Development of a novel five-dye panel for human identification insertion/deletion (INDEL) polymorphisms.

Area of Science:

• Forensic Science
• Genetics
• Molecular Biology

Background:

• Short tandem repeats (STRs) are standard for forensic DNA identification in systems like CODIS.
• Challenging samples (degraded, low-template DNA) limit STR analysis effectiveness.
• Single nucleotide polymorphisms (SNPs) and insertion/deletion (INDEL) polymorphisms offer alternative forensic markers.

Purpose of the Study:

• To develop and validate a novel 33-locus insertion/deletion (INDEL) marker panel for human identification.
• To assess the INDEL panel's performance with challenging forensic samples, including degraded and low-template DNA.
• To optimize INDEL markers for compatibility with existing multiplex electrophoresis systems.

Main Methods:

• Curated 33 INDEL Human Identification Markers (HID) from the 1000 Genomes Project based on F_ST and MAF criteria.
• Optimized and validated the 33-locus INDEL-HID panel using Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines.
• Employed a five-dye multiplex electrophoresis system for genotyping a sample set of 79 unrelated individuals.

Main Results:

• The 33-locus INDEL-HID panel demonstrated reproducibility and tolerance to PCR inhibitors.
• The assay successfully detected two-person mixtures across a range of ratios (4:1 to 1:6).
• Validation confirmed robustness with challenging samples and sensitivity down to 125 pg of DNA.

Conclusions:

• The developed 33-locus INDEL-HID panel provides robust recovery from low-template and degraded DNA samples.
• This INDEL panel is effective for individualization in forensic applications, particularly for challenging samples.
• INDEL markers offer a viable alternative or complement to STRs in forensic DNA analysis.