Arrayed primer extension in the "array of arrays" format: A rational approach for microarray-based SNP genotyping

Genetic Testing

Volumn 11, Issue 2, 2007, Pages 160-166

  Klitø, Niels G F ^a   Qihua, Tan ^a   Nyegaard, Mette ^b   Brusgaard, Klaus ^a   Thomassen, Mads ^a   Skouboe, Charlotte ^a   Dahlgaard, Jesper ^c   Kruse, Torben A ^a  

^a ODENSE UNIVERSITY HOSPITAL   (Denmark)

^b AARHUS UNIVERSITY   (Denmark)

^c AARHUS UNIVERSITY HOSPITAL   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ATOPY; CHROMOSOME 3Q; COST EFFECTIVENESS ANALYSIS; DENMARK; EUROPE; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC LINKAGE; GENOTYPE; HUMAN; HUMAN EXPERIMENT; MICROARRAY ANALYSIS; NORMAL HUMAN; PHENOTYPE; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 3; DNA PRIMERS; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 34447267924     PISSN: 10906576     EISSN: None     Source Type: Journal    
DOI: 10.1089/gte.2007.9998     Document Type: Article

References (26)

1. Abecasis GR, Cookson WO (2000) GOLD - graphical overview of linkage disequilibrium. Bioinformatics 16:182-183.
2. Brasch-Andersen C, Haagerup A, Borglum AD, Vestbo J, Kruse TA (2006) Highly significant linkage to chromosome 3q13.31 for rhinitis and related allergic diseases. J Med Genet. 43:e10.
3. Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR, Dunham I (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature 418:544-548.
4. Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927.
5. Fortina P, Delgrosso K, Sakazume T, Santacroce R, Moutereau S, Su HJ, Graves D, McKenzie S, Surrey S (2000) Simple two-color array-based approach for mutation detection. Eur J Hum Genet 8:884-894.
6. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225-2229.
7. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226-231.
8. Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307:1072-1079.
9. Jaakson K, Zernant J, Kulm M, Hutchinson A, Tonisson N, Glavac D, Ravnik-Glavac M, Hawlina M, Meltzer MR, Caruso RC, Testa F, Maugeri A, Hoyng CB, Gouras P, Simonelli F, Lewis RA, Lupski JR, Cremers FP, Allikmets R (2003) Genotyping microarray (gene chip) for the ABCR (ABCA4) gene. Hum Mutat 22:395-403.
10. Jorde LB (2000) Linkage disequilibrium and the search for complex disease genes. Genome Res 10:1435-1444.
11. Kaminski S, Ahman A, Ruse A, Wojcik E, Malewski T (2005) MilkProtChip - a microarray of SNPs in candidate genes associated with milk protein biosynthesis - development and validation. J Appl Genet 46:45-58.
12. Klitø NGF (2006) Implementing arrayed primer extension for specialised gene-phenotype association studies. PhD Thesis, 104 pages. Availability: Odense University Hospital library, http://www.sdu.dk/ videncenteret/english/index.php/.
13. Kurg A, Tonisson N, Georgiou I, Shumaker J, Tollett J, Metspalu A (2000) Arrayed primer extension: solid-phase four-color DNA resequencing and mutation detection technology. Genet Test 4:1-7.
14. Landi S, Gemignani F, Moreno V, Gioia-Patricola L, Chabrier A, Guino E, Navarro M, de Oca J, Capella G, Canzian F (2005) A comprehensive analysis of phase I and phase II metabolism gene polymorphisms and risk of colorectal cancer. Pharmacogenet Genomics 15:535-546.
15. Lewonttn RC (1964) The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49:49-67.
16. Lovmar L, Fredriksson M, Liljedahl U, Sigurdsson S, Syvanen AC (2003) Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA. Nucleic Acids Res 31:e129.
17. Maron E, Nikopensius T, Koks S, Altmae S, Heinaste E, Vabrit K, Tammekivi V, Hallast P, Koido K, Kurg A, Metspalu A, Vasar E, Vasar V, Shlik J (2005) Association study of 90 candidate gene polymorphisms in panic disorder. Psychiatr Genet 15:17-24.
18. Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen L, Syvanen AC (2000) A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res 10:1031-1042.
19. Schrijver I, Oitmaa E, Metspalu A, Gardner P (2005) Genotyping microarray for the detection of more than 200 CFTR mutations in ethnically diverse populations. J Mol Diagn 7:375-387.
20. Syvanen AC (2001) Accessing genetic variation: genotyping single nucleotide polymorphisms. Nature Rev Genet 2:930-942.
21. Syvanen AC (2005) Toward genome-wide SNP genotyping. Nature Genet 37:5-10.
22. Tebbutt SJ, He JQ, Burkett KM, Ruan J, Opushnyev IV, Tripp BW, Zeznik JA, Abara CO, Nelson CC, Walley KR (2004) Microarray genotyping resource to determine population stratification in genetic association studies of complex disease. Biotechniques 37:977-985.
23. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437:1299-1320.
24. Thorisson GA, Smith AV, Krishnan L, Stein LD (2005) The International HapMap Project Web site. Genome Res 15:1592-1593.
25. Tonisson N, Kurg A, Kaasik K, Lohmussaar E, Metspalu A (2000) Unravelling genetic data by arrayed primer extension. Clin Chem Lab Med 38:165-170.
26. Weiss KM, Clark AG (2002) Linkage disequilibrium and the mapping of complex human traits. Trends Genet 18:19-24.