title: Evaluation of nanofluidics technology for high-throughput SNP genotyping in a clinical setting.
abstract: The current need for high-throughput genotyping platforms for targeted validation of disease-associated single nucleotide polymorphisms (SNPs) motivated us to evaluate a novel nanofluidics platform for genotyping DNA extracted from peripheral blood and buccal wash samples. SNP genotyping was performed using a Fluidigm 48.48 Dynamic Array biochip on the BioMark polymerase chain reaction platform and results were compared against standard TaqMan assays and DNA sequencing. Pilot runs using these dynamic arrays on 90 samples against 20 SNP assays had an average call rate of 99.7%, with 100% call rates for 16 of the assays. Manual TaqMan genotyping of these samples against three SNPs demonstrated 100% correlation between the two platforms. To understand the influence of DNA template variability, three sources of blood samples (CH-1, n = 20; CH-2, n = 47; KK, n = 47) and buccal washes (n = 37) were genotyped for 24 SNPs. Although both CH-1 and CH-2 batches showed good base calling (≥98.8%), the KK batch and buccal wash samples exhibited lower call rates (82.1% and 94.0%). Importantly, repurification of the KK and buccal wash samples resulted in significant improvements in their call rates (to ≥97.9%). Scale-up for genotyping 1698 cases and controls for 24 SNPs had overall call rates of 97.6% for KK and 99.2% for CH samples. The Dynamic Array approach demonstrated accuracy similar to that of TaqMan genotyping, while offering significant savings in DNA, effort, time, and costs.
authors.affiliation: Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Republic of Singapore.
authors.forename: Maurice
authors.initials: M
authors.lastname: Chan
authors.forename: Mei Wen
authors.initials: MW
authors.lastname: Chan
authors.forename: Ting Wei
authors.initials: TW
authors.lastname: Loh
authors.forename: Hai Yang
authors.initials: HY
authors.lastname: Law
authors.forename: Chui Sheun
authors.initials: CS
authors.lastname: Yoon
authors.forename: Sint Sint
authors.initials: SS
authors.lastname: Than
authors.forename: Jia Mei
authors.initials: JM
authors.lastname: Chua
authors.forename: Chow Yin
authors.initials: CY
authors.lastname: Wong
authors.forename: Wei Sean
authors.initials: WS
authors.lastname: Yong
authors.forename: Yoon Sim
authors.initials: YS
authors.lastname: Yap
authors.forename: Gay Hui
authors.initials: GH
authors.lastname: Ho
authors.forename: Peter
authors.initials: P
authors.lastname: Ang
authors.forename: Ann Siew Gek
authors.initials: AS
authors.lastname: Lee
mesh_terms: D057166:High-Throughput Screening Assays; D006801:Humans; D046210:Microfluidic Analytical Techniques / Q000592:standards; D058889:Molecular Typing; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity