J. Microsatellites behaving badly: empirical evaluation of genotyping errors and subsequent impacts on population studies. Genet Mol Res 2011, 10:2534-53. 10.4238/2011.October.19.1, 22033936.
11. MouseDivGeno http://cgd.jax.org/tools/mousedivgeno, CEL Files http://cgd.jax.org/datasets/diversityarray/CELfiles.shtml, and Annotation Files http://cgd.jax.org/datasets/diversityarray/annotation.shtml.
12. R Development Core Team R: A Language and Environment for Statistical Computing 2011, Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team.
13. Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ, Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M, Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SN, Collins FS, Yang IV, Schwartz DA, Branstetter LA, Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L, Sarkar A, Wang J, et al. Genetic analysis of complex traits in the emerging collaborative cross. Genome Res 2011, 8:1213-1222.
14. VINO Visualization Tool. , http://compgen.unc.edu/Vino
15. Wright MH, Tung C-W, Zhao K, Reynolds A, McCouch SR, Bustamante CD. ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics 2010, 26:2952-2960. 10.1093/bioinformatics/btq533, 2982150, 20926420.
16. Agam A, Yalcin B, Bhomra A, Cubin M, Webber C, Holmes C, Flint J, Mott R. Elusive copy number variation in the mouse genome. PLoS One 2010, 5:e12839. 10.1371/journal.pone.0012839, 2943477, 20877625.
17. Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschleb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, et al. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 2009, 7:e1000112. 10.1371/journal.pbio.1000112, 2680341, 19468303.
18. Yang H, Bell TA, Churchill GA, Pardo-Manuel de Villena F. On the subspecific origin of the laboratory mouse. Nat Genet 2007, 39:1100-1107. 10.1038/ng2087, 17660819.
19. Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB, Pethiyagoda CL, Stuve LL, Johnson FM, Daly MJ, Wade CM, Cox DR. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 2007, 448:1050-1053. 10.1038/nature06067, 17660834.
20. The International HapMap 3 Consortium Integrating common and rare genetic variation in diverse human populations. Nature 2010, 467:52-58. 10.1038/nature09298, 3173859, 20811451, The International HapMap 3 Consortium.
21. Pardo-Manuel de Villena F, . The Collaborative Cross Consortium The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics The Collaborative Cross Consortium.
22. Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 2007, 8:485-499.
23. Hastie TJ. Generalized additive models. Statistical Models in S 1992, 136-173. Pacific Grove, California: Wadsworth & Brooks/Cole, Hastie TJ, Chambers JM.
24. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264. 10.1093/biostatistics/4.2.249, 12925520.
25. Bengtsson H, Irizarry R, Carvalho B, Speed TP. Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics 2008, 24:759-767. 10.1093/bioinformatics/btn016, 18204055.
26. Lovmar L, Ahlford A, Jonsson M, Syvänen A-C. Silhouette scores for assessment of SNP genotype clusters. BMC Genomics 2005, 6:35-40. 10.1186/1471-2164-6-35, 555759, 15760469.
27. Dempster AP, Laird NM, Rubin DB. Maximum Likelihood from Incomplete Data via the EM Algorithm. J R Stat Soc Series B Stat Methodol 1977, 39:1-38.
28. Johnson SC. Hierarchical clustering schemes. Psychometrika 1967, 32:241-254. 10.1007/BF02289588, 5234703.
29. Mosteller F, Tukey JW. Data Analysis and Regression: A Second Course in Statistics 1977, Reading, MA: Addison-Wesley.
30. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007, 17:1665-1674. 10.1101/gr.6861907, 2045149, 17921354.
31. Affymetrix Power Tools. , http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx
32. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
33. Krawitz P, Rödelsperger C, Jäger M, Jostins L, Bauer S, Robinson PN. Microindel detection in short-read sequence data. Bioinformatics 2010, 26:722-729. 10.1093/bioinformatics/btq027, 20144947.
34. Pohl A, Kent J. UCSC Genome Browser source code. , http://hgdownload.cse.ucsc.edu/downloads.html
35. Cox A, Ackert-Bicknell CL, Dumont BL, Ding Y, Bell JT, Brockmann GA, Wergedal JE, Bult C, Paigen B, Flint J, Tsaih S-W, Churchill GA, Broman KW. A new standard genetic map for the laboratory mouse. Genetics 2009, 182:1335-1344. 10.1534/genetics.109.105486, 2728870, 19535546.
36. The 1000 Genomes Consortium A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073. 10.1038/nature09534, 3042601, 20981092, The 1000 Genomes Consortium.
37. Wang J, Pardo-Manuel de Villena F, McMillan L. Dynamic visualization and comparative analysis of multiple collinear genomic data. Proceedings of 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine: 1-3 Aug 2011; Chicago
38. Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755. 10.1093/bioinformatics/17.8.754, 11524383.