Research on the method of setting depth thresholds for second generation sequencing of forensic genetic markers-Taking microhaplotypes as an example
10.13618/j.issn.1001-5728.2024.05.008
- VernacularTitle:法医遗传标记二代测序深度阈值设定方法研究
- Author:
Lin HE
1
,
2
;
Kelai KANG
;
Yaosen FENG
;
Jie ZHAO
;
Chi ZHANG
;
Wenhua MA
;
Kunpeng PAN
;
Fan CHEN
;
Anquan JI
;
Le WANG
Author Information
1. 昆明医科大学法医学院,云南 昆明 650500
2. 法医遗传学公安部重点实验室,公安部鉴定中心,北京 100038
- Keywords:
Forensic biological evidence;
Next generation sequencing;
Sequencing depth;
Analysis threshold
- From:
Chinese Journal of Forensic Medicine
2024;39(5):559-564
- CountryChina
- Language:Chinese
-
Abstract:
Objective Sequencing depth is a key parameter in next generation sequencing,which is closely related to the accuracy of sequencing results.Forensic biological evidence examination requires extremely high accuracy.It is crucial to scientifically and reasonably set the sequencing depth analysis threshold for forensic next generation sequencing testing.Methods This study used targeted sequencing data of microhaplotypes from 50 samples with known genotypes.By calculating the accuracy,precision,recall,and F1 score of each locus under various threshold conditions,two types of analysis threshold setting methods,which were based on fixed read count and fixed sequencing depth ratio,were studied extensively.Results The results showed that false positives were observed when the analysis threshold was set at 50×or 100×.When the analysis threshold was set at 200×,false negatives were observed.When the analysis threshold was set at 1.5%,3.0%,or 4.5%,false positives were observed.This study further proposed a third type of analysis threshold setting method,which was based on sequencing depth ratio scatter plots.With this method,no false positive or false negative was observed in the results.This article then explored four factors that lead to significant differences in the sequencing depth of forensic next generation sequencing experiments,compared with the analysis threshold setting method for capillary electrophoresis technology,and discussed the correlation between analysis thresholds and the ability to distinguish mixed DNA.Conclusion Employing the sequencing depth ratio scatter plot method to set analysis threshold has significant application value in next generation sequencing-based forensic genetic marker genotyping.
