SNPs, discovery

As SNP discovery technologies become mainstream research tools, the importance of genotype-phenotype relationships will continue to be a focus in pharma-cogenomic research. Not only will characterization of drug transporter polymorphisms enhance our insight of the molecular mechanisms involved in transporter function, it is likely that such findings will become important components of individualized drug therapy in the future. 

Optical gene chips dense arrays of oligonucleotides have been successfully applied to detect transcriptional profiling and SNP discovery, where massively parallel analysis is required. However, the fluorescence-based readout of these chips involves not only highly precise and expensive instrumentation but also sophisticated numerical algorithms to interpret the data, and therefore these methods have been commonly limited to use in research laboratories. In this way, thin-film arrays of 14, 20, 25, 48 and 64 electrodes have already been fabricated [12,15,39,40,44,48], using lithographic techniques. Readout systems for these arrays based on electrical detection have also been developed. 

Krebs S, Medugorac I, Seichter D, Forster M. RNaseCut a MALDI mass spectrometry-based method for SNP discovery. Nucleic Acids Res 2003 31 e37. 

Since microarrays are simply spots of DNA arrayed in a known pattern, they also can be used for DNA-DNA hybridization studies. This is the basis for using micro-arrays for comparative DNA hybridizations, single nucleotide polymorphism (SNP) discovery, and chromatin immunoprecipiation followed by microarray chip hybridization (ChIP on chip analyses) to identify transcription factor binding sites (discussed below). 

A variety of techniques are available for SNP discovery. DNA sequencing remains the most direct method to determine the sequence of a target gene and remains the gold standard for detecting mutations. In this mode, an individual s sequence can be compared with many wild-type sequences to identify new polymorphism-improvements in analytical software and platform have made modern automated DNA sequencers much more user friendly. Nonetheless, the use of DNA sequencing to identify population-wide variation is a costly, labor-intensive endeavor. Strategies to mini-... 

The requirements for SNP discovery- and SNP typing (or scoring) technologies are quite different. All of the above-mentioned methods for SNP discovery have merits. For large scale SNP scoring projects, however, they will fail to be efficient. The reasons are a lack of reasonable automation and an inherent susceptibility to errors. The first issue is mainly due to gel electrophoresis technology which is cumbersome to automate. Another issue is caused by indirect detection methods based on labels. 

Hyseq researchers have also performed comparative sequencing, re-sequenc-ing and SNP discovery experiments on several human, bacterial, and viral (e. g., HIV) genes. Reference sequences, although not required, were used to aid in the assembly steps of these applications. It was, however, not necessary to obtain... 

In general, SNP discovery and SNP genotyping take place on separate technological platforms. This is because SNP discovery technologies are... 

There is one other significant source of SNP validation—the simple observation of an SNP on independent occasions from different individuals. The massive scale of SNP discovery naturally has resulted in the repeated identification of SNPs across different individuals and populations. This determination usually indicates that an SNP is likely to be widely spread in populations and often of higher frequency. These so-called 2-hit SNPs have been identified in dbSNP and provide preliminary validation for approximately 45% of the SNPs in the database. This allows the user to specify 2-hit validation as a minimal requirement in a query of the database. As an aside, the problem of SNP validation is particularly pertinent to the study of nonsynonymous SNPs, as many nonsynonymous SNPs, particularly those that are nonconservative in nature, tend to be single-hit SNPs with no validation information. Attempts to validate these SNPs tend to be prone to failure. 

Haga, H., R. Yamada, Y. Ohnishi, Y. Nakamura, and T. Tanaka 2002. Gene-based SNP discovery as part of the Japanese Millennium Genome Project Identification of 190,562 genetic variations in the human genome. J Hum Genet 47 605-10. 

---