March 2007, SoftGenetics
- GeneMarker® Software for Single
Base Extension Analysis:
Introduction
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 
(713 Kb)
