Next generation sequencing of STR artifacts produced from historical bone samples

Area of Science:

• Forensic Science
• Molecular Biology
• Genetics

Background:

• Short tandem repeat (STR) artifacts complicate DNA profile interpretation, especially with degraded samples.
• Historical bone samples often yield low-quality DNA, necessitating sensitive analysis methods.
• Microbial DNA contamination can cross-react with primers during STR amplification, creating artifacts.

Purpose of the Study:

• To characterize STR artifacts in low-quality bone samples using next-generation sequencing (NGS).
• To identify the source of reproducible autosomal and Y-chromosomal STR (Y-STR) artifacts.
• To improve the interpretation of DNA profiles from challenging forensic samples.

Main Methods:

• Sequencing of PCR products from 17 degraded bone samples using NGS.
• Bioinformatic analysis with STRait Razor to validate alleles and CE profiles.
• Microbial identification using Kaiju to analyze sequence data and associated extracts.

Main Results:

• NGS and bioinformatic analysis confirmed STR alleles and identified artifact origins.
• A Y-STR artifact showed homology to Pseudomonas sp. DNA, a common soil bacterium.
• Observed homology between Pseudomonas genome and Y-STR primer binding sites.

Conclusions:

• Microbial DNA, specifically from soil bacteria like Pseudomonas, can cause Y-STR artifacts.
• Characterizing these artifacts enhances the interpretation of capillary electrophoresis (CE) data.
• This approach increases confidence in forensic DNA profile results from historical bone samples.