Establishing an integrated pipeline for automatic and efficient detection of trace DNA encountered in forensic applications

Chong Chen; Yuan Lin; Huan Yu; Yu Xue; Qiannan Xu; Lei Jiang; Ruxin Zhu; Anqi Chen; Yue Yang; Ruocheng Xia; Xiaochun Zhang; Qi Yang; Ruiyang Tao; Bofeng Zhu; Chengtao Li; Suhua Zhang

doi:10.1016/j.scijus.2021.10.008

Establishing an integrated pipeline for automatic and efficient detection of trace DNA encountered in forensic applications

Sci Justice. 2022 Jan;62(1):50-59. doi: 10.1016/j.scijus.2021.10.008. Epub 2021 Nov 14.

Authors

Chong Chen¹, Yuan Lin², Huan Yu³, Yu Xue⁴, Qiannan Xu⁵, Lei Jiang², Ruxin Zhu², Anqi Chen⁶, Yue Yang⁷, Ruocheng Xia⁸, Xiaochun Zhang³, Qi Yang³, Ruiyang Tao², Bofeng Zhu⁹, Chengtao Li¹⁰, Suhua Zhang¹¹

Affiliations

¹ College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China; Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China.
² Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China.
³ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China.
⁴ Bionewtech® Company., Ltd., Shanghai 201615, China.
⁵ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
⁶ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China.
⁷ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; School of Basic Medicine, Inner Mongolia Medical University, Hohhot 010030, China.
⁸ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China; Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou 325035, China.
⁹ College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China.
¹⁰ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China. Electronic address: lichengtaohla@163.com.
¹¹ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai 200063, China. Electronic address: zhangsh@ssfjd.cn.

PMID: 35033328
DOI: 10.1016/j.scijus.2021.10.008

Abstract

The analysis of trace DNA is a crucial component in forensic applications. Biological materials containing low-level DNA collected at crime scenes, such as fingerprints, can be valuable as evidence. Automatic detection of biological samples has been largely embraced in forensic applications to meet the increasing throughput requirements. However, the amount of DNA automatically retrieved from trace evidence often tends to be small and unstable, ultimately resulting in poor detection of DNA profiles. Thus, in this work, we introduced a robust DNA extraction and purification platform named Bionewtech® BN3200 (Bionewtech®, Shanghai, China) with the goal of constructing a rapid automatic detection system for trace DNA. The establishment of automatic detection system for trace DNA mainly encompassed two parts: assessing the sensitivity of automatic extraction platform and screening the optimal short tandem repeat (STR) typing kit. The sensitivity of Bionewtech® BN3200 platform based on Ultra-sensitive DNA Extraction kit was initially estimated, demonstrating that this extraction platform might contain large potential in the trace DNA extraction. For the amplification part, three sets of commercial multiplex STR typing kits were selected as candidates, and the amplified products were further genotyped on the Applied Biosystems 3500xl Genetic Analyzer. After comparation, SiFa™ 23 Plex Kit was determined as the most suitable amplification system for trace DNA. Eventually, the newly exploited trace DNA detection system was successfully implemented in the detection of fingerprints derived from glass surfaces with the five-seconds contact time. As a result, the DNA recovered from the fingerprints fluctuated approximately from 57.60 pg to 18.05 ng, in addition, over 70% of the total STR loci were detected in 75% of the fingerprint samples.

Keywords: Automatic detection; Fingerprints; Forensic science; STR genotyping; Trace DNA; qRT-PCR.

Publication types

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

MeSH terms

China
DNA Fingerprinting* / methods
DNA* / analysis
Forensic Genetics / methods
Genotype
Humans
Microsatellite Repeats

Substances

DNA