Microarray resources for genetic and genomic studies in chicken: A review

Genesis

Volumn 51, Issue 5, 2013, Pages 337-356

  Gheyas, Almas A ^a   Burt, David W ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

ACGH; Capture array; Gene expression array; Genotyping array

Indexed keywords

ALGORITHM; ALTERNATIVE RNA SPLICING; ANIMAL GENETICS; BODY WEIGHT; CHICKEN; CHROMOSOME 1; CHROMOSOME 4; CHROMOSOME 5; COMPARATIVE GENOMIC HYBRIDIZATION; DOMESTICATION; EMBRYO; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC IMPROVEMENT; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HAPLOTYPE MAP; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; IMMUNE RESPONSE; LIPID METABOLISM; LIVESTOCK; METAPHASE CHROMOSOME; MICROARRAY ANALYSIS; MITOCHONDRION; NONHUMAN; PHENOTYPE; POPULATION STRUCTURE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; REVIEW; RNA SEQUENCE; SEX CHROMOSOME; SIGNAL NOISE RATIO; THERMOSTABILITY;

ANIMALS; CHICKENS; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LIVESTOCK; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

AVES;

EID: 84878187143     PISSN: 1526954X     EISSN: 1526968X     Source Type: Journal    
DOI: 10.1002/dvg.22387     Document Type: Review

References (108)

