Only a subset of single-nucleotide polymorphisms (SNPs) can be genotyped in genome-wide association studies. Imputation methods can infer the alleles of 'hidden' variants and use those inferences to test the hidden variants for association.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Halperin, E. & Stephan, D.A. Nat. Biotechnol. 27, 255–256 (2009).
Nicolae, D.L. Genet. Epidemiol. 30, 718–727 (2006).
Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. Nat. Genet. 39, 906–913 (2007).
Pei, Y.F., Li, J., Zhang, L., Papasian, C.J. & Deng, H.W. PLoS One 3, e3551 (2008).
Scheet, P. & Stephens, M. Am. J. Hum. Genet. 78, 629–644 (2006).
Lin, D.Y., Hu, Y. & Huang, B.E. Am. J. Hum. Genet. 82, 444–452 (2008).
Li, Y. & Abecasis, G.R. Am. J. Hum. Genet. S79, 2290 (2006).
Kimmel, G. & Shamir, R. Proc. Natl. Acad. Sci. USA 102, 158–162 (2005).
Stephens, M., Smith, N.J. & Donnelly, P. Am. J. Hum. Genet. 68, 978–989 (2001).
Kimmel, G., Karp, R.M., Jordan, M.I. & Halperin, E. Am. J. Hum. Genet. 83, 675–683 (2008).
Minichiello, M.J. & Durbin, R. Am. J. Hum. Genet. 79, 910–922 (2006).
Huang, L. et al. Am. J. Hum. Genet. 84, 235–250 (2009).
Servin, B. & Stephens, M. PLoS Genet. 3, e114 (2007).
Barrett, J.C. et al. Nat. Genet. 40, 955–962 (2008).
Acknowledgements
E.H. is a faculty fellow of the Edmond J. Safra Bioinformatics program at Tel Aviv University. E.H. was supported by National Science Foundation grant IIS-071325412 and by the Israel Science Foundation grant no. 04514831.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Halperin, E., Stephan, D. SNP imputation in association studies. Nat Biotechnol 27, 349–351 (2009). https://doi.org/10.1038/nbt0409-349
Issue Date:
DOI: https://doi.org/10.1038/nbt0409-349
This article is cited by
-
Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra
BMC Genomics (2018)
-
The association study of nonsyndromic cleft lip with or without cleft palate identified risk variants of the \(\varvec{GLI3}\) G L I 3 gene in a Chinese population
Journal of Genetics (2017)
-
Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans
BMC Bioinformatics (2016)
-
Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping
BMC Genomics (2016)
-
Walking through the statistical black boxes of plant breeding
Theoretical and Applied Genetics (2016)
