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March 2007, SoftGenetics - GeneMarker® Software for Single Base Extension Analysis:


Single nucleotide polymorphisms (SNPs) occur every 100 to 300 bases along the human genome and make up to 90% of human genetic variation (1).Functional SNPs or non-synonymous SNPs (nsSNPs) occur in the coding region of a gene. Regulatory SNPs (rSNPs) occur in the promoter of a gene andmay alter protein function or gene expression (2, 3). Intronic or intergenic SNPs may not alter gene or protein function, but can be used to addressquestions in evolutionary biology (4) or in association studies with complex diseases, drug response, environmental insults (1) or quantitative trait loci(QTL) (5).
One method to determine SNP genotypes is single base primer extension or SBE. An unlabeled primer with its 3’ end directly flanking the SNP is extendedone nucleotide by Taq polymerase and fluorescently-labeled ddNTPs complementary to the polymorphic base are added. The resulting fragment is onenucleotide longer, but the observed fragment size on a gel will be greater than expected due to the influence of the fluorescent dye on theelectrophoretic mobility of these small fragments. SNPs can be identified by the one- or two-color peaks associated with the incorporated labeled ddNTPand the length of the primer.
The SBE technique can quickly interrogate a small number of SNPs. SNP genotyping using the MegaBACETM SNuPeTM Genotyping Kit (AmershamBioscience) demonstrated colocalization of Korrigan (beta 1-4 endo-glucanase) with a wood quality QTL of Pinus pinaster (5). SNaPshotTM GenotypingSystem (Applied Biosystems) was used to demonstrate the hybrid nature of the Baltic sturgeon by detecting both Acipenser sturio and A. oxyrinchusalleles in museum specimens of the extinct Baltic sturgeon (4). To fully utilize the investigative potential of SBE, a robust genotyping and data analysissystem should be employed. GeneMarker genotyping software is designed for fast, accurate and efficient analysis and reporting of primer extensiondata.
GeneMarker is user-friendly software containing a robust size calling algorithm that resolves fragment lengths to less than one base pair with highefficiency allele calling, adjusts for mobility shift of small fragments and displays two-color SNPs on one trace, essential for data generated by SNuPE andSNaPshot. The software is capable of analyzing data files from all major capillary electrophoresis systems including ABI, MegaBACE and Beckman.GeneMarker, in combination with our JelMarkerTM can also be used for analysis of slab gel output.


 For more details, download the Software for Single Base Extension Analysis PDF PDF icon (713 Kb)

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