Development of a novel five dye insertion/deletion (INDEL) panel for ancestry determination

Area of Science:

• Forensic Genetics
• Population Genetics
• Molecular Anthropology

Background:

• Short Tandem Repeats (STRs) are standard for identification, but other markers like Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion (INDEL) polymorphisms offer additional investigative avenues.
• INDELs are advantageous due to their size, lack of stutter, and suitability for degraded samples, enabling capillary electrophoresis genotyping.

Purpose of the Study:

• To develop and validate a robust 25 Insertion/Deletion Ancestry Informative Markers (INDEL-AIMs) multiplex assay for inferring ancestry.
• To assess the assay's performance across diverse ancestral populations relevant to the United States.

Main Methods:

• Selection of 25 INDEL-AIMs from the 1000 Genomes Project based on high fixation index (FST), allele frequency divergence, and genetic distance.
• Optimization and validation of the INDEL panel in a five-dye multiplex according to SWGDAM guidelines.
• Genotyping of 155 individuals from Caucasian, African, Hispanic, and East Asian ancestral groups, followed by Bayesian clustering and Principal Component Analysis (PCA).

Main Results:

• Clear genetic separation was observed among three ancestral groups (Caucasian, African, East Asian) with some overlap in the Hispanic group.
• PCA results showed consistency when compared against a large training set (793 samples) from the 1000 Genomes Project.
• The assay demonstrated reproducibility, inhibitor tolerance, robustness with casework samples, and high sensitivity (down to 125 pg).

Conclusions:

• The developed 25 loci INDEL system is a robust and effective tool for ancestry inference.
• This INDEL-based assay provides valuable supplementary data for forensic investigations involving individuals from common US ancestries.