1. Abasht B, Lamont SJ. 2007. Genome-wide association analysis reveals cryptic alleles as an important factor in heterosis for fatness in chicken F2 population. Anim Genet 38:491-498.
2. Aerts J, Megens HJ, Veenendaal T, Ovcharenko I, Crooijmans R, Gordon L, Stubbs L, Groenen M. 2007. Extent of linkage disequilibrium in chicken. Cytogenet Genome Res 117:338-345.
3. Afrakhte M, Schultheiss TM. 2004. Construction and analysis of a subtracted library and microarray of cDNAs expressed specifically in chicken heart progenitor cells. Dev Dyn 230:290-298.
4. Alkan C, Coe BP, Eichler EE. 2011. Genome structural variation discovery and genotyping. Nat Rev Genet 12:363-376.
5. Almomani R, van der Heijden J, Ariyurek Y, Lai Y, Bakker E, van Galen M, Breuning MH, den Dunnen JT. 2011. Experiences with array-based sequence capture; toward clinical applications. Eur J Hum Genet 19:50-55.
6. Andreescu C, Avendano S, Brown SR, Hassen A, Lamont SJ, Dekkers JCM. 2007. Linkage disequilibrium in related breeding lines of chickens. Genetics 177:2161-2169.
7. Avendaño S, Watson K, Kranis A. 2010. Genomics in poultry breeding: from Utopia to deliverables. In: Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, August 1-6, 2010, Leipzig, Germany. 761 Session 07-01. ISBN 978-3-00-031608-1.
8. Bailey MJ, Beremand PD, Hammer R, Bell-Pedersen D, Thomas TL, Cassone VM. 2003. Transcriptional profiling of the chick pineal gland, a photoreceptive circadian oscillator and pacemaker. Mol Endocrinol 17:2084-2095.
9. Bliss TW, Dohms JE, Emara MG, Keeler CL. 2005. Gene expression profiling of avian macrophage activation. Vet Immunol Immunopathol 105:289-299.
10. Blum Y, Le Mignon G, Causeur D, Filangi O, Desert C, Demeure O, Le Roy P, Lagarrigue S. 2011. Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken. BMC Genomics 12:567.
11. Boardman PE, Sanz-Ezquerro J, Overton IM, Burt DW, Bosch E, Fong WT, Tickle C, Brown WR, Wilson SA, Hubbard SJ. 2002. A comprehensive collection of chicken cDNAs. Curr Biol 12:1965-1969.
12. Bottje WG, Kong BW, Song JJ, Lee JY, Hargis BM, Lassiter K, Wing T, Hardiman J. 2012. Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K microarray. II. Differentially expressed focus genes. Poult Sci 91:2576-2587.
13. Brasch-Andersen C, Christiansen L, Tan Q, Haagerup A, Vestbo J, Kruse TA. 2004. Possible gene dosage effect of glutathione-S-transferases on atopic asthma: Using real-time PCR for quantification of GSTM1 and GSTT1 gene copy numbers. Hum Mutat 24:208-214.
14. Brown WR, Hubbard SJ, Tickle C, Wilson SA. 2003. The chicken as a model for large-scale analysis of vertebrate gene function. Nat Rev Genet 4:87-98.
15. Bureau C, Hennequet-Antier C, Couty M, Guemene D. 2009. Gene array analysis of adrenal glands in broiler chickens following ACTH treatment. BMC Genomics 10:430.
16. Burnside J, Neiman P, Tang JS, Basom R, Talbot R, Aronszajn M, Burt D, Delrow J. 2005. Development of a cDNA array for chicken gene expression analysis. BMC Genomics 6:13.
17. Caldwell RB, Kierzek AM, Arakawa H, Bezzubov Y, Zaim J, Fiedler P, Kutter S, Blagodatski A, Kostovska D, Koter M, Plachy J, Carninci P, Hayashizaki Y, Buerstedde JM. 2005. Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. Genome Biol 6:R6.
18. Carson AR, Feuk L, Mohammed M, Scherer SW. 2006. Strategies for the detection of copy number and other structural variants in the human genome. Hum Genomics 2:403-414.
19. Chiang H-I, Swaggerty CL, Kogut MH, Dowd SE, Li X, Pevzner IY, Zhou H. 2008. Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44 K Agilent microarray. BMC Genomics 9.
20. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613-619.
21. Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, Zhu JJ, Cheng HH, Dodgson JB, Burnside J. 2007. Functional genomics of the chicken-A model organism. Poult Sci 86:2059-2094.
22. Cogburn LA, Wang X, Carre W, Rejto L, Porter TE, Aggrey SE, Simon J. 2003. Systems-wide chicken DNA microarrays, gene expression profiling, and discovery of functional genes. Poult Sci 82:939-951.
23. Davison TF. 2003. The immunologists' debt to the chicken. Br Poult Sci 44:6-21.
24. de Koning DJ, Cabrera CP, Haley CS. 2007. Genetical genomics: Combining gene expression with marker genotypes in poultry. Poult Sci 86:1501-1509.
25. Dekkers JCM SC, Fernando RL, Garrick DJ, Lamont SJ, O'Sullivan NP, Fulton JE, Arango J, Settar P, Kranis A, McKay J, Watson KA, Koerhuis A, Preisinger R. 2010. Implementation of genomic selection in egg layer chickens. J Anim Sci 87 (E-Suppl. 2/J): iii.
26. Elferink MG, Megens HJ, Vereijken A, Hu XX, Crooijmans RPMA, Groenen MAM. 2012. Signatures of selection in the genomes of commercial and non-commercial chicken breeds. Plos One 7:e32720.
