Genome-wide screening for highly discriminative SNPs for personal identification and their assessment in world populations

Liming Li; Yi Wang; Shuping Yang; Mingying Xia; Yajun Yang; Jiucun Wang; Daru Lu; Xingwei Pan; Teng Ma; Pei Jiang; Ge Yu; Ziqin Zhao; Yuan Ping; Huaigu Zhou; Xueying Zhao; Hui Sun; Bing Liu; Dongtao Jia; Chengtao Li; Rile Hu; Hongzhou Lu; Xiaoyang Liu; Wenqing Chen; Qin Mi; Fuzhong Xue; Yongdong Su; Li Jin; Shilin Li

doi:10.1016/j.fsigen.2017.02.005

Genome-wide screening for highly discriminative SNPs for personal identification and their assessment in world populations

Forensic Sci Int Genet. 2017 May:28:118-127. doi: 10.1016/j.fsigen.2017.02.005. Epub 2017 Feb 16.

Authors

Liming Li¹, Yi Wang¹, Shuping Yang¹, Mingying Xia¹, Yajun Yang², Jiucun Wang², Daru Lu², Xingwei Pan¹, Teng Ma¹, Pei Jiang¹, Ge Yu¹, Ziqin Zhao³, Yuan Ping⁴, Huaigu Zhou⁴, Xueying Zhao⁴, Hui Sun⁵, Bing Liu⁶, Dongtao Jia⁷, Chengtao Li⁸, Rile Hu⁹, Hongzhou Lu¹⁰, Xiaoyang Liu¹¹, Wenqing Chen¹², Qin Mi¹³, Fuzhong Xue¹⁴, Yongdong Su¹⁵, Li Jin¹⁶, Shilin Li¹⁷

Affiliations

¹ MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China.
² MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China.
³ Department of Forensic Medicine, Shanghai Medicine College, Fudan University, Shanghai, 200000, China.
⁴ Shanghai Public Security Bureau-Fudan University Joint Laboratory of Human Biology and Forensic Techniques for Crime Scenes, Shanghai Research Institute of Criminal Science and Technology, Shanghai Key Laboratory of Crime Scene Evidence, Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Shanghai, 200000, China.
⁵ MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
⁶ Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
⁷ Nantong Bureau of Public Safety, Jiangsu, 226000, China.
⁸ National Institute of Forensics, Ministry of Justice, Shanghai, 200000, China.
⁹ MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Medical College of Inner Mongolia, Ulaanbaatar, Autonomous Region of Inner Mongolia, 010000, China.
¹⁰ Department of Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200000, China.
¹¹ China-Japan Friendship Hospital, Jilin University, Changchun, Jilin, 130000, China.
¹² Cancer Hospital, Changchun, Jilin, 130000, China.
¹³ Department of Biology and Geography, Qinghai Normal University, Xining, Qinghai, 810000, China.
¹⁴ School of Public Health, Shandong University, Jinan, Shandong, 250000, China.
¹⁵ Bureau of Public Safety, Lhasa, Autonomous Region of Tibet, 850000, China.
¹⁶ MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China. Electronic address: lijin@fudan.edu.cn.
¹⁷ MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Developmental Biology and School of Life Sciences, Fudan University, Shanghai, 200438, China; Fudan-Taizhou Institute of Health Sciences, Jiangsu, 225300, China. Electronic address: lishilin@fudan.edu.cn.

PMID: 28249201
DOI: 10.1016/j.fsigen.2017.02.005

Abstract

The applications of DNA profiling aim to identify perpetrators, missing family members and disaster victims in forensic investigations. Single nucleotide polymorphisms (SNPs) based forensic applications are emerging rapidly with a potential to replace short tandem repeats (STRs) based panels which are now being used widely, and there is a need for a well-designed SNP panel to meet such challenge for this transition. Here we present a panel of 175 SNP markers (referred to as Fudan ID Panel or FID), selected from ∼3.6 million SNPs, for the application of personal identification. We optimized and validated FID panel using 729 Chinese individuals using a next generation sequencing (NGS) technology. We showed that the SNPs in the panel possess very high heterozygosity as well as low within- and among-continent differentiations, enabling FID panel exhibit discrimination power in both regional and worldwide populations, with the average match probabilities ranging from 4.77×10^-71 to 1.06×10^-64 across 54 world populations. With the advent of biomedical research, the SNPs connecting physical anthropological, physiological, behavioral and phenotypic traits will be eventually added to the forensic panels that will revolutionize criminal investigation.

Keywords: Forensics; Ion Torrent; Next generation sequencing; Personal identification; Single nucleotide polymorphisms.

Publication types

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

MeSH terms

DNA Fingerprinting / methods*
Genetics, Population*
Genotyping Techniques
HapMap Project
Heterozygote
High-Throughput Nucleotide Sequencing
Humans
Polymorphism, Single Nucleotide*