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Identification of the efficacy of parentage testing based on bi-allelic autosomal single nucleotide polymorphism markers in Taiwanese population

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Abstract

Parentage testing is crucial for forensic DNA analysis, using short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) with high minor allele frequency (MAF) are promising for human identification. This study aimed to develop SNP markers for parentage testing in the Taiwanese population and compare their accuracy with STRs. The TPMv1 SNP microarray (714,457 SNPs) was used to screen 180,000 Taiwanese individuals and analyze the SNP data using PLINK. After quality control, allelic distribution, and MAF considerations, a set of SNPs with significant inheritance information was selected. Parentage testing was conducted on 355 single parent-child pairs using both STRs and SNPs, employing three kinship algorithms: identity by descent, kinship-based inference for genome-wide association studies, and the combined paternity index/probability of paternity (CPI/PP). An Affymetrix signature probe for kinship testing (ASP) was also used. Based on the quality control and selection criteria, 176 SNPs with MAF > 0.4995 were selected from the Taiwanese population. The CPI/PP results calculated using SNPs were consistent with the STR results. The accuracy of the SNPs used in the single-parent-child parentage testing was > 99.99%. The set of 176 SNPs had a higher identification rate in the single parent-child parentage test than in the ASP. The CPI/PP value calculated using 176 SNPs was also more accurate than that calculated using ASP. Our findings suggest that these 176 SNPs could be used for single-parent-child parentage identification in the Taiwanese population.

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Funding

This work was supported by a grant from the China Medical University Hospital, Taichung, Taiwan (# DMR 111-152).

Author information

Author notes

  1. Yu-Chia Chen and Wei-De Lin contributed equally to this work.

Authors and Affiliations

  1. Department of Medical Research, China Medical University Hospital, North District, No. 2, Yude Road, Taichung, 40447, Taiwan

    Yu-Chia Chen, Wei-De Lin, Ting-Yuan Liu & Fuu-Jen Tsai

  2. School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung, 40447, Taiwan

    Wei-De Lin

  3. Department of Medical Genetics, China , Medical University Hospital, Taichung, 40447, Taiwan

    Fuu-Jen Tsai

  4. Division of Genetics and Metabolism, China Medical University Children’s Hospital, Taichung, 40447, Taiwan

    Fuu-Jen Tsai

  5. School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan

    Fuu-Jen Tsai

  6. Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, 41354, Taiwan

    Fuu-Jen Tsai

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  1. Yu-Chia Chen
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Corresponding author

Correspondence to Fuu-Jen Tsai.

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Studies in humans and animals

Human sample collection was approved by the Research Ethics Committee, China Medical University Hospital, Taichung, Taiwan (CMUH REC No.: CMUH107-REC3-058 and CMUH110-REC3-005). All research is conducted in compliance with government laws and ethics.

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12024_2024_790_MOESM1_ESM.xlsx

Table S1. The signature probe for kinship testing from Affymetrix designed in TPMv1 chip. Table S2. The calculation formula for paternity index (PI). Table S3. The selected single nucleotide polymorphisms (SNPs) in combined paternity index computing. Table S4. Summary results of short tandem repeat (STR) parentage testing with single parent-child pairs. Table S5. Summary of results for identity by descent (IBD), kinship-based inference for genome-wide association (KING), and combined paternity index (CPI). Table S6. Parentage testing sensitivity and specificity of SNP method compared with STR results in 355 single-parent-child pairs. Table S7. Comparison of four SNP parentage testing population and their SNP minor allele frequency in Taiwanese population (XLSX 234 KB)

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Chen, YC., Lin, WD., Liu, TY. et al. Identification of the efficacy of parentage testing based on bi-allelic autosomal single nucleotide polymorphism markers in Taiwanese population. Forensic Sci Med Pathol (2024). https://doi.org/10.1007/s12024-024-00790-y

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