title: SNPstream UHT: ultra-high throughput SNP genotyping for pharmacogenomics and drug discovery.
abstract: Single nucleotide polymorphism (SNP) genotyping is playing an increasing role in genome mapping, pharmacogenetic studies, and drug discovery. To date, genome-wide scans and studies involving thousands of SNPs and samples have been hampered by the lack of a system that can perform genotyping with cost-effective throughput, accuracy, and reliability. To address this need, Orrhid has developed an automated, ultra-high throughput system, SNPstream UHT, which uses multiplexed PCR in conjunction with our next generation SNP-IT tag array single base extension genotyping technology The system employs oligonucleotide microarrays manufactured in a 384-well format on a novel glass-bottomed plate. Multiplexed PCR and genotyping are performed in homogeneous reactions, and assay results are read by direct two-color fluorescence on the SNPstream UHTArray Imager. The systems flexibility enables large projects involving thousands of SNPs and thousands of samples as well as small projects that have hundreds of SNPs and hundreds of samples to be done cost effectively. We have successfully demonstrated this system in greater than 1,000,000 genotyping assays with >96% of samples giving genotypes with >99% accuracy
authors.affiliation: Orchid BioSciences, Orchid Life Sciences, Princeton, NJ 08540, USA.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Bell
authors.forename: Surendra
authors.initials: S
authors.lastname: Chaturvedi
authors.forename: Craig A
authors.initials: CA
authors.lastname: Gelfand
authors.forename: Ching Yu
authors.initials: CY
authors.lastname: Huang
authors.forename: Michael
authors.initials: M
authors.lastname: Kochersperger
authors.forename: Rafael
authors.initials: R
authors.lastname: Kopla
authors.forename: Frank
authors.initials: F
authors.lastname: Modica
authors.forename: Mark
authors.initials: M
authors.lastname: Pohl
authors.forename: Shobha
authors.initials: S
authors.lastname: Varde
authors.forename: Renbin
authors.initials: R
authors.lastname: Zhao
authors.forename: Xiaojian
authors.initials: X
authors.lastname: Zhao
authors.forename: Michael T
authors.initials: MT
authors.lastname: Boyce-Jacino
authors.forename: Azzam
authors.initials: A
authors.lastname: Yassen
mesh_terms: D000483:Alleles; D004252:DNA Mutational Analysis / Q000295:instrumentation*; D017931:DNA Primers; D015195:Drug Design; D004867:Equipment Design; D005240:Feasibility Studies; D005787:Gene Frequency; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods; D010597:Pharmacogenetics / Q000295:instrumentation* / Q000379:methods; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers