The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping.
We developed the SNPlex Genotyping System to address the need for accurate genotyping data, high sample throughput, study design flexibility, and cost efficiency. The system uses oligonucleotide ligation/polymerase chain reaction and capillary electrophoresis to analyze bi-allelic single nucleotide polymorphism genotypes. It is well suited for single nucleotide polymorphism genotyping efforts in which throughput and cost efficiency are essential. The SNPlex Genotyping System offers a high degree of flexibility and scalability, allowing the selection of custom-defined sets of SNPs for medium- to high-throughput genotyping projects. It is therefore suitable for a broad range of study designs. In this article we describe the principle and applications of the SNPlex Genotyping System, as well as a set of single nucleotide polymorphism selection tools and validated assay resources that accelerate the assay design process. We developed the control pool, an oligonucleotide ligation probe set for training and quality-control purposes, which interrogates 48 SNPs simultaneously. We present performance data from this control pool obtained by testing genomic DNA samples from 44 individuals. in addition, we present data from a study that analyzed 521 SNPs in 92 individuals. Combined, both studies show the SNPlex Genotyping system to have a 99.32% overall call rate, 99.95% precision, and 99.84% concordance with genotypes analyzed by TaqMan probe-based assays. The SNPlex Genotyping System is an efficient and reliable tool for a broad range of genotyping applications, supported by applications for study design, data analysis, and data management.
Tobler
Andreas R
AR
Applied Biosystems, Foster City, CA 94404, USA. toblerar@appliedbiosystems.com
Short
Sabine
S
Andersen
Mark R
MR
Paner
Teodoro M
TM
Briggs
Jason C
JC
Lambert
Stephen M
SM
Wu
Priscilla P
PP
Wang
Yiwen
Y
Spoonde
Alexander Y
AY
Koehler
Ryan T
RT
Peyret
Nicolas
N
Chen
Caifu
C
Broomer
Adam J
AJ
Ridzon
Dana A
DA
Zhou
Hui
H
Hoo
Bradley S
BS
Hayashibara
Kathleen C
KC
Leong
Lilley N
LN
Ma
Congcong N
CN
Rosenblum
Barnet B
BB
Day
Joseph P
JP
Ziegle
Janet S
JS
De La Vega
Francisco M
FM
Rhodes
Michael D
MD
Hennessy
Kevin M
KM
Wenz
H Michael
HM
D001709:Biotechnology / Q000379:methods*; D004247:DNA / Q000235:genetics; D019075:Electrophoresis, Capillary; D005069:Evaluation Studies as Topic; D005787:Gene Frequency; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D010597:Pharmacogenetics; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D015203:Reproducibility of Results; D012984:Software; D044465:White People
D004247:DNA