Display options
Cite
Wang J, Lin M, Crenshaw A, et al. High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics. 2009;10:561doi: 10.1186/1471-2164-10-561.
Wang, J., Lin, M., Crenshaw, A., Hutchinson, A., Hicks, B., Yeager, M., Berndt, S., Huang, W. Y., Hayes, R. B., Chanock, S. J., Jones, R. C., & Ramakrishnan, R. (2009). High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC genomics, 10561. https://doi.org/10.1186/1471-2164-10-561
Wang, Jun, et al. "High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays." BMC genomics vol. 10 (2009): 561. doi: https://doi.org/10.1186/1471-2164-10-561
Wang J, Lin M, Crenshaw A, Hutchinson A, Hicks B, Yeager M, Berndt S, Huang WY, Hayes RB, Chanock SJ, Jones RC, Ramakrishnan R. High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics. 2009 Nov 28;10:561. doi: 10.1186/1471-2164-10-561. PMID: 19943955; PMCID: PMC2789104.
Copy Download .nbib Format: NLM
Share it on

BMC Genomics. 2009 Nov 28;10:561. doi: 10.1186/1471-2164-10-561.

High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays.

BMC genomics

Jun Wang, Min Lin, Andrew Crenshaw, Amy Hutchinson, Belynda Hicks, Meredith Yeager, Sonja Berndt, Wen-Yi Huang, Richard B Hayes, Stephen J Chanock, Robert C Jones, Ramesh Ramakrishnan

Affiliations

  1. Fluidigm Corporation, South San Francisco, CA, USA. [email protected]

PMID: 19943955 PMCID: PMC2789104 DOI: 10.1186/1471-2164-10-561

Abstract

BACKGROUND: Single nucleotide polymorphisms (SNPs) have emerged as the genetic marker of choice for mapping disease loci and candidate gene association studies, because of their high density and relatively even distribution in the human genomes. There is a need for systems allowing medium multiplexing (ten to hundreds of SNPs) with high throughput, which can efficiently and cost-effectively generate genotypes for a very large sample set (thousands of individuals). Methods that are flexible, fast, accurate and cost-effective are urgently needed. This is also important for those who work on high throughput genotyping in non-model systems where off-the-shelf assays are not available and a flexible platform is needed.

RESULTS: We demonstrate the use of a nanofluidic Integrated Fluidic Circuit (IFC) - based genotyping system for medium-throughput multiplexing known as the Dynamic Array, by genotyping 994 individual human DNA samples on 47 different SNP assays, using nanoliter volumes of reagents. Call rates of greater than 99.5% and call accuracies of greater than 99.8% were achieved from our study, which demonstrates that this is a formidable genotyping platform. The experimental set up is very simple, with a time-to-result for each sample of about 3 hours.

CONCLUSION: Our results demonstrate that the Dynamic Array is an excellent genotyping system for medium-throughput multiplexing (30-300 SNPs), which is simple to use and combines rapid throughput with excellent call rates, high concordance and low cost. The exceptional call rates and call accuracy obtained may be of particular interest to those working on validation and replication of genome- wide- association (GWA) studies.

References

  1. Nucleic Acids Res. 2005 Feb 24;33(4):e38 - PubMed
  2. Science. 2007 May 11;316(5826):889-94 - PubMed
  3. Nature. 2004 May 27;429(6990):446-52 - PubMed
  4. Nucleic Acids Res. 2008 Oct;36(18):e116 - PubMed
  5. Nat Methods. 2004 Nov;1(2):109-11 - PubMed
  6. Nat Genet. 1995 Apr;9(4):341-2 - PubMed
  7. Urol Oncol. 2004 Jul-Aug;22(4):358-61 - PubMed
  8. Nat Genet. 2007 Jul;39(7):870-4 - PubMed
  9. PLoS One. 2008 Feb 27;3(2):e1662 - PubMed
  10. Nat Genet. 2009 May;41(5):579-84 - PubMed
  11. Nat Rev Genet. 2005 Feb;6(2):95-108 - PubMed
  12. Science. 2001 Feb 16;291(5507):1304-51 - PubMed
  13. Nature. 2007 Oct 18;449(7164):851-61 - PubMed
  14. Nat Rev Genet. 2008 May;9(5):356-69 - PubMed
  15. Nature. 2001 Feb 15;409(6822):860-921 - PubMed
  16. Pharmacogenomics J. 2003;3(2):77-96 - PubMed
  17. Nat Methods. 2004 Nov;1(2):113-7 - PubMed
  18. Nat Biotechnol. 1998 Jan;16(1):49-53 - PubMed
  19. Nat Genet. 2008 Mar;40(3):310-5 - PubMed
  20. Genome Res. 2005 Feb;15(2):269-75 - PubMed
  21. Nature. 2005 Oct 27;437(7063):1299-320 - PubMed
  22. Nature. 2004 Oct 21;431(7011):931-45 - PubMed
  23. Methods Mol Biol. 2009;578:277-92 - PubMed
  24. Nature. 2003 Dec 18;426(6968):789-96 - PubMed
  25. Annu Rev Genomics Hum Genet. 2001;2:235-58 - PubMed
  26. Science. 2006 Dec 1;314(5804):1461-3 - PubMed

Substances

MeSH terms

Publication Types

Grant support