title: High-throughput SNP genotyping by single-tube PCR with Tm-shift primers.
abstract: Despite many recent advances in high-throughput single nucleotide polymorphism (SNP) genotyping technologies, there is still a great need for inexpensive and flexible methods with a reasonable throughput. Here we report substantial modifications and improvements to an existing homogenous allele-specific PCR-based SNP genotyping method, making it an attractive new option for researchers engaging in candidate gene studies or following up on genome-wide scans. In this advanced version of the melting temperature (Tm)-shift SNP genotyping method, we attach two GC-rich tails of different lengths to allele-specific PCR primers, such that SNP alleles in genomic DNA samples can be discriminated by the Tms of the PCR products. We have validated 306 SNP assays using this method and achieved a success rate in assay development of greater than 83% under uniform PCR conditions. We have developed a standalone software application to automatically assign genotypes directly from melting curve data. To demonstrate the accuracy of this method, we typed 592 individuals for 6 SNPs and showed a high call rate (>98%) and high accuracy (>99.9%). With this method, 6-10,000 samples can be genotyped per day using a single 384-well real-time thermal cycler with 2-4 standard 384-well PCR instruments.
authors.affiliation: Human Genetics Department, Roche Molecular Systems, Alameda, CA 94501, USA. jun.wang@roche.com
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Karen
authors.initials: K
authors.lastname: Chuang
authors.forename: Mandeep
authors.initials: M
authors.lastname: Ahluwalia
authors.forename: Sarika
authors.initials: S
authors.lastname: Patel
authors.forename: Nanette
authors.initials: N
authors.lastname: Umblas
authors.forename: Daniel
authors.initials: D
authors.lastname: Mirel
authors.forename: Russell
authors.initials: R
authors.lastname: Higuchi
authors.forename: Soren
authors.initials: S
authors.lastname: Germer
mesh_terms: D017931:DNA Primers; D005838:Genotype; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D044366:Transition Temperature
chemical_list: D017931:DNA Primers