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Microsatellite Analysis with Linked Pedigree

Microsatellite Analysis (SSR, STR, VNTR, MLVA)
Microsatellites (also known as simple-sequence-repeats, simple-tandem-repeats, variable-nucleotidetandem-repeats in eukaryote research; and Multiple-Loci-VNTR-Analysis in microbial research) are widely used to determine the genotype of organisms based on naturally occuring 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 decreases analysis set-up time, in comparison to GeneMapper®, Genotyper™, GeneScan®, CEQ™ Fragment Analysis 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. GeneMarker’s automated Run Wizard is designed to make analysis quick, easy, and accurate; compatible with ABI PRISM® 310-3100-3130-3500, 3730, Beckman CEQ™ or MegaBACE™ genetic analyzers. Visit our webinar for additional details on Microsatellite Analysis Tools in GeneMarker Software.

  1. Saturation Correction: Analysis of saturated data points by creating a synthetic peak based upon the peak
    shape before and after saturation.
  2. Baseline Subtraction: The software removes the baseline so that the Y axis is above the noise level.
  3. Pull-up Correction: This function removes peaks caused by wavelength bleeding.
  4. Spike Correction: The software automatically removes peaks from voltage spikes caused by micro- air
    bubbles or debris in the laser path.
  5. Stutter Peak Correction: The software automatically filters for stutter peaks caused by PCR slippage.

Linked Pedigree Tool

The user can either open an existing pedigree file of type ped or pre or create a new pedigree file in GeneMarker’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 showing inheritance conflicts in Family 5005

Download Microsatellite Analysis Application Note

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Research use only (RUO)

GeneMarker Applications:
Fragile X
MLPA® (Multiplex Ligation‐dependent Probe Amplification)
MS‐MLPA®
Trisomy Analysis
Macromolecule Analysis Tool
ARMs & Comparative Analysis (Cystic Fibrosis Analysis)
MSI (Microsatellite Instability) Analysis
Merge Project
Kinship Analysis of Wild Populations and data base
AFLP
t‐RFLP
Microsatellite (SSR, STR, VNTR)
MLVA
SBE/ SnapShot®
Cluster Analysis
TILLING® & EcoTilling with slabgel or capillary data
SNPWave®/SNPlex®
Haplotype Analysis
Loss of Heterozygosity Analysis (LOH)









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