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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 561.
Published online 2009 November 28. doi:  10.1186/1471-2164-10-561
PMCID: PMC2789104
Copyright ©2009 Wang et al; licensee BioMed Central Ltd.
High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays
Jun Wang,1 Min Lin,1 Andrew Crenshaw,2,3 Amy Hutchinson,2,3 Belynda Hicks,2,3 Meredith Yeager,2,3 Sonja Berndt,3 Wen-Yi Huang,3 Richard B Hayes,3 Stephen J Chanock,3 Robert C Jones,1 and Ramesh Ramakrishnancorresponding author1
1Fluidigm Corporation, South San Francisco, CA, USA
2Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Advanced Technology Program, NCI-FCRDC, Frederick, MD, USA
3Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
corresponding authorCorresponding author.
Jun Wang: jun.wang/at/fluidigm.com; Min Lin: min.lin/at/fluidigm.com; Andrew Crenshaw: crenshaw/at/broad.mit.edu; Amy Hutchinson: hutchiam/at/mail.nih.gov; Belynda Hicks: hicksbel/at/mail.nih.gov; Meredith Yeager: yeagerm/at/mail.nih.gov; Sonja Berndt: berndts/at/mail.nih.gov; Wen-Yi Huang: huangw/at/mail.nih.gov; Richard B Hayes: richard.hayes2/at/nyumc.org; Stephen J Chanock: chanocks/at/mail.nih.gov; Robert C Jones: bob.jones/at/fluidigm.com; Ramesh Ramakrishnan: ramesh.ramakrishnan/at/fluidigm.com
Received July 8, 2009; Accepted November 28, 2009.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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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.
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