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Updated: Apr 18, 2026

qPCRTag Analysis - A High Throughput, Real Time PCR Assay for Sc2.0 Genotyping

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Published on: May 25, 2015

Short-read, high-throughput sequencing technology for STR genotyping.

Daniel M Bornman¹, Mark E Hester², Jared M Schuetter³

¹Battelle Memorial Institute, Columbus, OH, USA.

Biotechniques. Rapid Dispatches

|January 27, 2015

Summary

This summary is machine-generated.

High-throughput sequencing offers a powerful new method for human identification using short tandem repeat (STR) loci. This validated approach accurately genotypes CODIS STR loci and identifies genetic variants in forensic samples.

Keywords:

Bridge PCR Illumina SNP STR forensic genotyping high-throughput sequencing next-generation sequencing

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Last Updated: Apr 18, 2026

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Published on: August 29, 2025

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Published on: March 15, 2019

Area of Science:

Forensic Science
Genetics
Molecular Biology

Background:

DNA-based human identification relies on short tandem repeat (STR) genotyping.
Current electrophoretic methods have limitations in throughput and sequence information.
High-throughput sequencing (HTS) technology is not yet validated for forensic casework.

Purpose of the Study:

To develop and validate a systematic method for HTS-based genotyping of CODIS STR loci.
To evaluate the accuracy and sensitivity of HTS for human identification.
To explore the potential of HTS for identifying variant alleles and analyzing mixed DNA samples.

Main Methods:

Utilized short-read (150 bp) massively parallel sequencing.
Optimized open-source reference alignment tools with a custom STR genome reference.
Analyzed Polymerase Chain Reaction (PCR)-amplified CODIS STR loci and the amelogenin (AMEL) locus.

Main Results:

Accurate genotyping of 13 CODIS STR loci and AMEL from individual and mixture samples was achieved.
Sensitivity analysis indicated that as few as 18,500 reads were sufficient for confident individual genotyping.
Identified variant alleles with single nucleotide polymorphisms (SNPs) and developed quantitative measurements for mixed samples.

Conclusions:

HTS provides a powerful, accurate, and sensitive method for forensic STR genotyping.
This validated approach enhances human identification capabilities by providing sequence-level detail.
The method supports the identification of genetic variants and the resolution of complex forensic samples.