An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis
Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and...
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MDPI AG
2023-04-01
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| Online Access: | https://www.mdpi.com/2073-4425/14/4/865 |
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| author | Ranran Zhang Jiaming Xue Mengyu Tan Dezhi Chen Yuanyuan Xiao Guihong Liu Yazi Zheng Qiushuo Wu Miao Liao Meili Lv Shengqiu Qu Weibo Liang |
| author_facet | Ranran Zhang Jiaming Xue Mengyu Tan Dezhi Chen Yuanyuan Xiao Guihong Liu Yazi Zheng Qiushuo Wu Miao Liao Meili Lv Shengqiu Qu Weibo Liang |
| author_sort | Ranran Zhang |
| collection | DOAJ |
| description | Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform. The sizes of markers and amplicons ranged between 11–81 bp and 123–198 bp, respectively. The sensitivity was 0.25 ng, and the calling results were consistent with Sanger sequencing and the Integrative Genomics Viewer (IGV). It showed measurable polymorphism among sequenced 137 Southwest Chinese Han individuals. No significant deviations in the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were found at all MHs after Bonferroni correction. Furthermore, the specificity was 1:40 for simulated two-person mixtures, and the detection rates of highly degraded single samples and mixtures were 100% and 93–100%, respectively. Moreover, animal DNA testing was incomplete and low depth. Overall, our MPS-based 50-plex MH panel is a powerful forensic tool that provides a strong supplement and enhancement for some existing panels. |
| first_indexed | 2024-03-11T04:59:16Z |
| format | Article |
| id | doaj.art-a516e35546d94b9a87e0b3814d95d1fc |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T04:59:16Z |
| publishDate | 2023-04-01 |
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| series | Genes |
| spelling | doaj.art-a516e35546d94b9a87e0b3814d95d1fc2023-11-17T19:23:37ZengMDPI AGGenes2073-44252023-04-0114486510.3390/genes14040865An MPS-Based 50plex Microhaplotype Assay for Forensic DNA AnalysisRanran Zhang0Jiaming Xue1Mengyu Tan2Dezhi Chen3Yuanyuan Xiao4Guihong Liu5Yazi Zheng6Qiushuo Wu7Miao Liao8Meili Lv9Shengqiu Qu10Weibo Liang11Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaWest China Forensics Center, Sichuan University, No. 16, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, No. 17, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, ChinaMicrohaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform. The sizes of markers and amplicons ranged between 11–81 bp and 123–198 bp, respectively. The sensitivity was 0.25 ng, and the calling results were consistent with Sanger sequencing and the Integrative Genomics Viewer (IGV). It showed measurable polymorphism among sequenced 137 Southwest Chinese Han individuals. No significant deviations in the Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) were found at all MHs after Bonferroni correction. Furthermore, the specificity was 1:40 for simulated two-person mixtures, and the detection rates of highly degraded single samples and mixtures were 100% and 93–100%, respectively. Moreover, animal DNA testing was incomplete and low depth. Overall, our MPS-based 50-plex MH panel is a powerful forensic tool that provides a strong supplement and enhancement for some existing panels.https://www.mdpi.com/2073-4425/14/4/865microhaplotypemassively parallel sequencing (MPS)Southwest Chinese Hanforensic DNA analysisdegraded mixturesnoninvasive prenatal paternity testing (NIPPT) |
| spellingShingle | Ranran Zhang Jiaming Xue Mengyu Tan Dezhi Chen Yuanyuan Xiao Guihong Liu Yazi Zheng Qiushuo Wu Miao Liao Meili Lv Shengqiu Qu Weibo Liang An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis Genes microhaplotype massively parallel sequencing (MPS) Southwest Chinese Han forensic DNA analysis degraded mixtures noninvasive prenatal paternity testing (NIPPT) |
| title | An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis |
| title_full | An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis |
| title_fullStr | An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis |
| title_full_unstemmed | An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis |
| title_short | An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis |
| title_sort | mps based 50plex microhaplotype assay for forensic dna analysis |
| topic | microhaplotype massively parallel sequencing (MPS) Southwest Chinese Han forensic DNA analysis degraded mixtures noninvasive prenatal paternity testing (NIPPT) |
| url | https://www.mdpi.com/2073-4425/14/4/865 |
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