High-throughput Single Nucleotide Polymorphism Genotyping Using Nanofluidic Dynamic Arrays

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2009 Dec 1

PMID 19943955

Citations 69

Authors

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

Soon will be listed here.

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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References

Ehrich M, Bocker S, Van Den Boom D . Multiplexed discovery of sequence polymorphisms using base-specific cleavage and MALDI-TOF MS. Nucleic Acids Res. 2005; 33(4):e38. PMC: 549577. DOI: 10.1093/nar/gni038. View

Frayling T, Timpson N, Weedon M, Zeggini E, Freathy R, Lindgren C . A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science. 2007; 316(5826):889-94. PMC: 2646098. DOI: 10.1126/science.1141634. View

Carlson C, Eberle M, Kruglyak L, Nickerson D . Mapping complex disease loci in whole-genome association studies. Nature. 2004; 429(6990):446-52. DOI: 10.1038/nature02623. View

Qin J, Jones R, Ramakrishnan R . Studying copy number variations using a nanofluidic platform. Nucleic Acids Res. 2008; 36(18):e116. PMC: 2566873. DOI: 10.1093/nar/gkn518. View

Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E . Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods. 2005; 1(2):109-11. DOI: 10.1038/nmeth718. View

Livak K, Marmaro J, Todd J . Towards fully automated genome-wide polymorphism screening. Nat Genet. 1995; 9(4):341-2. DOI: 10.1038/ng0495-341. View

Andriole G, Reding D, Hayes R, Prorok P, Gohagan J . The prostate, lung, colon, and ovarian (PLCO) cancer screening trial: Status and promise. Urol Oncol. 2004; 22(4):358-61. DOI: 10.1016/j.urolonc.2004.04.013. View

Hunter D, Kraft P, Jacobs K, Cox D, Yeager M, Hankinson S . A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet. 2007; 39(7):870-4. PMC: 3493132. DOI: 10.1038/ng2075. View

Spurgeon S, Jones R, Ramakrishnan R . High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS One. 2008; 3(2):e1662. PMC: 2244704. DOI: 10.1371/journal.pone.0001662. View

10.

Thomas G, Jacobs K, Kraft P, Yeager M, Wacholder S, Cox D . A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat Genet. 2009; 41(5):579-84. PMC: 2928646. DOI: 10.1038/ng.353. View

11.

Hirschhorn J, Daly M . Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005; 6(2):95-108. DOI: 10.1038/nrg1521. View

12.

Venter J, Adams M, Myers E, Li P, Mural R, Sutton G . The sequence of the human genome. Science. 2001; 291(5507):1304-51. DOI: 10.1126/science.1058040. View

13.

Frazer K, Ballinger D, Cox D, Hinds D, Stuve L, Boudreau A . A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007; 449(7164):851-61. PMC: 2689609. DOI: 10.1038/nature06258. View

14.

McCarthy M, Abecasis G, Cardon L, Goldstein D, Little J, Ioannidis J . Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008; 9(5):356-69. DOI: 10.1038/nrg2344. View

15.

Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J . Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860-921. DOI: 10.1038/35057062. View

16.

Chen X, Sullivan P . Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J. 2003; 3(2):77-96. DOI: 10.1038/sj.tpj.6500167. View

17.

Murray S, Oliphant A, Shen R, McBride C, Steeke R, Shannon S . A highly informative SNP linkage panel for human genetic studies. Nat Methods. 2005; 1(2):113-7. DOI: 10.1038/nmeth712. View

18.

Tyagi S, Bratu D, Kramer F . Multicolor molecular beacons for allele discrimination. Nat Biotechnol. 1998; 16(1):49-53. DOI: 10.1038/nbt0198-49. View

19.

Thomas G, Jacobs K, Yeager M, Kraft P, Wacholder S, Orr N . Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet. 2008; 40(3):310-5. DOI: 10.1038/ng.91. View

20.

Hardenbol P, Yu F, Belmont J, MacKenzie J, Bruckner C, Brundage T . Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 2005; 15(2):269-75. PMC: 546528. DOI: 10.1101/gr.3185605. View