A microhaplotypes panel for massively parallel sequencing analysis of DNA mixtures

Peng Chen; Chuwei Deng; Zheng Li; Yan Pu; Jiawen Yang; Yanfang Yu; Kai Li; Ding Li; Weibo Liang; Lin Zhang; Feng Chen

doi:10.1016/j.fsigen.2019.02.018

A microhaplotypes panel for massively parallel sequencing analysis of DNA mixtures

Forensic Sci Int Genet. 2019 May:40:140-149. doi: 10.1016/j.fsigen.2019.02.018. Epub 2019 Feb 22.

Authors

Peng Chen¹, Chuwei Deng², Zheng Li², Yan Pu³, Jiawen Yang², Yanfang Yu², Kai Li², Ding Li², Weibo Liang⁴, Lin Zhang⁴, Feng Chen⁵

Affiliations

¹ Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China. Electronic address: chenpeng@njmu.edu.cn.
² Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China.
³ School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, PR China.
⁴ Department of Forensic Biology, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, PR China.
⁵ Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China; Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China. Electronic address: fchen@njmu.edu.cn.

PMID: 30836262
DOI: 10.1016/j.fsigen.2019.02.018

Abstract

Massively parallel sequencing (MPS) technology enables the simultaneous analysis of different kinds of forensic genetic markers as well as the detection of the alleles with minor contributions in a highly unbalanced DNA mixture. In our previous study, we presented a novel set of microhaplotype loci and evaluated their application value in analyzing the DNA mixtures. However, several issues remain unclear, for example (i) whether the major or the minor donor in an unbalanced DNA mixture can be compared with a known suspect, (ii) whether the proportion of each contributor in a DNA mixture can be inferred, (iii) whether the captured alleles can be assigned to the major or the minor donor. To further address these issues, during the present study, we increased the number of loci in a single multiplex system to 25 (all the microhaplotypes have a length less than 50 bp). The DNA samples of 60 unrelated Han Chinese individuals, 40 artificially made DNA mixtures with different mixing proportions were analyzed with MPS by using the microhaplotypes panel. By comparing the population genetic data of the 25 microhaplotypes in 26 populations from 1000 Genome Project (1000 G), the microhaplotypes were found to have similar high A_e values in different populations. The likelihood ratios were further employed to compare the mixtures and known suspects. The major contributor could be well identified in both balanced and unbalanced samples. The minor contributor could also be identified if capturing enough loci. When we divided the microhaplotypes into different subgroups, significant correlation was found between the allele depth ratio and the gradual mixing ratios. The allele depth patterns in balanced, mildly imbalanced and severely imbalanced mixtures were clarified, and we found that certain loci could be discriminated from the contributors and they could be used for direct individual identification.

Keywords: Effect number of alleles; Massively parallel sequencing; Microhaplotype; Unbalanced DNA mixture.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

China
DNA / analysis*
DNA Fingerprinting*
Ethnicity / genetics
Gene Frequency
Genetics, Population
Genotype
Haplotypes*
High-Throughput Nucleotide Sequencing*
Humans
Likelihood Functions
Sequence Analysis, DNA*

Substances

DNA