Nanogen microelectronic chip for large-scale genotyping.

Abstract

To increase the speed and reduce the cost of single-nucleotide polymorphism (SNP) genotyping, we evaluated a new potential high-throughput genotyping method, the Nanogen™ NMW 1000 Nanochip™ Molecular Biology Workstation (1). We tested the Nanogen microelectronic chip for SNP genotyping with respect to throughput, accuracy, and cost-effectiveness. To increase throughput we first developed two different multiplex methods by which three different SNPs are determined sequentially at each test site. We then validated accuracy by genotyping 3637 individuals for three SNPs, using the microelectronic chip as well as restriction fragment length polymorphism (RFLP) analysis. Finally, we compared the cost-effectiveness of SNP genotyping by the Nanogen microelectronic chip and RFLP and evaluated the reuse of microelectronic chips to decrease the cost per SNP genotyped. As a first step, we developed two different protocols for multiplex SNP analyses: (a) PCR amplification of 557 bp of the β2-adrenergic receptor gene, including three known SNPs detected sequentially at each test site, and (b) multiplex PCR to amplify three regions of the hepatic lipase gene, each with one known SNP, addressed simultaneously and detected sequentially at each test site. To test accuracy we next genotyped three β2-adrenergic receptor SNPs in 3637 individuals from the Danish general population, The Copenhagen City Heart Study (2)(3)(4), using Nanogen microelectronic chips as well as RFLP analysis. Any samples showing discordance between the two methods were sequenced. We then compared total running cost (supplies and wages) when SNPs were genotyped with Nanogen microelectronic chips and by RFLP analysis. In addition, in 376 individuals we compared genotype outcome for three hepatic lipase SNPs between four new microelectronic chips and four microelectronic chips already used to genotype the three SNPs in the β2-adrenergic receptor gene. The Danish ethics committee for Copenhagen and Frederiksberg approved …