Distribution of human SNPs and its effect on high-throughput genotyping

Human Mutation

Volumn 27, Issue 3, 2006, Pages 249-254

  Koboldt, Daniel C ^a   Miller, Raymond D ^a   Kwok, Pui Yan ^b  

^a WASHINGTON UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Allele dropout; Assay design; Genotyping; HapMap Project; Primer site variants; SNPs

Indexed keywords

PRIMER DNA;

ACCURACY; ALLELE DROPOUT; ANALYTICAL ERROR; ARTICLE; BIOASSAY; DIAGNOSTIC KIT; GENETIC SCREENING; GENOMICS; GENOTYPE; GENOTYPE FAILURE; GENOTYPING ASSAY DESIGN; HAPLOTYPE; HIGH THROUGHPUT SCREENING; HUMAN; INTERNATIONAL HAPMAP PROJECT; MUTATION; PRIMER SITE MUTATION; PRIORITY JOURNAL; PROCESS DESIGN; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; BASE SEQUENCE; BINDING SITES; CALIBRATION; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DNA PRIMERS; GENOTYPE; MOLECULAR SEQUENCE DATA; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 33645213803     PISSN: 10597794     EISSN: None     Source Type: Journal    
DOI: 10.1002/humu.20286     Document Type: Article

References (12)

1. 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.
2. Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. 2005. Multispecies microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res 15:674-680.
3. Hardenbol P, Yu F, Belmont J, Mackenzie J, Bruckner C, Brundage T, Boudreau A, Chow S, Eberle J, Erbilgin A, Falkowski M, Fitzgerald R, Ghose S, Iartchouk O, Jain M, Karlin-Neumann G, Lu X, Miao X, Moore B, Moorhead M, Namsaraev E, Pasternak S, Prakash E, Tran K, Wang Z, Jones HB, Davis RW, Willis TD, Gibbs RA. 2005. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res 15:269-275.
4. 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.
5. International HapMap Consortium. 2003. The International HapMap Project. Nature 426:789-796.
6. International HapMap Consortium. 2004. Integrating ethics and science in the International HapMap Project. Nat Rev Genet 5:467-475.
7. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. 2001. Nature 409:860-921.
8. International SNP Map Working Group. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933.
9. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ. 2003. The UCSC Genome Browser Database. Nucl Acids Res 31:51-54.
10. Leibelt C, Budowle B, Collins P, Daoudi Y, Moretti T, Nunn G, Reeder D, Roby R. 2003. Identification of a D8S1179 primer binding site mutation and the validation of a primer designed to recover null alleles. Forensic Sci Int 133:220-227.
11. Marth G, Yeh R, Minton M, Donaldson R, Li Q, Duan S, Davenport R, Miller RD, Kwok PY. 2001. Single-nucleotide polymorphisms in the public domain: how useful are they? Nat Genet 27:371-372.
12. Miller RD, Phillips MS, Jo I, Donaldson MA, Studebaker JF, Addleman N, Alfisi SV, Ankener WM, Bhatti HA, Callahan CE, Carey BJ, Conley CL, Cyr JM, Derohannessian V, Donaldson RA, Elosua C, Ford SE, Forman AM, Gelfand CA, Grecco NM, Gutendorf SM, Hock CR, Hozza MJ, Hur S, In SM, Jackson DL, Jo SA, Jung SC, Kim S, Kimm K, Kloss EF, Koboldt DC, Kuebler JM, Kuo FS, Lathrop JA, Lee JK, Leis KL, Livingston SA, Lovins EG, Lundy ML, Maggan S, Minton M, Mockler MA, Morris DW, Nachtman EP, Oh B, Park C, Park CW, Pavelka N, Perkins AB, Restine SL, Sachidanandam R, Reinhart AJ, Scott KE, Shah GJ, Tate JM, Varde SA, Walters A, White JR, Yoo YK, Lee JE, Boyce-Jacino MT, Kwok PY, SNP Consortium Allele Frequency Project. 2005. High-density single-nucleotide polymorphism maps of the human genome. Genomics 86:117-126.