27. Elferink MG, Vallee AA, Jungerius AP, Crooijmans RP, Groenen MA. 2008. Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken. BMC Genomics 9:391.
28. Elferink MG, van As P, Veenendaal T, Crooijmans RP, Groenen MA. 2010. Regional differences in recombination hotspots between two chicken populations. BMC Genet 11:11.
29. Ellestad LE, Carre W, Muchow M, Jenkins SA, Wang XF, Cogburn LA, Porter TE. 2006. Gene expression profiling during cellular differentiation in the embryonic pituitary gland using cDNA microarrays. Physiol Genomics 25:414-425.
30. Fadista J, Nygaard M, Holm LE, Thomsen B, Bendixen C. 2008. A snapshot of CNVs in the pig genome. Plos One 3:e3916.
31. Fanciulli M, Norsworthy PJ, Petretto E, Dong R, Harper L, Kamesh L, Heward JM, Gough SC, de Smith A, Blakemore AI, Froguel P, Owen CJ, Pearce SH, Teixeira L, Guillevin L, Graham DS, Pusey CD, Cook HT, Vyse TJ, Aitman TJ. 2007. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat Genet 39:721-723.
32. Fontanesi L, Beretti F, Martelli PL, Colombo M, Dall'Olio S, Occidente M, Portolano B, Casadio R, Matassino D, Russo V. 2011. A first comparative map of copy number variations in the sheep genome. Genomics 97:158-165.
33. Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Rovin BH, Bradley W, Clark RA, Anderson SA, O'Connell R J, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ, Ahuja SK. 2005. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307:1434-1440.
34. Griffin DK, Robertson LB, Tempest HG, Vignal A, Fillon V, Crooijmans RP, Groenen MA, Deryusheva S, Gaginskaya E, Carre W, Waddington D, Talbot R, Volker M, Masabanda JS, Burt DW. 2008. Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics 9:168.
35. Groenen MAM, Megens HJ, Zare Y, Warren WC, Hillier LW, Crooijmans RPMA, Vereijken A, Okimoto R, Muir WM, Cheng HH. 2011. The development and characterization of a 60K SNP chip for chicken. BMC Genomics 12:274.
36. Groenen MAM, Wahlberg P, Foglio M, Cheng HH, Megens HJ, Crooijmans RPMA, Besnier F, Lathrop M, Muir WM, Wong GKS, Gut I, Andersson L. 2009. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res 19:510-519.
37. Gu X, Feng C, Ma L, Song C, Wang Y, Da Y, Li H, Chen K, Ye S, Ge C, Hu X, Li N. 2011. Genome-wide association study of body weight in chicken F2 resource population. Plos One 6:e21872.
38. Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS. 2005. A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet 37:549-554.
39. Habier D, Fernando RL, Dekkers JCM. 2009. Genomic selection using low-density marker panels. Genetics 182:343-353.
40. Habig C, Geffers R, Distl O. 2012. Differential gene expression from genome-wide microarray analyses distinguishes Lohmann selected leghorn and Lohmann brown layers. Plos One 7:e46787.
41. Hackam AS, Bradford RL, Bakhru RN, Shah RM, Farkas R, Zack DJ, Adler R. 2003. Gene discovery in the embryonic chick retina. Mol Vis 9:262-276.
42. Hardiman G. 2004. Microarray platforms--Comparisons and contrasts. Pharmacogenomics 5:487-502.
43. Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA. 2009. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 10:R32.
44. Heidari M, Sarson AJ, Huebner M, Sharif S, Kireev D, Zhou H. 2010. Marek's disease virus-induced immunosuppression: Array analysis of chicken immune response gene expression profiling. Viral Immunol 23:309-319.
45. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106:9362-9367.
46. Hou Y, Liu GE, Bickhart DM, Cardone MF, Wang K, Kim ES, Matukumalli LK, Ventura M, Song J, VanRaden PM, Sonstegard TS, Van Tassell CP. 2011. Genomic characteristics of cattle copy number variations. BMC Genomics 12:127.
47. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342-347.
48. Hurd PJ, Nelson CJ. 2009. Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomic Proteomic 8:174-183.
49. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36:949-951.
50. International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.
51. International Chicken Polymorphism Map Consortium. 2004. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432:717-722.
52. Kano R, Konnai S, Onuma M, Ohashi K. 2009. Microarray analysis of host immune responses to marek's disease virus infection in vaccinated chickens. J Vet Med Sci 71:603-610.
53. Kranis A, Gheyas AA, Boschiero C, Turner F, Yu L, Smith S, Talbot R, Pirani A, Brew F, Kaiser P, Hocking PM, Fife M, Salmon N, Fulton J, Strom TM, Haberer G, Weigend S, Preisinger R, Gholami M, Qanbari S, Simianer H, Watson KA, Woolliams JA, Burt DW. 2013. Development of a high density 600K SNP genotyping array for chicken. BMC Genomics 14:59.
54. Kong BW, Song JJ, Lee JY, Hargis BM, Wing T, Lassiter K, Bottje W. 2011. Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K oligo microarray. I. Top differentially expressed genes. Poult Sci 90:2535-2547.
