CLC number:
On-line Access: 2024-08-27
Received: 2023-10-17
Revision Accepted: 2024-05-08
Crosschecked: 2023-09-13
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Yating FANG, Man CHEN, Bofeng ZHU. Construction and evaluation of in-house methylation-sensitive SNaPshot system and three classification prediction models for identifying the tissue origin of body fluid[J]. Journal of Zhejiang University Science B, 2023, 24(9): 839-852.
@article{title="Construction and evaluation of in-house methylation-sensitive SNaPshot system and three classification prediction models for identifying the tissue origin of body fluid",
author="Yating FANG, Man CHEN, Bofeng ZHU",
journal="Journal of Zhejiang University Science B",
volume="24",
number="9",
pages="839-852",
year="2023",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B2200555"
}
%0 Journal Article
%T Construction and evaluation of in-house methylation-sensitive SNaPshot system and three classification prediction models for identifying the tissue origin of body fluid
%A Yating FANG
%A Man CHEN
%A Bofeng ZHU
%J Journal of Zhejiang University SCIENCE B
%V 24
%N 9
%P 839-852
%@ 1673-1581
%D 2023
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B2200555
TY - JOUR
T1 - Construction and evaluation of in-house methylation-sensitive SNaPshot system and three classification prediction models for identifying the tissue origin of body fluid
A1 - Yating FANG
A1 - Man CHEN
A1 - Bofeng ZHU
J0 - Journal of Zhejiang University Science B
VL - 24
IS - 9
SP - 839
EP - 852
%@ 1673-1581
Y1 - 2023
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B2200555
Abstract: The identification of tissue origin of body fluid can provide clues and evidence for criminal case investigations. To establish an efficient method for identifying body fluid in forensic cases, eight novel body fluid-specific DNA methylation markers were selected in this study, and a multiplex single base extension reaction (SNaPshot) system for these markers was constructed for the identification of five common body fluids (venous blood, saliva, menstrual blood, vaginal fluid, and semen). The results indicated that the in-house system showed good species specificity, sensitivity, and ability to identify mixed biological samples. At the same time, an artificial body fluid prediction model and two machine learning prediction models based on the support vector machine (SVM) and random forest (RF) algorithms were constructed using previous research data, and these models were validated using the detection data obtained in this study (n=95). The accuracy of the prediction model based on experience was 95.79%; the prediction accuracy of the SVM prediction model was 100.00% for four kinds of body fluids except saliva (96.84%); and the prediction accuracy of the RF prediction model was 100.00% for all five kinds of body fluids. In conclusion, the in-house SNaPshot system and RF prediction model could achieve accurate tissue origin identification of body fluids.
[1]AlderdenJ, PepperGA, WilsonA, et al., 2018. Predicting pressure injury in critical care patients: a machine-learning model. Am J Crit Care, 27(6):461-468.
[2]Benn TorresJ, MartucciV, AldrichMC, et al., 2019. Analysis of biogeographic ancestry reveals complex genetic histories for indigenous communities of St. Vincent and Trinidad. Am J Phys Anthropol, 169(3):482-497.
[3]BiQF, GoodmanKE, KaminskyJ, et al., 2019. What is machine learning? A primer for the epidemiologist. Am J Epidemiol, 188(12):2222-2239.
[4]CheDS, LiuQ, RasheedK, et al., 2011. Decision tree and ensemble learning algorithms with their applications in bioinformatics. In: Arabnia HR, Tran QN (Eds.), Software Tools and Algorithms for Biological Systems. Springer, New York, p.191-199.
[5]ChenCJ, ChenH, ZhangY, et al., 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant, 13(8):1194-1202.
[6]ChoungCM, LeeJW, ParkJH, et al., 2021. A forensic case study for body fluid identification using DNA methylation analysis. Leg Med, 51:101872.
[7]ChowdhuryAR, ChatterjeeT, BanerjeeS, 2019. A random forest classifier-based approach in the detection of abnormalities in the retina. Med Biol Eng Comput, 57(1):193-203.
[8]DeoRC, 2015. Machine learning in medicine. Circulation, 132(20):1920-1930.
[9]de RaadtA, WarrensMJ, BoskerRJ, et al., 2019. Kappa coefficients for missing data. Educ Psychol Meas, 79(3):558-576.
[10]DiasHC, CordeiroC, PereiraJ, et al., 2020. DNA methylation age estimation in blood samples of living and deceased individuals using a multiplex SNaPshot assay. Forensic Sci Int, 311:110267.
[11]EngstrandRD, MoellerG, 1967. Confusion matrix analysis for form perception. Hum Factors, 9(5):439-446.
[12]ForatS, HuettelB, ReinhardtR, et al., 2016. Methylation markers for the identification of body fluids and tissues from forensic trace evidence. PLoS ONE, 11(2):e0147973.
[13]HaddrillPR, 2021. Developments in forensic DNA analysis. Emerg Top Life Sci, 5(3):381-393.
[14]HaoT, GuoJL, LiuJD, et al., 2021. Predicting human age by detecting DNA methylation status in hair. Electrophoresis, 42(11):1255-1261.
[15]HuangHZ, LiuXZ, ChengJB, et al., 2022. A novel multiplex assay system based on 10 methylation markers for forensic identification of body fluids. J Forensic Sci, 67(1):136-148.
[16]HuangSJ, CaiNG, PachecoPP, et al., 2018. Applications of support vector machine (SVM) learning in cancer genomics. Cancer Genomics Proteomics, 15(1):41-51.
[17]KaderF, GhaiM, OlaniranAO, 2020. Characterization of DNA methylation-based markers for human body fluid identification in forensics: a critical review. Int J Legal Med, 134(1):1-20.
[18]LeeHY, AnJH, JungSE, et al., 2015. Genome-wide methylation profiling and a multiplex construction for the identification of body fluids using epigenetic markers. Forensic Sci Int Genet, 17:17-24.
[19]LeeJE, LeeJM, NaueJ, et al., 2022. A collaborative exercise on DNA methylation-based age prediction and body fluid typing. Forensic Sci Int Genet, 57:102656.
[20]MartinNC, ClaysonNJ, ScrimgerDG, 2006. The sensitivity and specificity of Red-Starch paper for the detection of saliva. Sci Justice, 46(2):97-105.
[21]MatteiAL, BaillyN, MeissnerA, 2022. DNA methylation: a historical perspective. Trends Genet, 38(7):676-707.
[22]PanC, YiSH, XiaoC, et al., 2020. The evaluation of seven age-related CpGs for forensic purpose in blood from Chinese Han population. Forensic Sci Int Genet, 46:102251.
[23]ParkJL, KwonOH, KimJH, et al., 2014. Identification of body fluid-specific DNA methylation markers for use in forensic science. Forensic Sci Int Genet, 13:147-153.
[24]SijenT, HarbisonS, 2021. On the identification of body fluids and tissues: a crucial link in the investigation and solution of crime. Genes, 12(11):1728.
[25]TianH, BaiP, TanY, et al., 2020. A new method to detect methylation profiles for forensic body fluid identification combining ARMS-PCR technique and random forest model. Forensic Sci Int Genet, 49:102371.
[26]VirklerK, LednevIK, 2009. Analysis of body fluids for forensic purposes: from laboratory testing to non-destructive rapid confirmatory identification at a crime scene. Forensic Sci Int, 188(1-3):1-17.
[27]ZhaoC, YangJ, XuH, et al., 2022. Genetic diversity analysis of forty-three insertion/deletion loci for forensic individual identification in Han Chinese from Beijing based on a novel panel. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 23(3):241-248.
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