Enhancing animal breeding through quality control in genomic data - a review

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참고문헌 (50)

1. Hayes BJ, "Invited review: genomic selection in dairy cattle: progress and challenges", J Dairy Sci, 92, pp.433~443 (2009)[DOI]
2. Meuwissen THE, "Prediction of total genetic value using genome-wide dense marker maps", Genetics, 157, pp.1819~1829 (2001)[DOI]
3. Wiggans GR, "The genomic evaluation system in the United States : past, present, future", J Dairy Sci, 94, pp.3202~3211 (2011)[DOI]
4. Anderson CA, "Data quality control in genetic case-control association studies", Nat Protoc, 5, pp.1564~1573 (2010)[DOI]
5. Purcell S, "PLINK : a tool set for whole-genome association and population-based linkage analyses", Am J Hum Genet, 81, pp.559~575 (2007)[DOI]
6. García-Ruiz A, "Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection", Proc Natl Acad Sci USA, 113, pp.E3995~E4004 (2016)[DOI]
7. Laurie CC, "Quality control and quality assurance in genotypic data for genome-wide association studies", Genet Epidemiol, 34, pp.591~602 (2010)[DOI]
8. Marees AT, "A tutorial on conducting genome-wide association studies : quality control and statistical analysis", Int J Methods Psychiatr Res, 27, pp.e1608~ (2018)[DOI]
9. "FastQC: a quality control tool for high throughput sequence data" (2010)[URL]
10. Bolger AM, "Trimmomatic: a flexible trimmer for Illumina sequence data", Bioinformatics, 30, pp.2114~2120 (2014)[DOI]
11. Martin M, "Cutadapt removes adapter sequences from high-throughput sequencing reads", EMBnet J, 17, pp.10~12 (2011)[DOI]
12. Li H, Durbin R, "Fast and accurate short read alignment with Burrows–Wheeler transform", Bioinformatics, 25, pp.1754~1760 (2009)[DOI]
13. Langmead B, "Fast gapped-read alignment with Bowtie 2", Nat Methods, 9, pp.357~359 (2012)[DOI]
14. Li H, "The sequence alignment", map format and SAMtools, 2009, pp.25, 2078~2079
15. McKenna A, "The Genome Analysis Toolkit : a MapReduce framework for analyzing next-generation DNA sequencing data", Genome Res, 20, pp.1297~1303 (2010)[DOI]
16. Danecek P, "The variant call format and VCFtools", Bioinformatics, 27, pp.2156~2158 (2011)[DOI]
17. "Haplotype-based variant detection from short-read sequencing" (2012)[URL]
18. Cingolani P, "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3", Fly, 6, pp.80~92 (2012)[DOI]
19. Wang K, "ANNOVAR : functional annotation of genetic variants from high-throughput sequencing data", Nucleic Acids Res, 38, pp.e164~ (2010)[DOI]
20. Robinson JT, "Integrative genomics viewer", Nat Biotechnol, 29, pp.24~26 (2011)[DOI]
21. Kennedy GC, "Large-scale genotyping of complex DNA", Nat Biotechnol, 21, pp.1233~1237 (2003)[DOI]
22. Matsuzaki H, "Genotyping over 100, 000 SNPs on a pair of oligonucleotide arrays", Nat Methods, 1, pp.109~111 (2004)[DOI]
23. Matukumalli LK, "Development and characterization of a high density SNP genotyping assay for cattle", PLOS ONE, 4, pp.e5350~ (2009)[DOI]
24. BovineSNP50 Genotyping BeadChip, "llumina", llumina, ~, pp.Pub. No.: 370-2007-029 (2009)
25. "GenomeStudio Software" (2010)[URL]
26. Pryce JE, "Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle", Genet Sel Evol, 46, pp.71~ (2014)[DOI]
27. Kim S, "Genome-wide identification of candidate genes for milk production traits in Korean Holstein cattle", Animals, 11, pp.1392~ (2021)[DOI]
28. Verma SS, "Imputation and quality control steps for combining multiple genome-wide datasets", Front Genet, 5, pp.370~ (2014)[DOI]
29. Lee J, "Genomic analysis using Bayesian methods under different genotyping platforms in Korean Duroc pigs", Animals, 10, pp.752~ (2020)[DOI]
30. "SNP & Variation Suite™(Version 8.x)" (2024)[URL]
31. Edwards AWF, "G. H. Hardy (1908) and Hardy–Weinberg equilibrium", Genetics, 179, pp.1143~1150 (2008)[DOI]
32. Nielsen E, "An introduction to population genetics: theory and application" (2013), Sinauer Associates
33. Mayo O, "A century of Hardy–Weinberg equilibrium", Twin Res Hum Genet, 11, pp.249~256 (2008)[DOI]
34. Graffelman J, "Testing for Hardy–Weinberg equilibrium at biallelic genetic markers on the X chromosome", Heredity, 116, pp.558~568 (2016)[DOI]
35. Hill WG, "Understanding and using quantitative genetic variation", Philos Trans R Soc B Biol, 365, pp.73~85 (2010)[DOI]
36. Alexander DH, "Fast model-based estimation of ancestry in unrelated individuals", Genome Res, 19, pp.1655~1664 (2009)[DOI]
37. Minelli C, "How should we use information about HWE in the meta-analyses of genetic association studies?", Int J Epidemiol, 37, pp.136~146 (2008)[DOI]
38. McVean G, "A genealogical interpretation of principal components analysis", PLOS Genet, 5, pp.e1000686~ (2009)[DOI]
39. Browning BL, "A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals", Am J Hum Genet, 84, pp.210~223 (2009)[DOI]
40. Sargolzaei M, "A new approach for efficient genotype imputation using information from relatives", BMC Genomics, 15, pp.478~ (2014)[DOI]
41. Pearson TA, "How to interpret a genome-wide association study", JAMA, 299, pp.1335~1344 (2008)[DOI]
42. Kohavi R, "A study of cross-validation and bootstrap for accuracy estimation and model selection", Proceedings of the 14th International Joint Conference on Artificial Intelligence (IJCAI), pp.1137~1143 (1995)
43. Meuwissen T, "Genomic selection : a paradigm shift in animal breeding", Anim Front, 6, pp.6~14 (2016)[DOI]
44. Zhang Z, "Advances in genomic selection in domestic animals", Chin Sci Bull, 56, pp.2655~2663 (2011)[DOI]
45. Berry DP, "Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection", Animal, 5, pp.1162~1169 (2011)[DOI]
46. Howie BN, "A flexible and accurate genotype imputation method for the next generation of genome-wide association studies", PLOS Genet, 5, pp.e1000529~ (2009)[DOI]
47. Howie B, "Fast and accurate genotype imputation in genome-wide association studies through pre-phasing", Nat Genet, 44, pp.955~959 (2012)[DOI]
48. VanRaden PM, "Symposium review : how to implement genomic selection", J Dairy Sci, 103, pp.5291~5301 (2020)
49. Habier D, "Extension of the Bayesian alphabet for genomic selection", BMC Bioinformatics, 12, pp.186~ (2011)[DOI]
50. Misztal I, "Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information", J Dairy Sci, 92, pp.4648~4655 (2009)[DOI]

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