55. Le Bihan-Duval E, Nadaf J, Berri C, Pitel F, Graulet B, Godet E, Leroux SY, Demeure O, Lagarrigue S, Duby C, Cogburn LA, Beaumont CM, Duclos MJ. 2011. Detection of a Cis [corrected] eQTL controlling BCMO1 gene expression leads to the identification of a QTG for chicken breast meat color. Plos One 6:e14825.
56. Le Mignon G, Desert C, Pitel F, Leroux S, Demeure O, Guernec G, Abasht B, Douaire M, Le Roy P, Lagarrigue S. 2009. Using transcriptome profiling to characterize QTL regions on chicken chromosome 5. BMC Genomics 10:575.
57. Ledford H. 2008. The death of microarrays? Nature 455:847-847.
58. Li CL, Wang XL, Li N, Wu CX. 2012. Microarray analysis revealed that immunity-associated genes are primarily regulated by roxarsone in promoting broiler chicken (Gallus gallus domesticus) growth. Poult Sci 91:3184-3190.
59. Li XY, Chiang HI, Zhu J, Dowd SE, Zhou HJ. 2008. Characterization of a newly developed chicken 44K Agilent microarray. BMC Genomics 9:60.
60. Liu GE, Hou Y, Zhu B, Cardone MF, Jiang L, Cellamare A, Mitra A, Alexander LJ, Coutinho LL, Dell'Aquila ME, Gasbarre LC, Lacalandra G, Li RW, Matukumalli LK, Nonneman D, Regitano LC, Smith TP, Song J, Sonstegard TS, Van Tassell CP, Ventura M, Eichler EE, McDaneld TG, Keele JW. 2010. Analysis of copy number variations among diverse cattle breeds. Genome Res 20:693-703.
61. Maher B. 2008. Personal genomes: The case of the missing heritability. Nature 456:18-21.
62. Marchini J, Howie B. 2010. Genotype imputation for genome-wide association studies. Nat Rev Genet 11:499-511.
63. McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette P, Zody MC, Hall JL, Brant SR, Cho JH, Duerr RH, Silverberg MS, Taylor KD, Rioux JD, Altshuler D, Daly MJ, Xavier RJ. 2008. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet 40:1107-1112.
64. McKinney C, Merriman ME, Chapman PT, Gow PJ, Harrison AA, Highton J, Jones PB, McLean L, O'Donnell JL, Pokorny V, Spellerberg M, Stamp LK, Willis J, Steer S, Merriman TR. 2008. Evidence for an influence of chemokine ligand 3-like 1 (CCL3L1) gene copy number on susceptibility to rheumatoid arthritis. Ann Rheum Dis 67:409-413.
65. Megens HJ, Crooijmans RPMA, Bastiaansen JWM, Kerstens HHD, Coster A, Jalving R, Vereijken A, Silva P, Muir WM, Cheng HH, Hanotte O, Groenen MAM. 2009. Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken. BMC Genet 10:86.
66. Meuwissen THE, Hayes BJ, Goddard ME. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
67. Miller MB, Tang YW. 2009. Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev 22:611-633.
68. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621-628.
69. Muir WM, Wong GK, Zhang Y, Wang J, Groenen MA, Crooijmans RP, Megens HJ, Zhang H, Okimoto R, Vereijken A, Jungerius A, Albers GA, Lawley CT, Delany ME, MacEachern S, Cheng HH. 2008a. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci USA 105:17312-17317.
70. Muir WM, Wong GK, Zhang Y, Wang J, Groenen MAM, Crooijmans RPMA, Megens H-J, Zhang HM, Mckay JC, Mcleod S, Okimoto R, Fulton JE, Settar P, O'sullivan NP, Vereijken A, Jungerius-Rattink A, Albers GAA, Taylor LC, Delany ME, Cheng HH. 2008b. Review of the initial validation and characterization of a 3K chicken SNP array. Worlds Poult Sci J 64:219-226.
71. Murphy D. 2002. Gene expression studies using microarrays: Principles, problems, and prospects. Adv Physiol Educ 26:256-270.
72. Neiman PE, Grbic JJ, Polony TS, Kimmel R, Bowers SJ, Delrow J, Beemon KL. 2003. Functional genomic analysis reveals distinct neoplastic phenotypes associated with c-myb mutation in the bursa of Fabricius. Oncogene 22:1073-1086.
73. Neiman PE, Ruddell A, Jasoni C, Loring G, Thomas SJ, Brandvold KA, Lee RM, Burnside J, Delrow J. 2001. Analysis of gene expression during myc oncogene-induced lymphomagenesis in the bursa of Fabricius. Proc Natl Acad Sci USA 98:6378-6383.
74. Nielsen R, Paul JS, Albrechtsen A, Song YS. 2011. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12:443-451.
75. Perez-Enciso M, Ferretti L. 2010. Massive parallel sequencing in animal genetics: Wherefroms and wheretos. Anim Genet 41:561-569.
76. Pinto D, Darvishi K, Shi XH, Rajan D, Rigler D, Fitzgerald T, Lionel AC, Thiruvahindrapuram B, MacDonald JR, Mills R, Prasad A, Noonan K, Gribble S, Prigmore E, Donahoe PK, Smith RS, Park JH, Hurles ME, Carter NP, Lee C, Scherer SW, Feuk L. 2011. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 29:U512-U576.
77. Preisinger R. 2012. Genome-wide selection in poultry. Anim Prod Sci 52:121-125.
78. Qanbari S, Hansen M, Weigend S, Preisinger R, Simianer H. 2010. Linkage disequilibrium reveals different demographic history in egg laying chickens. BMC Genet 11:103.
