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Microsatellite
Analysis (SSR, STR, VNTR) with Embedded
Pedigree Functionality
Microsatellites
(also known as simple-sequence-repeats,
simple-tandem-repeats, variable-nucleotide-tandem-repeats
in eukaryote research, or Multiple-Loci-VNTR-Analysis
in microbial research) are widely
used to determine the genotype of
organisms based on naturally
occurring variation. With eukaryotes,
the genotypes are used in areas like
population
genetics, forensics,
agriculture advancement. With bacteria
and other microbes, MLVA is used for
population genetics, to study transmission
routes, sources
of infection and the impact of
vaccination and use of antibiotics
on antibiotic
resistance.
GeneMarker software decreases
analysis set-up time, in
comparison to GeneMapper® software
through automated correction of common
genotyping problems including saturated
and pull-up peaks, instrument spikes,
and stutter peaks. A flexible panel
editor provides custom
panels required for microsatellite
analysis, and the software's automated
Run Wizard
is designed to make analysis quick,
easy, and accurate.
GeneMarker software is compatible
with outputs from all major sequencing
systems, including ABI®PRISM, Applied
Biosystems® SeqStudio and Spectrum
Compact CE genetic analyzers, as well
as custom primers or commercially
available 4-6 dye chemistries.
Read the Plant Animal Genome Poster
for additional Relationship Testing
Tools.
Download
Microsatellite Analysis Application
Note
View
the Microsatellite Analysis Webinar
GeneMarker
software is equipped with several
data processing options that make
Microsatellite analysis more accurate:
- Saturation Correction: Analysis
of saturated data points by creating
a synthetic peak based upon the
peak shape before and after saturation.
- Baseline Subtraction: The software
removes the baseline so that the
Y axis is above the noise level.
- Pull-up Correction: This function
removes peaks caused by wavelength
bleeding.
- Spike Correction: The software
automatically removes peaks from
voltage spikes caused by micro-
air bubbles or debris in the laser
path.
- Stutter Peak Correction: The software
automatically filters for stutter
peaks caused by PCR slippage.
Microsatellite
Analysis Results
Figure 1:
Review genotyping results and export
or print electropherogram and genotype
table results.
Linked Pedigree Tool
The user can either open an existing
pedigree file of type .ped or create
a new pedigree file in GeneMarker
software's pedigree tool. The pedigree
chart is designed to aid identification
of inheritance patterns and abnormalities.
All individuals in the pedigree with
sample files are directly linked to
the corresponding electropherograms
with a mouse click, and individuals
with illogical or abnormal allele
calls are highlighted in red. The
link between the pedigree and the
electropherograms displaying allele
calls for each marker make analysis
makes analysis quick and efficient.
Pedigree Chart
Figure 2:
The pedigree chart above shows the
inheritance conflicts
MLPA® is the registered
trademark of MRC Holland
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