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

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

The Illumina® MiSeq FGx™, in conjunction with the ForenSeq™ DNA Signature Prep kit, produces genotypes of the CODIS-required short tandem repeats and provides phenotype and biogeographical ancestry estimations via phenotype-informative and ancestry-informative markers, respectively. Although both ma...

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Bibliographic Details
Published in:International journal of legal medicine Vol. 135; no. 6; pp. 2221 - 2233
Main Authors: Weisz, Naomi A., Roberts, Katherine A., Hardy, W. Reef
Format: Journal Article
Language:English
Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-11-2021
Springer Nature B.V
Subjects:
Accuracy
Color
Deoxyribonucleic acid
DNA
DNA Fingerprinting
Eye Color - genetics
Forensic Medicine
Genotype
Genotype & phenotype
Hair
High-Throughput Nucleotide Sequencing
Humans
Markers
Medical Law
Medicine
Medicine & Public Health
Original Article
Phenotype
Polymorphism, Single Nucleotide
Reproducibility of Results
Statistical methods
Decedent missing persons
Next-generation sequencing
Phenotype and ancestry estimation
Investigative leads
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Summary:The Illumina® MiSeq FGx™, in conjunction with the ForenSeq™ DNA Signature Prep kit, produces genotypes of the CODIS-required short tandem repeats and provides phenotype and biogeographical ancestry estimations via phenotype-informative and ancestry-informative markers, respectively. Although both markers have been validated for use in forensic biology, there is little data to determine the practical utility of these estimations to assist in identifying missing persons using decedent casework samples. The accuracy and utility of phenotypic and ancestral estimations were investigated for 300 samples received by the Los Angeles County Department of Medical Examiner-Coroner. piSNP genotypes were translated into hair and eye colors using the Forenseq™ Universal Analysis Software (UAS) on the MiSeq FGx™ and the HIrisPlex System, and statistical accuracy was evaluated in context with the reported decedent characteristics. Similarly, estimates of each decedent’s biogeographical ancestry were compared to assess the efficacy of these markers to predict ancestry correctly. The average UAS and the HIrisPlex system prediction accuracy for brown and blue eyes were 95.3% and 96.2%, respectively. Intermediate eye color could not be predicted with high accuracy using either system. Other than the black hair phenotype reporting an accuracy that exceeded 90% using either system, hair color was also too variable to be predicted with high accuracy. The FROG-kb database distinguishes decedents adequately beyond the Asian, African, European, and Admixed American global ancestries provided by the MiSeq FGx™ UAS PCA plots. FROG-kb correctly identified Middle Eastern, Pacific Islander, Latin American, or Jewish ancestries with accuracies of 70.0%, 81.8%, 73.8%, and 86.7%, respectively.
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ISSN:0937-9827
1437-1596
DOI:10.1007/s00414-021-02631-x