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

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Abstract

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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Acknowledgements

From the Los Angeles County Department of Medical Examiner-Coroner, the authors wish to thank Dr. Ruby Javed-Ghaffar, the Chief of the Forensic Labs, Mr. Eric Wahoske, the previous supervisor of the Human Genomics Unit, and Sarah de Quintana, who served as the Chair of the Research and Publication Committee during this project, for providing approval for the use of postmortem blood samples. Also, we would like to acknowledge and thank DNA Analyst, Oscar Pleitez, for sharing in the training of Ms. Weisz and for helping with the logistics of charging in and out the postmortem blood samples. The authors want to extend thanks to Verogen for reagents and for the scientific collaboration provided by Ann Allison, John Walsh, Melissa Kotkin, Meghan Didier, and Cydne Holt in data review.

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Authors and Affiliations

  1. School of Criminal Justice and Criminalistics, California State University, Los Angeles, 1800 Paseo Rancho Castilla, Los Angeles, CA, 90032, USA

    Naomi A. Weisz & Katherine A. Roberts

  2. California Forensic Science Institute, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA, 90032, USA

    Katherine A. Roberts

  3. Human Genomics Unit, Los Angeles County Department of Medical Examiner-Coroner, 1104 N Mission Road, Los Angeles, CA, 90033, USA

    W. Reef Hardy

Authors
  1. Naomi A. Weisz
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Correspondence to Katherine A. Roberts.

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Ethics approval

The LACDoME-C Research and Publication Committee approved this study before initiating the research. The use of decedent samples is permitted to validate new technologies and analysis methods at the LACDoME-C. The results for all samples utilized in this study were reported without personal identifying information (PII) other than the decedent’s hair and eye color and biogeographical ancestry. Living subjects gave informed consent for the collection and use of their buccal swabs for research purposes. All samples were coded to provide confidentiality.

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Supplementary Information

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Supplementary file1 (PDF 481 KB) EMS 1 (LACDoME-C HGU-003 Manual Setup of Plexor HY Quantification Assay).

414_2021_2631_MOESM2_ESM.pdf

Supplementary file2 (PDF 166 KB) EMS 2 (LACDoME-C HGU-004 Analysis and Interpretation of Plexor HY Quantification Assay).

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Weisz, N.A., Roberts, K.A. & Hardy, W.R. Reliability of phenotype estimation and extended classification of ancestry using decedent samples. Int J Legal Med 135, 2221–2233 (2021). https://doi.org/10.1007/s00414-021-02631-x

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  • DOI: https://doi.org/10.1007/s00414-021-02631-x

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