PPC: An algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays

Nucleic Acids Research

Volumn 33, Issue 17, 2005, Pages 1-7

  Brohede, Jesper ^a   Dunne, Rob ^a   McKay, James D ^b,c   Hannan, Garry N ^a  

^a CSIRO   (Australia)

^b UNIVERSITY OF TASMANIA   (Australia)

^c INTERNATIONAL AGENCY FOR RESEARCH ON CANCER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYZER; ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; DNA MICROARRAY; GENE FREQUENCY; GENE MAPPING; GENE PROBE; GENETIC ALGORITHM; GENOTYPE; HUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; ALGORITHM; COMPARATIVE STUDY; GENOMICS; METHODOLOGY; REPRODUCIBILITY; VALIDATION STUDY;

ALGORITHMS; GENE FREQUENCY; GENOMICS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 27644510907     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni142     Document Type: Article

References (37)

1. Collins,F.S., Guyer,M.S. and Charkravarti,A. (1997) Variations on a theme: Cataloging human DNA sequence variation. Science, 278, 1580-1581.
2. Risch,N. and Merikangas,K. (1996) The future of genetic studies of complex human diseases. Science, 273, 1516-1517.
3. Kruglyak,L. (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genet., 22, 139-144.
4. Risch,N. and Teng,J. (1998) The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases I. DNA pooling. Genome Res., 8, 1273-1288.
5. Pharoah,P.D., Dunning,A.M., Ponder,B.A. and Easton,D.F. (2004) Association studies for finding cancer-susceptibility genetic variants. Nature Rev. Cancer, 4, 850-860.
6. 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 the HLA class II loci. Proc. Natl Acad. Sci. USA, 82, 6970-6974.
7. Michelmore,R.W., Paran,I. and Kesseli,R.V. (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl Acad. Sci. USA, 88, 9828-9832.
8. Butcher,L.M., Meaburn,E., Dale,P.S., Sham,P., Schalkwyk,L.C., Craig,I.W. and Plomin,R. (2005) Association analysis of mild mental impairment using DNA pooling to screen 432 brain-expressed single-nucleotide polymorphisms. Mol. Psychiatry, 10, 384-392.
9. Hinds,D.A., Seymour,A.B., Durham,L.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.
10. Kirov,G., Williams,N., Sham,P., Craddock,N. and Owen,M.J. (2000) Pooled genotyping of microsatellite markers in parent-offspring trios. Genome Res., 10, 105-115.
11. 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.
12. König,I.R. and Ziegler,A. (2004) Analysis of SNPs in pooled DNA: A decision theoretic model. Genet. Epidemiol., 26, 31-43.
13. Butcher,L.M., Meaburn,E., Knight,J., Sham,P.C., Schalkwyk,L.C., Craig,I.W. and Plomin,R. (2005) SNPs, microarrays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children. Hum. Mol. Genet., 14, 1315-1325.
14. Law,G.R., Rollinson,S., Feltbower,R., Allan,J.M., Morgan,G.J. and Roman,E. (2004) Application of DNA pooling to large studies of disease. Stat. Med., 23, 3841-3850.
15. Matsuzaki,H., Loi,H., Dong,S., Tsai,Y.Y., Fang,J., Law,J., Di,X., Liu,W.M., Yang,G., Liu,G. et al. (2004) Parallel genotyping of over 10 000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res., 14, 414-425.
16. 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.
17. Di,X., Matsuzaki,H., Webster,T.A., Hubbell,E., Liu,G., Dong,S., Bartell,D., Huang,J., Chiles,R., Yang,G. et al. (2005) Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. Bioinformatics, 21, 1958-1963.
18. Uhl,G.R., Liu,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.
19. Butcher,L.M., Meaburn,E., Liu,L., Fernandes,C., Hill,L., Al-Chalabi,A., Plomin,R., Schalkwyk,L. and Craig,I.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.
20. 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.
21. 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, e52.
22. 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.
23. Perlin,M.W., Lancia,G. and Ng,S.K. (1995) Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution. Am. J. Hum. Genet., 57, 1199-1210.
24. 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.
25. 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.
26. Pfeiffer,R.M., Rutter,J.L., Gail,M.H., Struewing,J. and Gastwirth,J.L. (2002) Efficiency of DNA pooling to estimate joint allele frequencies and measure linkage disequilibrium. Genet. Epidemiol., 22, 94-102.
27. Barratt,B.J., Payne,F., Rance,H.E., Nutland,S., Todd,J.A. and Clayton,D.G. (2002) Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Ann. Hum. Genet., 66, 393-405.
28. 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.
29. Huber,P.J. (1981) Robust Statistics. Wiley, NY.
30. Germer,S., Holland,M.J. and Higuchi,R. (2000) High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res., 10, 258-266.
31. Chen,J., Germer,S., Higuchi,R., Berkowitz,G., Godbold,J. and Wetmur,J.G. (2002) Kinetic polymerase chain reaction on pooled DNA: A high-throughput, high-efficiency alternative in genetic epidemiological studies. Cancer Epidemiol. Biomarkers Prev., 11, 131-136.
32. Lavebratt,C., Sengul,S., Jansson,M. and Schalling,M. (2004) Pyrosequencing-based SNP allele frequency estimation in DNA pools. Hum. Mutat., 23, 92-97.
33. Wasson,J., Skolnick,G., Love-Gregory,L. and Permutt,M.A. (2002) Assessing allele frequencies of single nucleotide polymorphisms in DNA pools by pyrosequencing technology. Biotechniques, 32, 1144-1150.
34. Norton,N., Williams,N.M., Williams,H.J., Spurlock,G., Kirov,G., Morris,D.W., Hoogendoorn,B., Owen,M.J. and O'Donovan,M.C. (2002) Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum. Genet., 110, 471-478.
35. Giordano,M., Mellai,M., Hoogendoorn,B. and Momigliano-Richiardi,P. (2001) Determination of SNP allele frequencies in pooled DNAs by primer extension genotyping and denaturing high-performance liquid chromatography. J. Biochem. Biophys, Methods, 47, 101-110.
36. Downes,K., Barratt,B.J., Akan,P., Bumpstead,S.J., Taylor,S,D., Clayton,D.G. and Deloukas,P. (2004) SNP allele frequency estimation in DNA pools and variance components analysis. Biotechniques, 36, 840-845.
37. Sasaki,T., Tahira,T., Suzuki,A., Higasa,K., Kukita,Y., Baba,S. and Hayashi,K. (2001) Precise estimation of allele frequencies of single-nucleotide polymorphisms by a quantitative SSCP analysis of pooled DNA. Am. J. Hum. Genet., 68, 214-218.