A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments

Nucleic Acids Research

Volumn 34, Issue 15, 2006, Pages

  Yang, H C ^a   Liang, Y J ^a   Huang, M C ^a   Li, L H ^a   Lin, C H ^a   Wu, J Y ^a   Chen, Y T ^a   Fann, C S J ^a  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE;

AFRICAN AMERICAN; ARTICLE; ASIAN; CAUCASIAN; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DNA DETERMINATION; DNA HYBRIDIZATION; DNA MICROARRAY; ETHNIC DIFFERENCE; GENE AMPLIFICATION; GENE FREQUENCY; GENETIC DATABASE; GENETIC HETEROGENEITY; GENOME ANALYSIS; GENOTYPE; HUMAN; HUMAN CELL; HUMAN GENOME; MOLECULAR MODEL; NORMAL DISTRIBUTION; OBSERVATIONAL STUDY; PRIORITY JOURNAL; PROTEIN CONTENT; PROTEIN DETERMINATION; RELIABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; GENOME; METHODOLOGY; NUCLEIC ACID AMPLIFICATION; NUCLEIC ACID DATABASE; NUCLEIC ACID HYBRIDIZATION;

DATABASES, NUCLEIC ACID; GENE FREQUENCY; GENOME, HUMAN; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 33749157376     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl446     Document Type: Article

References (48)

