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Updated: Jan 2, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

Understanding the characteristics of sequence-based single-source DNA profiles.

Sarah Riman¹, Hari Iyer², Lisa A Borsuk¹

¹U.S. National Institute of Standards and Technology, Biomolecular Measurement Division, 100 Bureau Drive, Gaithersburg, MD 20899-8314, USA.

Forensic Science International. Genetics

|December 6, 2019

Summary

This study characterizes short tandem repeat (STR) sequencing data, revealing how common genotyping challenges like stutter and noise appear in next-generation sequencing (NGS) profiles. A statistical framework helps interpret these targeted sequencing results for forensic applications.

Keywords:

Analytical threshold Next generation sequencing (NGS)Noise Receiver operating characteristic (ROC) plots Short tandem repeat (STR)Zygosity

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Published on: March 9, 2015

Area of Science:

Forensic genetics
Molecular biology
Bioinformatics

Background:

Traditional fragment-based genotyping of short tandem repeat (STR) markers masks underlying sequence variation.
Targeted sequencing offers deeper insights but faces interpretation challenges similar to capillary electrophoresis, including stochastic effects, noise, and allelic dropout.

Purpose of the Study:

To characterize and understand the behavior of common genotyping artifacts in targeted STR sequencing datasets.
To develop a statistical framework for interpreting single-source DNA profiles generated by targeted sequencing.

Main Methods:

Sensitivity studies using known single-source samples with varying DNA input (15-500 pg) amplified with the PowerSeq 46GY System Prototype.
STR library preparation using two commercial kits, followed by sequencing on the Illumina MiSeq platform.
Analysis of raw FASTQ data using STRait Razor v2.0 without thresholds (coverage ≥ 1), investigating library normalization and threshold setting.

Main Results:

Investigated the impact of DNA quantity and library preparation methods on STR profile characteristics.
Evaluated methods for setting analytical and zygosity thresholds in targeted sequencing data.
Demonstrated that analyses can be adapted for similar targeted sequencing panels and next-generation sequencing platforms.

Conclusions:

Established a framework for systematically interpreting STR profiles from targeted sequencing.
Characterized key factors influencing STR profile quality and interpretation in sequencing data.
Provided a methodology applicable to diverse targeted sequencing panels and NGS platforms for forensic analysis.