Identification of disease causing loci using an array-based genotyping approach on pooled DNA

BMC Genomics

Volumn 6, Issue , 2005, Pages

  Craig, David W ^a   Huentelman, Matthew J ^a   Hu Lince, Diane ^a   Zismann, Victoria L ^a   Kruer, Michael C ^a   Lee, Anne M ^a   Puffenberger, Erik G ^b   Pearson, John M ^a   Stephan, Dietrich A ^a  

^a TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^b CLINIC FOR SPECIAL CHILDREN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; DNA;

ACCURACY; ALLELE; ARTICLE; BIOINFORMATICS; CORRELATION FUNCTION; DATA BASE; DNA MICROARRAY; GENE FREQUENCY; GENE LOCUS; GENE MUTATION; GENETIC PREDISPOSITION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HUMAN; RELATIVE ALLELE SIGNAL; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; GENETIC DATABASE; GENETICS; GENOME; HUMAN GENOME; METABOLISM; METHODOLOGY; MUTATION; NEWBORN; SUDDEN INFANT DEATH SYNDROME;

ALLELES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; GENE FREQUENCY; GENOME; GENOME, HUMAN; GENOTYPE; HUMANS; INFANT, NEWBORN; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SUDDEN INFANT DEATH;

EID: 27644523251     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-6-138     Document Type: Article

References (23)

1. Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E. Law J, Berntsen T, Chadha M, Hui H, Yang G, Kennedy GC, Webster TA, Cawley S, Walsh E, Jones KW, Fodor SP, Mei R: Genotyping over 100,000 SNPs on a pair of olignucleoticle arrays. Nature Methods 2004, 1:109-111.
2. Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS: Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 2003, 68:69-78.
3. Marnellos G: High-throughput SNP analysis for genetic association studies. Curr Opin Drug Discov Devel 2003, 6:317-321.
4. Cardon LR, Bell JI: Association study designs for complex diseases. Nat Rev Genet 2001, 2:91-99.
5. Risch N, Teng J: The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases I. DNA pooling. Genome Res 1998, 8:1273-1288.
6. Hirschhorn JN, Daly MJ: Genome-wide association studies for common diseases and complex traits. Not Rev Genet 2005, 6:95-108.
7. Carlson CS, Eberle MA, Kruglyak L, Nickerson DA: Mapping complex disease loci in whole-genome association studies. Nature 2004, 429:446-452.
8. Butcher LM, Meaburn E, Knight J, Sham PC, Schalkwyk LC, Craig IW, Plomin R: SNPs, microarrays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children. Hum Mol Genet 2005, 14:1315-1325.
9. Meaburn E, Butcher LM, Liu L, Fernandes C, Hansen V, Al-Chalabi A. Plomin R, Craig I, Schalkwyk LC: Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs. BMC Genomics 2005, 6:52.
10. Butcher LM, Meaburn E, Liu L, Fernandes C, Hill L. Al-Chalabi A, Plomin R, Schalkwyk L, Craig IW: Genotyping pooled DNA on microarrays: a systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits. Behav Genet 2004, 34:549-555.
11. Simpson CL, Knight J, Butcher LM, Hansen VK, Meaburn E, Schalkwyk LC, Craig IW, Powell JF, Sham PC, Al-Chalabi A: A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. Nucleic Acids Res 2005, 33:e2S.
12. Butcher LM, Meaburn E, Dale PS, Sham P, Schalkwyk LC, Craig IW, Plomin R: Association analysis of mild mental impairment using DNA pooling to screen 432 brain-expressed single-nucleotide polymorphisms. Mol Psychiatry 2005, 10:384-92.
13. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, Mei R: Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res 2004, 14:414-425.
14. Puffenberger EG, Hu-Lince D, Parod JM, Craig DW, Dobrin SE, Conway AR, Donarum EA, Strauss KA, Dunckley T, Cardenas JF, Melmed KR, Wright CA, Liang W, Stafford P, Flynn CR, Morton DH, Stephan DA: Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function. Proc Natl Acad Sci U S A 2004, 101:11689-11694.
15. Hoogendoorn B, Norton N, Kirov G, Williams N, Hamshere ML, Spurlock G, Austin J, Stephens MK, Buckland PR, Owen MJ, O'Donovan MC: Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Hum Genet 2000, 107:488-493.
16. Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW, Thomson ML, Semple CA, Muir WJ, Blackwood DH, Porteous DJ, Evans KL: SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res 2002, 30:e74.
17. Norton N, Williams NM, Williams HJ, Spurlock G, Kirov G, Morris DW, Hoogendoorn B, Owen MJ, O'Donovan MC: Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum Genet 2002, 110:471-478.
18. Giordano M, Mellai M, Hoogendoorn B, Momigliano-Richiardi P: Determination of SNP allele frequencies in pooled DNAs by primer extension genotyping and denaturing high-performance liquid chromatography. J Biochem Biophys Methods 2001, 47:101-110.
19. Moskvina V, Norton N, Williams N, Holmans P, Owen M, O'Donovan M: Streamlined analysis of pooled genotype data in SNP-based association studies. Genet Epidemiol 2005, 28:273-282.
20. Website: [http://www.tgen.org/neurogenomics/data].
21. Puffenberger EG: Genetic heritage of the Old Order Mennonites of southeastern Pennsylvania. Am J Med Genet C Semin Med Genet 2003, 121:18-31.
22. Hinds DA, Seymour AB, Durham LK, Banerjee P, Ballinger DG, Milos PM, Cox DR, Thompson JF, Frazer KA: Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels. Hum Genomics 2004, 1:421-434.
23. Website2: [http://bioinformatics.tgen.org/software/tgen-array/].