1. The International Human Genome Mapping Consortium (2001) A physical map of the human genome. Nature, 409, 934-941.
2. The International HapMap Consortium (2003) The International HapMap project. Nature, 426, 789-796.
3. The ENCODE Project Consortium (2004) The ENCODE (encyclopedia of DNA elements) project. Science, 306, 636-640.
4. Pusch,W., Wurmbach,J.-H., Tiele,H. and Kostrzewa,M. (2002) MALDI-TOF mass spectrometry-based SNP genotyping. Pharmacogenomics, 3, 537-548.
5. Kennedy,G.C., Matsuzaki,H., Dong,S., Liu,W.M., Huang,J., Liu,G., Su,X., Cao,M., Chen,W., Zhang,J. et al. (2003) Large-scale genotyping of complex DNA. Nat. Biotechnol., 21, 1233-1237.
6. Barcellos,L.F., Klitz,W., Field,L.L., Tobias,R., Bowcock,A.M., Wilson,R., Nelson,M.P., Nagatomi,J. and Thomson,G. (1997) Association mapping of disease loci, by use of a pooled DNA genomic screen. Am. J. Hum. Genet., 61, 734-747.
7. Mohlke,K.L., Erdos,M.R., Scott,L.J., Fingerlin,T.E., Jackson,A.U., Silander,K., Hollstein,P., Boehnke,M. and Collins,F.S. (2002) High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools. Proc. Natl Acad. Sci. USA, 99, 16928-16933.
8. Bansal,A., van den Boom,D., Kammerer,S., Honisch,C., Adam,G., Cantor,C.R., Kleyn,P. and Braun,A. (2002) Association testing in DNA pooling: An effective initial screen. Proc. Natl Acad. Sci. USA, 99, 16871-16874.
9. Jawadi,A., Bader,J.S., Purcell,S., Cherny,S.S. and Sham,P. (2002) Family-based association tests for quantitative traits using pooled DNA. Eur. J. Hum. Genet., 20, 125-132.
10. Hinds,D.A., Seymour,A.B., Durham,K., Banerjee,P., Ballinger,D.G., Milos,P.M., Cox,D.R., Thompson,J.F. and Frazer,K.A. (2004) Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels. Hum. Genomics, 1, 421-434.
11. Zou,G. and Zhao,H. (2005) Family-based association tests for different family structures using pooled DNA. Ann. Hum. Genet., 69, 429-442.
12. Wolford,J.K., Blunt,D., Ballecer,C. and Prochazka,M. (2000) High-throughput SNP detection by using DNA pooling and denaturing high performance liquid chromatography (DHPLC). Hum. Genet., 107, 483-487.
13. Buetow,K.H., Edmonson,M., MacDonald,R., Clifford,R., Yip,P., Kelley,J., Little,D.P., Strausberg,R., Koester,H., Cantor,C.R. et al. (2001) High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl Acad. Sci. USA, 98, 581-584.
14. Nelson,M.R., Marnellos,G., Kammerer,S., Hoyal,C.R., Shi,M.M., Cantor,C.R. and Braun,A. (2004) Large-scale validation of single nucleotide polymorphisms in gene regions. Genome Res., 14, 1664-1668.
15. Yang,H.C., Lin,C.H., Hung,S.I. and Fann,C.S.J. (2006) Polymorphism validation using DNA pools prior to conducting large-scale genetic studies. Ann. Hum. Genet., 70, 350-359.
16. Dubreuil,P., Rebourg,C., Merlino,M. and Charcosset,A. (1999) Evaluation of a DNA pooled-sampling strategy for estimating the RFLP diversity of maize populations. Plant Mol. Biol. Rep., 17, 123-138.
17. Hillel,J., Groenen,M.A.M., Tixier-Boichard,M., Korol,A.B., David,L., Kirzhner,V.M., Burke,T., Barre-Dirie, A., Crooijmans,R.P.M.A., Elo,K. et al. (2003) Biodiveristy of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet. Sel. Evol., 35, 533-557.
18. Werner,M., Sych,M., Herbon,N., Illig,T., König,I.R. and Wjst,M. (2002) Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum. Mutat., 20, 57-64.
19. Le Hellard,S., Ballereau,S.J., Visscher,P.M., Torrance,H.S., Pinson,J., Morris,S.W., Thomson,M.L., Semple,C.A., Muir,W.J., Blackwood,D.H. et al. (2002) SNP genotyping on pooled DNAs: Comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res., 30, e74.
20. Barratt,B.J., Payne,F., Rance,H.E., Nutland,S., Todd,J.A. and Clayton,D.G. (2003) Identification of the sources of error in allele freqeuncy estimations from pooled DNA indicates an optimal experimental design. Ann. Hum. Genet., 66, 393-405.
21. Shaw,S.H., Carrasquillo,M.M., Kashuk,C., Puffenberger,E.G. and Chakravarti,A. (1998) Allele frequency distributions in pooled DNA samples: Applications to mapping complex disease genes. Genome Res., 8, 111-123.
22. Arnheim,N., Strange,C. and Erlich,H. (1985) Use of pooled DNA samples to detect linkage disequilibrium of polymorphic restriction fragments and human disease: Studies of HLA class II loci. Proc. Natl Acad. Sci. USA, 85, 6970-6974.
23. Sham,P., Bader,J.S., Craig,I., O'Donovan,M. and Owen,M. (2002) DNA pooling: A tool for large-scale association studies. Nature Rev. Genet., 3, 862-871.
24. Yang,H.C. and Fann,C.S.J. (2007) Association mapping using pooled DNA. In Collins,A. (ed.), Linkage Disequilibrium and Association Mapping. The Humana Press, Inc, USA. In Press.
