Reliability of phenotype estimation and extended classification of ancestry using decedent samples

Area of Science:

• Forensic genetics
• Human identification
• Population genetics

Background:

• The Illumina® MiSeq FGx™ platform, with the ForenSeq™ DNA Signature Prep kit, generates short tandem repeat (STR) genotypes for CODIS (Combined DNA Index System) and estimates phenotype and biogeographical ancestry.
• While validated for forensic applications, the practical utility of these estimations for identifying missing persons from decedent samples is not well-established.

Purpose of the Study:

• To evaluate the accuracy and utility of phenotypic (hair and eye color) and biogeographical ancestry estimations for missing persons identification using decedent casework samples.
• To assess the performance of the ForenSeq™ Universal Analysis Software (UAS) and the HIrisPlex System for predicting phenotypes and the FROG-kb database for predicting ancestry.

Main Methods:

• Analysis of 300 decedent samples from the Los Angeles County Department of Medical Examiner-Coroner.
• Translation of piSNP genotypes to hair and eye colors using ForenSeq™ UAS and HIrisPlex System.
• Statistical evaluation of prediction accuracy against reported decedent characteristics.
• Comparison of predicted biogeographical ancestry with FROG-kb database and MiSeq FGx™ UAS PCA (Principal Component Analysis) plots.

Main Results:

• High prediction accuracy for brown (95.3% UAS) and blue (96.2% UAS, 96.2% HIrisPlex) eyes was observed.
• Prediction accuracy for intermediate eye colors and most hair colors (except black, >90%) was not high due to variability.
• The FROG-kb database provided more granular ancestry information than MiSeq FGx™ UAS PCA plots, correctly identifying Middle Eastern (70.0%), Pacific Islander (81.8%), Latin American (73.8%), and Jewish (86.7%) ancestries.

Conclusions:

• Phenotypic estimations, particularly for eye color and black hair, show potential utility in missing persons investigations, but limitations exist for intermediate eye colors and other hair colors.
• Biogeographical ancestry estimation using the FROG-kb database offers valuable insights beyond broad continental classifications, aiding in the identification of diverse populations.
• The combined use of STR genotyping, phenotypic, and biogeographical ancestry estimations on platforms like Illumina® MiSeq FGx™ can enhance missing persons identification efforts, despite current limitations in predicting certain traits.