Whole-genome genotyping of haplotype tag single nucleotide polymorphisms

Pharmacogenomics

Volumn 7, Issue 4, 2006, Pages 641-648

  Gunderson, Kevin L ^a   Kuhn, Kenneth M ^a   Steemers, Frank J ^a   Ng, Pauline ^a   Murray, Sarah S ^a   Shen, Richard ^a  

^a ILLUMINA INC   (United States)

Author keywords

ASPE; Association; Genotyping; Haplotype; Infinium; Linkage disequilibrium; SBE; SNP; Tag SNP; Whole genome genotyping

Indexed keywords

2,4 DINITROPHENOL; BIOTIN; DNA POLYMERASE; GENOMIC DNA;

AUTOMATION; BIOCHEMISTRY; COMPUTER PROGRAM; COST EFFECTIVENESS ANALYSIS; DRUG RESPONSE; GENE CLUSTER; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE TARGETING; GENETIC DISORDER; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY LOSS; HUMAN; HUMAN GENOME; MAJOR HISTOCOMPATIBILITY COMPLEX; PHARMACOGENOMICS; REPRODUCIBILITY; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

AUTOMATION; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHARMACOGENETICS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 33745159993     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/14622416.7.4.641     Document Type: Review

References (17)

1. Walgren RA, Meucci MA, McLeod HL: Pharmacogenomic discovery approaches: will the real genes please stand up? J. Clin. Oncol. 23 (29), 7342-7349 (2005).
2. Evans WE, McLeod HL: Pharmacogenomics - drug disposition, drug targets, and side effects. N. Engl. J. Med. 348(6), 538-549 (2003).
3. Hirschhorn JN. Daly MJ: Genome-wide association studies for common diseases and complex traits. Nature Rev. Genet. 6(2), 95-108 (2005).
4. Lin M, Aquilante C, Johnson JA, Wu R: Sequencing drug response with HapMap Pharmacogenomics 5(3), 149-156 (2005).
5. Gabriel SB, Schaffner SF, Nguyen H et al.: The structure of haplotype blocks in the human genome. Science 296(5576), 2225-2229 (2002).
6. Salisbury BA, Pungliya M, Choi JY, Jiang R, Sun XJ, Stephens JC: SNP and haplotype variation in the human genome. Mutat. Res. 526(1-2), 53-61 (2003).
7. Johnson GC, Esposito L, Barratt BJ et al.: Haplotype tagging for the identification of common disease genes. Nature Genet. 29 (2), 233-237 (2001).
8. Cardon LR, Abecasis GR: Using haplotype blocks to map human complex trait loci. Trends Genet. 19(3), 135-140 (2003).
9. Hinds DA, Stuve LL, Nilsen GB et al.: Whole-genome patterns of common DNA variation in three human populations. Science 307(5712), 1072-1079 (2005).
10. Altshuler D, Brooks LD, Chakravarti A et al.: A haplotype map of the human genome. Nature, 437(7063), 1299-1320 (2005).
11. Gunderson KL, Steemers FJ, Kuhn K et al.: Whole Genome Genotyping on BeadChips with Illuminas Infinium™ - Assay. DNA Press, Cold Spring Harbor, NY, USA, p264 (2005).
12. Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen L, Syvanen AC: A system for specific, high throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10(7), 1031-1042 (2000).
13. Pastinen T, Kurg A, Metspalu A, Peltonen L, Syvanen AC: Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7(6), 606-614 (1997).
14. Steemers FJ, Chang W, Lee G, Barker DL, Shen R. Gunderson KL: Whole-genome genotyping with the single-base extension assay. Nature Methods 3(1), 31-33 (2006).
15. Gunderson KL, Kruglyak S, Graige MS et al.: Decoding randomly ordered DNA arrays. Genome Res. 14(5), 870-877 (2004).
16. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA: Selecting a maximally informative set of single nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74(1), 106-120 (2004).
17. Zhang K, Qin Z, Chen T, Liu JS, Waterman MS, Sun F: HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics 21(1), 131-134 (2005).