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Developmental validations of a self-developed 39 AIM-InDel panel and its forensic efficiency evaluations in the Shaanxi Han population

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Abstract

Most of insertion/deletion polymorphisms are diallelic molecular markers characterized as small amplicon sizes, high inter-population diversities, and low mutation rates, which make them the promising genetic markers in biogeographic ancestor inference field. The developmental validations of a 39 ancestry informative marker-insertion/deletion (AIM-InDel) panel and the genetic polymorphic investigations of this panel were performed in the Shaanxi Han population of China. The developmental validation included the optimizations of PCR-related indicators, repeatability, reproducibility, precision, accuracy, sensitivity, species specificity, stability of the panel, and the abilities in analyzing degraded, casework, and mixture samples, and the present results demonstrated that this 39 AIM-InDel panel was robust, sensitive, and accurate. For the population diversity analyses, the combined discrimination power value of 38 AIM-InDel loci except for rs36038238 locus was 0.999999999931257, indicating that this novel panel was highly polymorphic, biogeographic informative, and could be also used in individual identifications in the Shaanxi Han population.

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Data availability

The datasets generated during the current study are available from the corresponding author on reasonable request.

Code availability

Not applicable.

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Funding

This study was supported by the National Natural Science Foundation of China (81471824 and 81525015).

Author information

Author notes

  1. Xingru Zhang and Chunmei Shen contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an, 710004, China

    Xingru Zhang, Xiaoye Jin, Yuxin Guo & Bofeng Zhu

  2. Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, 710004, China

    Xingru Zhang, Xiaoye Jin & Yuxin Guo

  3. College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an, 710004, China

    Xingru Zhang, Xiaoye Jin & Bofeng Zhu

  4. Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi’an, 710062, China

    Chunmei Shen

  5. Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China

    Tong Xie & Bofeng Zhu

Authors
  1. Xingru Zhang
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  2. Chunmei Shen
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  5. Tong Xie
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  6. Bofeng Zhu
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Contributions

All authors contributed to the study conception and design. X-RZ and C-MS wrote the main text; C-MS collected samples; X-YJ performed the experiment and analyzed data; Y-XG revised the manuscript; B-FZ and XT designed the work and provided the conception. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Tong Xie or Bofeng Zhu.

Ethics declarations

Ethics approval

This study was performed in accordance with the principles of Declaration of Helsinki and was approved by the Ethics Committees of Xi’an Jiaotong University (No. 2019–1039).

Consent to participate

Informed consent was obtained from all individual participants included in the study.

Consent for publication

All individuals signed the informed consent regarding publishing their data.

Conflict of interest

The authors declare no competing interests.

Additional information

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Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary Figure 1.

Electrophoretogram of F312 DNA sample amplified by 39 AIM-InDel panel (PNG 23 kb)

Supplementary Figure 2.

Electrophoretogram of F312 DNA sample amplified by 39 AIM-InDel panel at different annealing temperatures. (PNG 34 kb)

Supplementary Figure 3.

Electrophoretogram of F312 DNA sample amplified by 39 AIM-InDel panel at different concentrations of Master mix. (PNG 258 kb)

Supplementary Figure 4.

Electrophoretogram of F312 DNA sample amplified by 39 AIM-InDel panel at different concentrations of Primer mix. (PNG 210 kb)

Supplementary Figure 5.

Electrophoretogram of F312 DNA sample amplified by 39 AIM-InDel panel at different cycle numbers. (PNG 233 kb)

Supplementary Figure 6.

Electrophoretogram of F312 DNA sample amplified by 39 AIM-InDel panel at different reaction volumes. (PNG 29 kb)

Supplementary Figure 7.

Electrophoretogram of F312 DNA sample amplified by 39 AIM-InDel panel in Beijing (A) and Suzhou (B) labs. (PNG 23 kb)

Supplementary Figure 8.

Electrophoretogram of different biological samples from individual A amplified by 39 AIM-InDel panel. (PNG 29 kb)

Supplementary Figure 9.

Electrophoretogram of different biological samples from individual B amplified by 39 AIM-InDel panel. (PNG 364 kb)

Supplementary Figure 10.

Electrophoretogram of artificially degraded F312 DNA samples amplified by 39 AIM-InDel panel with different incubation time. (PNG 188 kb)

Supplementary Figure 11.

Electrophoretogram of challenging samples amplified by 39 AIM-InDel panel (A) and Microreader™ 21 (Direct) ID System (B). (PNG 264 kb)

Supplementary Figure 12.

Electrophoretogram of F312 DNA sample amplified by 39 39 AIM-InDel panel in a gradient dilution. (PNG 273 kb)

Supplementary Figure 13.

The sensitivity study of the developed 39 AIM-InDel panel among a dilution series of F312 DNA sample. (PNG 119 kb)

Supplementary Figure 14.

Electrophoretogram of different non-human species DNA samples amplified by 39 AIM-InDel panel. (PNG 133 kb)

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Zhang, X., Shen, C., Jin, X. et al. Developmental validations of a self-developed 39 AIM-InDel panel and its forensic efficiency evaluations in the Shaanxi Han population. Int J Legal Med 135, 1359–1367 (2021). https://doi.org/10.1007/s00414-021-02600-4

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  • DOI: https://doi.org/10.1007/s00414-021-02600-4

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