A real-time Taqman method for hepatitis C virus genotyping and methods for further subtyping of isolates.
Methods Mol Biol. 2009;510:55-71
Authors: Rolfe KJ, Wreghitt TG, Alexander GJ, Curran MD
The HCV genome is highly heterogeneous; more and more genotypes, each with several distinct subtypes, are being identified around the world. Knowledge of genotype is important for planning of treatment regimes, whereas subtype identification is useful in epidemiological studies and outbreak investigation. We describe HCV genotyping and subtyping assays, based on real-time PCR, that are sensitive, specific, and reliable. These assays provide fast, accurate, and convenient methods for HCV genotyping/subtyping to support clinical practice.
PMID: 19009253 [PubMed - indexed for MEDLINE]
[Genotyping of AKAP10 gene 2073A/G single nucleotide polymorphism by TaqMan probe real-time PCR].
Sichuan Da Xue Xue Bao Yi Xue Ban. 2009 Mar;40(2):275-8
Authors: Wang MJ, Zhou ZG, Wang L, Li Y, Zhang P, Zhang Y, Cui CF, Zhou B
To detect AKAP10 gene 2073A/G single nucleotide polymorphism (SNP) genotyping by TaqMan probe real-time PCR.
PMID: 19462906 [PubMed - indexed for MEDLINE]
Apolipoprotein E genotyping method by real time PCR, a fast and cost-effective alternative to the TaqMan and FRET assays.
J Neurosci Methods. 2009 Oct 15;183(2):238-40
Authors: Calero O, Hortigüela R, Bullido MJ, Calero M
The apolipoprotein E gene (APOE) polymorphism genotyping has an allegedly important predictive value for coronary heart disorders and Alzheimer's disease. We developed a simple, fast, cost-effective and suited for high-throughput protocol for determining APOE genotypes by Real Time PCR monitored by SYBR Green. The method is based on differential amplification by allele-specific primers. These primers have variations in their 3'-end nucleotides such that are specific for one of the two variants in each polymorphic position. By this protocol, we obtained a 100% concordance with the APOE genotypes determined by sequencing analysis. The main advantages of this method are its relative simplicity and the reduced cost compared to other methodologies, such as the TaqMan and FRET assays.
PMID: 19583979 [PubMed - indexed for MEDLINE]
The TaqMan method for SNP genotyping.
Methods Mol Biol. 2009;578:293-306
Authors: Shen GQ, Abdullah KG, Wang QK
Single nucleotide polymorphisms (SNPs) are common DNA sequence variations that occur at single bases within the genome. SNPs have been instrumental in elucidating the genetic basis of common, complex diseases using genome-wide association studies, candidate gene case-control association studies, and genome-wide linkage analyses. A key to these studies is genotyping of SNPs. Various methods for SNP genotyping have been developed. For a particular genotyping project, the choice of method is dependent on the number of SNPs (n) and the number of DNA samples (m) to be genotyped. For a genome-wide or large-scale project with very high n and small m, the Affymetrix SNP GeneChip and Illumina GoldenGate BeadChips assays are the ideal methods. For a project involving a small number of SNPs (small n) and a large population (high m), the TaqMan assay is the preferred technology as it has high throughput and is highly accurate, precise, time-efficient, and cost-effective. Here, we describe the detailed procedures for TaqMan SNP genotyping assay, including preparation of high-quality DNA samples, the operating protocol, clarification of technical issues, and discussion of several cautionary notes.
PMID: 19768602 [PubMed - indexed for MEDLINE]