79. Ramayo-Caldas Y, Castello A, Pena RN, Alves E, Mercade A, Souza CA, Fernandez AI, Perez-Enciso M, Folch JM. 2010. Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip. BMC Genomics 11:593.
80. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles ME. 2006. Global variation in copy number in the human genome. Nature 444:444-454.
81. Ren C, Lee MK, Yan B, Ding K, Cox B, Romanov MN, Price JA, Dodgson JB, Zhang HB. 2003. A BAC-based physical map of the chicken genome. Genome Res 13:2754-2758.
82. Rincon G, Weber KL, Van Eenennaam AL, Golden BL, Medrano JF. 2011. Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys. J Dairy Sci 94:6116-6121.
83. Robb EA, Delany ME. 2012. Case study of sequence capture enrichment technology: Identification of variation underpinning developmental syndromes in an amniote model. Genes 3:233-247.
84. Roh SW, Abell GC, Kim KH, Nam YD, Bae JW. 2010. Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends Biotechnol 28:291-299.
85. Rubin CJ, Zody MC, Eriksson J, Meadows JRS, Sherwood E, Webster MT, Jiang L, Ingman M, Sharpe T, Ka S, Hallbook F, Besnier F, Carlborg O, Bed'hom B, Tixier-Boichard M, Jensen P, Siegel P, Lindblad-Toh K, Andersson L. 2010. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464:U587-U145.
86. Schmutz J, Grimwood J. 2004. Genomes: fowl sequence. Nature 432:679-680.
87. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. 2004. Large-scale copy number polymorphism in the human genome. Science 305:525-528.
88. Shendure J. 2008. The beginning of the end for microarrays? Nat Methods 5:585-587.
89. Shendure J. 2011. Next-generation human genetics. Genome Biol 12:408.
90. Skinner BM, Robertson LB, Tempest HG, Langley EJ, Ioannou D, Fowler KE, Crooijmans RP, Hall AD, Griffin DK, Volker M. 2009. Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis. BMC Genomics 10:357.
91. Smith J, Sadeyen JR, Paton IR, Hocking PM, Salmon N, Fife M, Nair V, Burt DW, Kaiser P. 2011. Systems analysis of immune responses in Marek's disease virus-infected chickens identifies a gene involved in susceptibility and highlights a possible novel pathogenicity mechanism. J Virol 85:11146-11158.
92. Smith J, Speed D, Hocking PM, Talbot RT, Degen WGJ, Schijns VEJC, Glass EJ, Burt DW. 2006. Development of a chicken 5 K microarray targeted towards immune function. BMC Genomics 7:49.
93. Stern CD. 2005. The chick; a great model system becomes even greater. Dev Cell 8:9-17.
94. Syvanen AC. 2005. Toward genome-wide SNP genotyping. Nat Genet 37(Suppl): S5-S10.
95. The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437:1299-1320.
96. Theisen A. 2008. Microarray-based comparative genomic hybridization (aCGH). Nat Educ 1:1. In: http://www.nature.com/scitable/topicpage/microarray-based-comparative-genomic-hybridization-acgh-45432.
97. Tsuchihashi Z, Dracopoli NC. 2002. Progress in high throughput SNP genotyping methods. Pharmacogenomics J 2:103-110.
98. Volker M, Backstrom N, Skinner BM, Langley EJ, Bunzey SK, Ellegren H, Griffin DK. 2010. Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Res 20:503-511.
99. Wang H-B, Li H, Wang Q-G, Zhang X-Y, Wang S-Z, Wang Y-X, Wang X-P. 2007. Profiling of chicken adipose tissue gene expression by genome array. BMC Genomics 8:193.
100. Wang J, Jiang J, Fu W, Jiang L, Ding X, Liu JF, Zhang Q. 2012. A genome-wide detection of copy number variations using SNP genotyping arrays in swine. BMC Genomics 13:273.
101. Wang X, Nahashon S, Feaster TK, Bohannon-Stewart A, Adefope N. 2010. An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics 11:351.
102. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63.
103. Wolc A, Stricker C, Arango J, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Habier D, Fernando R, Garrick DJ, Lamont SJ, Dekkers JCM. 2011. Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model. Genet Select Evol 43:5.
104. Wong KK, deLeeuw RJ, Dosanjh NS, Kimm LR, Cheng Z, Horsman DE, MacAulay C, Ng RT, Brown CJ, Eichler EE, Lam WL. 2007. A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet 80:91-104.
105. Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G. 2004. A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech 15:276-284.
106. Wright D, Boije H, Meadows JR, Bed'hom B, Gourichon D, Vieaud A, Tixier-Boichard M, Rubin CJ, Imsland F, Hallbook F, Andersson L. 2009. Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genet 5:e1000512.
107. Yang TL, Chen XD, Guo Y, Lei SF, Wang JT, Zhou Q, Pan F, Chen Y, Zhang ZX, Dong SS, Xu XH, Yan H, Liu X, Qiu C, Zhu XZ, Chen T, Li M, Zhang H, Zhang L, Drees BM, Hamilton JJ, Papasian CJ, Recker RR, Song XP, Cheng J, Deng HW. 2008. Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis. Am J Hum Genet 83:663-674.
108. Yauk CL, Berndt ML. 2007. Review of the literature examining the correlation among DNA microarray technologies. Environ Mol Mutagen 48:380-394.