SNP genotyping methods

Tab. 4.3 Examples of current SNP genotyping methods. Information given in the table are based on the manufacturer s data provided in Q4 2000... 

Storm N, Darnhofer-Patel B, van den Boom D, Rodi CP. MALDI-TOF mass spectrometry-based SNP genotyping. Methods Mol Biol 2003 212 241-262. 

Fig. 5. Schematic representation of the SNP genotyping method based on a combination of surface ligation chemistry and nanoparticles enhanced SPRi. The two array elements (P and P,) differ only by their last nucleotide at the 3 end. Target DNA (T), ligation probe (L), and Taq DNA ligase are simultaneously introduced. Ligation only occurs with perfect complementary duplexes on the array, leading to extension with the L sequence. The presence of L is detected by gold nanoparticles carrying oligonucleotides (L ) complementary to L. For further details see text. Reprinted from ref. (23) with permission.

The major reaction principles that form the basis of the genotyping technologies available today are primer extension, ligation, and hybridization. Many of the methods for SNP genotyping rely on PCR amplification of the sequence of interest prior to allele determination. Primer design and assay optimization for multiplexed and reproducible genotyping of SNPs in large sample sets have become major bottle necks in most methods used today. 

Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW, Thomson ML, Semple CA, Muir WJ, Blackwood DH, Porteous DJ, Evans KL. SNP genotyping on pooled DNAs comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res... 

There are maii)7 methods for SNP genotyping and the method of choice depends on several factors, including turnaround time and throughput requirements. The necessities of high-volume genomic research are different from a clinical reference laboratory, a medical clinic, or the STAT laboratories of the future. 

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