25. Liu,W.M., Di,X., Yang,G., Matsuzaki,H., Huang,J., Mei,R., Ryder,T.B., Webster,T.A., Dong,S., Liu,G. et al. (2003) Algorithms for large-scale genotyping microarrays. Bioinformatics, 19, 2397-2403.
26. Matsuzaki,H., Dong,S., Loi,H., Di,X., Liu,G., Hubbell,E., Law,J., Berntsen,T., Chadha,T., Chadha,M. et al. (2004) Genotyping over 100 000 SNPs on a pair of oligonucleotide arrays. Nature Meth., 1, 109-111.
27. Uhl,G.R., Lin,Q.R., Walther,D., Hess,J. and Naiman,D. (2001) Polysubstance abuse-vulnerability genes: Genome scans for association, using 1004 subjects and 1494 single-nucleotide polymorphisms. Am. J. Hum. Genet., 69, 1290-1300.
28. Lindroos,K., Sigurdsson,S., Johansson,K., Ronnblom,L. and Syvanen,A.-C. (2002) Multiplex SNP genotyping in pooled DNA samples by a four-color microarray system. Nucleic Acids Res., 30, e70.
29. Butcher,L.M., Meaburn,E., Liu,L., Fernandes,C., Hill,L., Al-Chalabi,A., Plomin,R., Schalkwyk,L. and Craig,J.W. (2004) Genotyping pooled DNA on microarrays: A systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits. Behav. Genet., 34, 549-555.
30. Meaburn,E., Butcher,L.M., Liu,L., Fernandes,C., Hansen,V., Al-Chalabi,A., Plomin,R., Craig,I. and Schalkwyk,L.C. (2005) Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs. BMC Genomics, 6, 52.
31. Meaburn,E., Butcher,L.M., Schalkwyk,L.C. and Plomin,R. (2006) Genotyping pooled DNA using 100K SNP microarrays: A step towards genomewide association scans. Nucleic Acids Res., 34, e28.
32. Macgregor,S., Visscher,P.M. and Montgomery,G. (2006) Analysis of pooled DNA samples on high density arrays without prior knowledge of differential hybridization rates. Nucleic Acids Res., 34, e55.
33. Norton,N., Williams,N.M., O'Donovan,M.C. and Owen,M.J. (2004) DNA pooling as a tool for large-scale association studies in complex traits. Ann. Med., 36, 146-152.
34. Yang,H.C., Pan,C.C., Lu,R.C.Y. and Fann,C.S.J. (2005) New adjustment factors and sample size calculation in a DNA-pooling experiment with preferential amplification. Genetics, 169, 399-410.
35. Hoogendoorn,B., Norton,N., Kirov,G., Williams,N., Hamshere,M.L., Spurlock,G., Austin,J., Stephens,M.K., Buckland,P.R., Owen,M.J. et al. (2000) Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Hum. Genet., 107, 488-493.
36. Moskvina,V., Norton,N., Williams,N., Holmans,P., Owen,M. and O'Donovan,M. (2005) Streamlined analysis of pooled genotype data in SNP-based association studies. Genet. Epidemiol., 28, 273-282.
37. Xu,H., Knight,J., Brookes,K., Mill,J., Sham,P., Craig,I., Taylor,E. and Asherson,P. (2005) DNA pooling analysis of 21 norepinephrine transporter gene SNPs with attention deficit hyperactivity disorder. Am. J. Med. Genet. B, 134, 115-118.
38. Simpson,C.L., Knight,J., Butcher,L.M., Hansen,V.K., Meaburn,E., Schalkwyk,L.C., Craig,I.W., Powell,J.F., Sham,P.C. and Al-Chalabi,A. (2005) A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. Nucleic Acids Res., 33, e25.
39. Pan,W.H., Fann,C.S.J., Wu,J.Y., Hung,Y.T., Ho,M.S., Tai,T.H., Chen,Y.J., Liao,C.J., Yang,M.L., Cheng,A.T.A. et al. (2006) Han Chinese cell and genome bank in Taiwan: Purpose, design and ethical considerations. Hum. Hered., 61, 27-30.
40. Huang,J., Wei,W., Zhang,J., Liu,G., Bignell,G.R., Stratton,M.R., Futreal,P.A., Wooster,R., Jones,K.W. and Shapero,M.H. (2004) Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum. Genomics, 1, 287-299.
41. Yang,H.C., Pan,C.C., Lin,C.Y. and Fann,C.S.J. (2006) PDA: Pooled DNA analyzer. BMC Bioinformatics, 7, 233.
42. Shapiro,S.S. and Wilks,M.B. (1965) An analysis of variance test for normaility (complete samples). Biometrika, 52, 591-611.
43. Holm,S. (1979) A simple sequentially rejective multiple test procedure. Scand. J. Stat., 6, 65-70.
44. Vilsscher,P.M. and Le Hellard,S. (2003) Simple method to analyze SNP-based association studies using DNA pools. Genet. Epidemiol., 24, 291-296.
45. Johnson,M.P. and Griffiths,L.R. (2005) A genetic analysis of serotonergic biosynthetic and metabolic enzymes in migraine using a DNA pooling approach. J. Hum. Genet., 50, 607-610.
46. Akey,J.M., Eberle,M.A., Rieder,M.J., Carlson,C.S., Shriver,M.D., Nickerson,D.A. and Kruglyak,L. (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLos Biol., 2, 1591-1599.
47. Hinds,D.A., Stuve,L.L., Nilsen,G.B., Halperin,E., Eskin,E., Ballinger,D.G., Frazer,K.A. and Cox,D.R. (2005) Whole-genome patterns of common DNA variation in three human populations. Science, 307, 1072-1079.
48. Guo,S.W. and Thompson,E.A. (1992) Performing the exact test for Hardy-Weinberg proportion for multiple alleles. Biometrics, 48, 361-372.