Genomic position mapping discrepancies of commercial SNP chips

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Fadista, João ^a   Bendixen, Christian ^b  

^a LUND UNIVERSITY   (Sweden)

^b AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; COW; DNA FLANKING REGION; DNA MICROARRAY; GENE LOCATION; GENE MAPPING; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; MOUSE; NONHUMAN; PROMOTER REGION; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; CATTLE; CHROMOSOME; CHROMOSOME MAP; GENETICS; GENOME; GENOMICS; GENOTYPING TECHNIQUE; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ANIMALS; BASE SEQUENCE; CATTLE; CHROMOSOME MAPPING; CHROMOSOMES, MAMMALIAN; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPING TECHNIQUES; HUMANS; MICE; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84857179035     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031025     Document Type: Article

References (13)

1. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Schmitt AO, Bortfeldt RH, Brockmann GA, (2010) Tracking chromosomal positions of oligomers- a case study with Illumina's BovineSNP50 beadchip. BMC Genomics 11: 80-87.
4. Zhang Z, Schwartz S, Wagner L, Miller W, (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-214.
5. Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, et al. (2010) The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330: 1551-1557.
6. Pelak K, Goldstein DB, Walley NM, Fellay J, Ge D, et al. (2010) Host determinants of HIV-1 control in African Americans. J Infect Dis 201: 1141-1149.
7. Macgregor S, Hewitt AW, Hysi PG, Ruddle JB, Medland SE, et al. (2010) Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. Hum Mol Genet 19: 2716-2724.
8. Anderson CA, Pettersson FH, Barrett JC, Zhuang JJ, Ragoussis J, et al. (2008) Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms. Am J Hum Genet 83: 112-119.
9. Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, et al. (2004) Complex SNP-related sequence variation in segmental genome duplications. Nat Genet 36: 861-866.
10. Ho MR, Tsai KW, Chen CH, Lin WC, (2011) dbDNV: a resource of duplicated gene nucleotide variants in human genome. Nucleic Acids Res 39: D920-925.
11. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522-528.
12. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, et al. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 10: R42.
13. Luethy R, Hoover C, (2004) Hardware and software systems for accelerating common bioinformatics sequence analysis algorithms. Biosilico 2: 12-17.