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Related Experiment Video

Updated: May 26, 2026

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe

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Variants observed for STR locus SE33: a concordance study.

Carey Davis¹, Jianye Ge, Jonathan King

¹Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA.

Forensic Science International. Genetics

|January 3, 2012

Summary

Short tandem repeat (STR) typing kits can show discordant results for the SE33 marker due to primer differences. A single nucleotide polymorphism (SNP) in the flanking region, not an indel, causes these size variations.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Area of Science:

Forensic genetics
Molecular biology
Population genetics

Background:

Short tandem repeat (STR) typing is crucial for forensic identification and population studies.
Discordance in STR typing results can arise from variations in amplification kits, particularly at complex loci like SE33.
Primer selection and sequence-dependent conformational changes can influence electrophoretic migration and allele calls.

Purpose of the Study:

To compare the concordance of allele calls for the SE33 marker among three different STR typing kits: AmpFlSTR® NGM SElect™ (Life Technologies), PowerPlex® ESX 17 (Promega), and PowerPlex® ESI 17 (Promega).
To investigate the cause of discordant SE33 allele calls observed in selected samples.

Main Methods:

Comparative analysis of SE33 allele calls using AmpFlSTR® NGM SElect™, PowerPlex® ESX 17, and PowerPlex® ESI 17 kits.
Identification of samples with discordant SE33 allele calls.
Sequence analysis of the SE33 locus and flanking regions in discordant samples.

Main Results:

Sixteen samples exhibited discordant SE33 allele calls, appearing as a one-nucleotide size difference.
The AmpFlSTR® NGM SElect™ and PowerPlex® ESX 17 kits produced concordant results, while the PowerPlex® ESI 17 kit showed discrepancies.
Sequence analysis revealed that the size variation was caused by single nucleotide polymorphisms (SNPs) in the flanking region of SE33, with one novel SNP identified. These SNPs were observed in individuals of African and European descent.

Conclusions:

The observed discordance in SE33 allele calls is attributed to SNPs in the flanking region, not indels, and can be kit-dependent.
While observed with the ESI 17 kit, similar migration anomalies may occur with other kits as datasets grow.
Understanding STR kit discordance is vital for accurate forensic profile comparisons and database searches.