TY - GEN
T1 - Finding more effective microsatellite markers for forensics
AU - Tan, Bowen
AU - Zhang, Zhe
AU - Zhao, Zicheng
AU - Li, Shengbin
AU - Li, Shuai Cheng
N1 - Publisher Copyright:
© 2016 IEEE.
PY - 2017/1/17
Y1 - 2017/1/17
N2 - Published by the Combined DNA Index System (CODIS) program of the Federal Bureau of Investigation (FBI) in 1997, the 13 core short tandem repeat (STR) loci are widely adopted as genetic markers in forensic applications, e.g., identity testing and paternity testing. However, these loci may be biased and suffer from reduced sensitivities towards specific population groups. In addition, the rapid growth of entries in forensic databases raises the chance of random hits, which can cause false judgments of innocents as criminals. A solution to these problems is to introduce more effective STR markers. The availability of whole genome sequencing enables us to identify more reliable STR markers for forensic applications computationally. In this study, we proposed an algorithm to identify STR markers with high discriminative abilities from the next-generation sequencing (NGS) data. Our algorithm could select a customized set of loci for a given population with pre-specified discriminative thresholds. We have applied the method to 320 Chinese individuals from the 1,000 Genomes Project and obtained various numbers of loci, which were able to statistically identify an individual worldwide and had higher combined powers of discrimination (CPD) and combined probabilities of exclusion (CPE) than the existing CODIS 13 loci. For identity testing, the mean frequency of DNA profile (FDP) with the selected 11 STRs was smaller than that with CODIS 13 STRs by student's t-test. With more loci, much smaller FDPs were obtained. The database matching probabilities (DMP) for selected loci were also lower than that for CODIS 13 STRs in a database with 10 billion entries. Moreover, the selected loci were able to provide considerably low chance of random profile matches so that statistically no false judgments could occur. The selected loci also reduced the risk of random allele matches when doing the familial search, with lower random allele matching probabilities. In addition, the selected STRs were statistically better than CODIS STRs for paternity testing in our simulated data, with lower probabilities of false inclusions and exclusions.
AB - Published by the Combined DNA Index System (CODIS) program of the Federal Bureau of Investigation (FBI) in 1997, the 13 core short tandem repeat (STR) loci are widely adopted as genetic markers in forensic applications, e.g., identity testing and paternity testing. However, these loci may be biased and suffer from reduced sensitivities towards specific population groups. In addition, the rapid growth of entries in forensic databases raises the chance of random hits, which can cause false judgments of innocents as criminals. A solution to these problems is to introduce more effective STR markers. The availability of whole genome sequencing enables us to identify more reliable STR markers for forensic applications computationally. In this study, we proposed an algorithm to identify STR markers with high discriminative abilities from the next-generation sequencing (NGS) data. Our algorithm could select a customized set of loci for a given population with pre-specified discriminative thresholds. We have applied the method to 320 Chinese individuals from the 1,000 Genomes Project and obtained various numbers of loci, which were able to statistically identify an individual worldwide and had higher combined powers of discrimination (CPD) and combined probabilities of exclusion (CPE) than the existing CODIS 13 loci. For identity testing, the mean frequency of DNA profile (FDP) with the selected 11 STRs was smaller than that with CODIS 13 STRs by student's t-test. With more loci, much smaller FDPs were obtained. The database matching probabilities (DMP) for selected loci were also lower than that for CODIS 13 STRs in a database with 10 billion entries. Moreover, the selected loci were able to provide considerably low chance of random profile matches so that statistically no false judgments could occur. The selected loci also reduced the risk of random allele matches when doing the familial search, with lower random allele matching probabilities. In addition, the selected STRs were statistically better than CODIS STRs for paternity testing in our simulated data, with lower probabilities of false inclusions and exclusions.
UR - https://www.scopus.com/pages/publications/85013277200
U2 - 10.1109/BIBM.2016.7822596
DO - 10.1109/BIBM.2016.7822596
M3 - 会议稿件
AN - SCOPUS:85013277200
T3 - Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
SP - 658
EP - 663
BT - Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
A2 - Burrage, Kevin
A2 - Zhu, Qian
A2 - Liu, Yunlong
A2 - Tian, Tianhai
A2 - Wang, Yadong
A2 - Hu, Xiaohua Tony
A2 - Jiang, Qinghua
A2 - Song, Jiangning
A2 - Morishita, Shinichi
A2 - Burrage, Kevin
A2 - Wang, Guohua
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Y2 - 15 December 2016 through 18 December 2016
ER -