The cost effectiveness of duplicate genotyping for testing genetic association

Annals of Human Genetics

Volumn 73, Issue 3, 2009, Pages 370-378

  Tintle, Nathan ^a   Gordon, Derek ^b   Van Bruggen, Dirk ^a   Finch, Stephen ^c  

^a HOPE COLLEGE   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c Stony Brook University   (United States)

Author keywords

Duplicate genotype; Genome wide association study; Genotype error; Power; Re genotype; Two stage

Indexed keywords

ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; COST EFFECTIVENESS ANALYSIS; DISEASE MODEL; GENE DUPLICATION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC RISK; GENOTYPE; MATHEMATICAL COMPUTING; PENETRANCE; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

COST-BENEFIT ANALYSIS; DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 65449170784     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2009.00516.x     Document Type: Article

References (28)

1. Ahn, K., Haynes, C., Kim, W., Fleur, R. S., Gordon, D. & Finch, S. J. (2007) The effects of SNP genotyping errors on the power of the Cochran-Armitage linear trend test for case/control association studies. Ann Hum Genet 71, 249-261.
2. Amos, C. I. (2007) Successful design and conduct of genome-wide association studies. Hum Mol Genet 16, R220-R225.
3. Barral, S., Haynes, C., Stone, M. & Gordon, D. (2006) LRTae: improving statistical power for genetic association with case/control data when phenotype and/or genotype misclassification errors are present. BMC Genet 7, 24.
4. Douglas, J. A., Skol, A. D. & Boehnke, M. (2002) Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear-family data. Am J Hum Genet 70, 487-495.
5. Edwards, A. O., Ritter, R., 3rd, Abel, K. J., Manning, A., Panhuysen, C. & Farrer, L. A. (2005) Complement factor H polymorphism and age-related macular degeneration. Science (New York, N.Y.) 308, 421-424.
6. Gordon, D. & Finch, S. J. (2005a) Consequences of Error. In Encyclopedia of genetics, genomics, proteomics and bioinformatics (eds. M. J. Dunn, L. B. Jorde, P. F. R. Little & S. Subramanian), Wiley.
7. Gordon, D. & Finch, S. J. (2005b) Factors affecting statistical power in the detection of genetic association. J Clin Invest 115, 1408-1418.
8. Gordon, D., Finch, S. J., Nothnagel, M. & Ott, J. (2002) Power and sample size calculations for case-control genetic association tests when errors are present: Application to single nucleotide polymorphisms. Hum Hered 54, 22-33.
9. Gordon, D. & Ott, J. (2001) Assessment and management of single nucleotide polymorphism genotype errors in genetic association analysis. Pac Symp Biocomput 18-29.
10. Gordon, D., Yang, Y., Haynes, C., Finch, S. J., Mendell, N. R., Brown, A. M. & Haroutunian, V. (2004) Increasing power for tests of genetic association in the presence of phenotype and/or genotype error by use of double-sampling. Stat Appl Genet Mol Biol 3, Article 26.
11. Hampe, J., Franke, A., Rosenstiel, P., Till, A., Teuber, M., Huse, K., Albrecht, M., Mayr, G., De La Vega, F. M., Briggs, J., Gunther, S., Prescott, N. J., Onnie, C. M., Hasler, R., Sipos, B., Folsch, U. R., Lengauer, T., Platzer, M., Mathew, C. G., Krawczak, M. & Schreiber, S. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 39, 207-211.
12. Ji, F., Yang, Y., Haynes, C., Finch, S. J. & Gordon, D. (2005) Computing asymptotic power and sample size for case-control genetic association studies in the presence of phenotype and/or genotype misclassification errors. Stat Appl Genet Mol Biol 4, Article 37.
13. Kang, S. J., Finch, S. J., Haynes, C. & Gordon, D. (2004a) Quantifying the percent increase in minimum sample size for SNP genotyping errors in genetic model-based association studies. Hum Hered 58, 139-144.
14. Kang, S. J., Gordon, D. & Finch, S. J. (2004b) What SNP genotyping errors are most costly for genetic association studies? Genet Epidemiol 26, 132-141.
15. Kim, W., Gordon, D., Sebat J., Ye, K. Q. & Finch, S. J. (2008) Computing power and sample size for case-control association studies with copy number polymorphism: Application of mixture-based likelihood ratio test. PLoS ONE 3, e3475.
16. Lai, R. Z., Zhang, H. & Yang, Y. N. (2007) Repeated measurement sampling in genetic association analysis with genotyping errors. Genet Epidemiol 31, 143-153.
17. Levenstien, M. A., Ott, J. & Gordon, D. (2006) Are molecular haplotypes worth the time and expense? A cost-effective method for applying molecular haplotypes. PLoS Genet 2, e127.
18. Moskvina, V., Craddock, N., Holmans, P., Owen, M. J. & O'Donovan, M. C. (2006) Effects of differential genotyping error rate on the type I error probability of case-control studies. Hum Hered 61, 55-64.
19. Muller, H., Pahl, R. & Schafer, H. (2007) Including sampling and phenotyping costs into the optimization of two stage designs for genomewide association studies. Genet Epidemiol 31, 844-852.
20. Rice, K. M. & Holmans, P. (2003) Allowing for genotyping error in analysis of unmatched case-control studies. Ann Hum Genet 67, 165-174.
21. Satagopan, J. M. & Elston, R. C. (2003) Optimal two-stage genotyping in population-based association studies. Genet Epidemiol 25, 149-157.
22. Saunders, I. W., Brohede, J. & Hannan, G. N. (2007) Estimating genotyping error rates from Mendelian errors in SNP array genotypes and their impact on inference. Genomics 90, 291-296.
23. Schaid, D. J. & Sommer, S. S. (1993) Genotype relative risks: methods for design and analysis of candidate-gene association studies.
24. Skol, A. D., Scott, L. J., Abecasis, G. R. & Boehnke, M. (2007) Optimal designs for two-stage genome-wide association studies. Genet Epidemiol 31, 776-788.
25. Tintle, N. L., Ahn, K., Mendell, N. R., Gordon, D. & Finch, S. J. (2005) Characteristics of replicated single-nucleotide polymorphism genotypes from COGA: Affymetrix and Center for Inherited Disease Research. BMC Genetics [Computer File]6, S154.
26. Tintle, N. L., Gordon, D., McMahon, F. J. & Finch, S. J. (2007) Using duplicate genotyped data in genetic analyses: Testing association and estimating error rates. Stat Appl Genet Mol Biol 6, Article 4.
27. Wang, H., Thomas, D. C., Pe'er, I. & Stram, D. O. (2006) Optimal two-stage genotyping designs for genome-wide association scans. Genet Epidemiol 30, 356-368.
28. Zuo, Y., Zou, G., Wang, J., Zhao, H. & Liang, H. (2008) Optimal two-stage design for case-control association analysis incorporating genotyping errors. Ann Hum Genet 72, 375-387.