Detection of Single Nucleotide Polymorphisms SNPs, Genome, Oligonucleotide, Microarray, Affymetrix technoology, Mutations

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Home >> Biotechnology and Genomics >> DNA Chip Technology and Microarrays >> Detection of Single Nucleotide Polymorphisms SNPs

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Detection of single nucleotide polymorphisms (SNPs)
Identification of single base mismatches in the known DNA sequences of a genome, can be achieved by resequencing DNA segments using SBH. In this case one needs to distinguish a perfect match from a single base mismatch and precise sequencing is not required. It is also known that a single base mutation leads to general reduction of signal. Further, the mismatching in the centre of the oligonucleotide sequence has a greater destabilizing effect than mispairing at the distal position.

A tiling strategy of microarrays production has been used by Affymetrix, where a set of four possible oligonucleotides for each base to be sequenced, is utilized (e.g. TACGCA, TCCGCA, TGCGCA, TTCGCA). For resequencing a 10kb gene by this method, a microarray of 40,000 oligonucleotides is needed. This can be achieved by Affymetix technology. A hypothetical example of tilling strategy is shown in the table. Utilizing this approach, a chip based or reported sequence of the human

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mitochondrial DNA (mtDNA) has been prepared. In this study, complete sequence of human mtDNA was organized as a set of 16,000 oligonucleotides (20-mer). Since, for each base to be sequenced, four possible oligonucleotides are needed, a chip with 64,000 features was used to detect mutations anywhere in the mitochondrial genome in a single hybridization. Using this method, 179 of the 180 known polymorphisms could be identified.

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