PeakSeeker: a program for interpreting genotypes of mononucleotide repeats
James M Thompson1, Stephen J Salipante
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, USA. tex@u.washington.edu
BMC Research Notes
|February 5, 2009
Summary
A new software, PeakSeeker, interprets genotypes of mononucleotide repeats, overcoming stutter issues. This enables the use of highly informative mononucleotide microsatellite markers in genetic research.
Area of Science:
- Genetics
- Molecular Biology
- Bioinformatics
Background:
- Mononucleotide repeats are abundant, polymorphic DNA sequences with potential as genetic markers.
- PCR amplification causes "stutter" in mononucleotide repeats, complicating genotype interpretation.
- Larger microsatellite repeats (di- and tri-nucleotide) produce less stutter but are less informative.
Purpose of the Study:
- To develop a method for interpreting genotypes of mononucleotide repeats.
- To enable the widespread use of highly informative mononucleotide microsatellite markers.
Main Methods:
- Developed a software program named PeakSeeker.
- PeakSeeker interprets experimental electropherograms to identify individual allele signals.
- Defined locus-specific stutter patterns for each marker, approximated by genotyping single DNA molecules or homozygotes.
Main Results:
- Evaluated PeakSeeker's ability to discriminate homozygous and heterozygous mononucleotide loci using simulated and experimental data.
- Demonstrated that PeakSeeker can accurately interpret mononucleotide repeat genotypes.
Conclusions:
- Mononucleotide tracts offer advantages over di- and tri-nucleotide microsatellite markers.
- PeakSeeker provides a high-throughput method for typing mononucleotide tracts using fragment length polymorphism genotyping.
- The PeakSeeker algorithm may be adaptable to improve and standardize conventional microsatellite genotype analysis.
