Body Fluid Identification in Samples Collected After Intimate and Social Contact: A Comparison of Two MRNA Profiling Methods and the Additional Information Gained by CSNP Genotypes

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2023 Mar 29

PMID 36980908

Authors

Helen Johannessen

Erin Hanson

Peter Gill

Cordula Haas

Erik Francisco Bergseth

Jack Ballantyne

Ane Elida Fonnelop

Affiliations

Soon will be listed here.

Abstract

The ability to associate a contributor with a specific body fluid in a crime stain can aid casework investigation. The detection of body fluids combined with DNA analyses may supply essential information, but as the two tests are independent, they may not be associated. Recently, the analysis of coding region SNPs (cSNPs) within the RNA transcript has been proven to be a promising method to face this challenge. In this study, we performed targeted RNA sequencing of 158 samples (boxershorts, fingernail swabs and penile swabs) collected from 12 couples at different time points post-intimate contact and after non-intimate contact, using the Ion S5™ System and BFID-cSNP-6F assay. The aim of the study was to compare the performance of the MPS and CE methods in the detection of mRNA markers, and to associate body fluids with contributors by their cSNP genotypes. The results of the study show a lower success rate in the detection of vaginal mucosa by the MPS compared to the CE method. However, the additional information obtained with the cSNP genotypes could successfully associate body fluids with contributors in most cases.

Citing Articles

Application of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen-vaginal fluid mixtures.

Wen D, Xing H, Tang X, Wang Y, Jiang B, Li J R Soc Open Sci. 2025; 12(1):241565.

PMID: 39816748 PMC: 11732431. DOI: 10.1098/rsos.241565.

References

Ingold S, Dorum G, Hanson E, Ballard D, Berti A, Gettings K . Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach - results of a second EUROFORGEN / EDNAP collaborative exercise. Forensic Sci Int Genet. 2019; 45:102208. DOI: 10.1016/j.fsigen.2019.102208. View

Hanson E, Dorum G, Zamborlin M, Wang S, Gysi M, Ingold S . Targeted S5 RNA sequencing assay for the identification and direct association of common body fluids with DNA donors in mixtures. Int J Legal Med. 2022; 137(1):13-32. DOI: 10.1007/s00414-022-02908-9. View

Johannessen H, Gill P, Shanthan G, Fonnelop A . Transfer, persistence and recovery of DNA and mRNA vaginal mucosa markers after intimate and social contact with Bayesian network analysis for activity level reporting. Forensic Sci Int Genet. 2022; 60:102750. DOI: 10.1016/j.fsigen.2022.102750. View

Zubakov D, Kokmeijer I, Ralf A, Rajagopalan N, Calandro L, Wootton S . Towards simultaneous individual and tissue identification: A proof-of-principle study on parallel sequencing of STRs, amelogenin, and mRNAs with the Ion Torrent PGM. Forensic Sci Int Genet. 2015; 17:122-128. DOI: 10.1016/j.fsigen.2015.04.002. View

van den Berge M, Carracedo A, Gomes I, Graham E, Haas C, Hjort B . A collaborative European exercise on mRNA-based body fluid/skin typing and interpretation of DNA and RNA results. Forensic Sci Int Genet. 2014; 10:40-48. DOI: 10.1016/j.fsigen.2014.01.006. View

Ingold S, Dorum G, Hanson E, Ballantyne J, Haas C . Assigning forensic body fluids to donors in mixed body fluids by targeted RNA/DNA deep sequencing of coding region SNPs. Int J Legal Med. 2020; 134(2):473-485. DOI: 10.1007/s00414-020-02252-w. View

Salzmann A, Russo G, Aluri S, Haas C . Transcription and microbial profiling of body fluids using a massively parallel sequencing approach. Forensic Sci Int Genet. 2019; 43:102149. DOI: 10.1016/j.fsigen.2019.102149. View

Akutsu T, Motani H, Watanabe K, Iwase H, Sakurada K . Detection of bacterial 16S ribosomal RNA genes for forensic identification of vaginal fluid. Leg Med (Tokyo). 2012; 14(3):160-2. DOI: 10.1016/j.legalmed.2012.01.005. View

Lindenbergh A, de Pagter M, Ramdayal G, Visser M, Zubakov D, Kayser M . A multiplex (m)RNA-profiling system for the forensic identification of body fluids and contact traces. Forensic Sci Int Genet. 2012; 6(5):565-77. DOI: 10.1016/j.fsigen.2012.01.009. View

10.

Liu J, Cheng X, Liu F, Hao T, Wang J, Guo J . Identification of coding region SNPs from specific and sensitive mRNA biomarkers for the deconvolution of the semen donor in a body fluid mixture. Forensic Sci Int Genet. 2021; 52:102483. DOI: 10.1016/j.fsigen.2021.102483. View

11.

Virkler K, Lednev I . Analysis of body fluids for forensic purposes: from laboratory testing to non-destructive rapid confirmatory identification at a crime scene. Forensic Sci Int. 2009; 188(1-3):1-17. DOI: 10.1016/j.forsciint.2009.02.013. View

12.

Albani P, Fleming R . Developmental validation of an enhanced mRNA-based multiplex system for body fluid and cell type identification. Sci Justice. 2019; 59(3):217-227. DOI: 10.1016/j.scijus.2019.01.001. View

13.

Dorum G, Bleka O, Gill P, Haas C . Source level interpretation of mixed biological stains using coding region SNPs. Forensic Sci Int Genet. 2022; 59:102685. DOI: 10.1016/j.fsigen.2022.102685. View

14.

Ingold S, Dorum G, Hanson E, Berti A, Branicki W, Brito P . Body fluid identification using a targeted mRNA massively parallel sequencing approach - results of a EUROFORGEN/EDNAP collaborative exercise. Forensic Sci Int Genet. 2018; 34:105-115. DOI: 10.1016/j.fsigen.2018.01.002. View

15.

Fleming R, Harbison S . The use of bacteria for the identification of vaginal secretions. Forensic Sci Int Genet. 2010; 4(5):311-5. DOI: 10.1016/j.fsigen.2009.11.008. View

16.

Sidstedt M, Steffen C, Kiesler K, Vallone P, Radstrom P, Hedman J . The impact of common PCR inhibitors on forensic MPS analysis. Forensic Sci Int Genet. 2019; 40:182-191. DOI: 10.1016/j.fsigen.2019.03.001. View

17.

Juusola J, Ballantyne J . Multiplex mRNA profiling for the identification of body fluids. Forensic Sci Int. 2005; 152(1):1-12. DOI: 10.1016/j.forsciint.2005.02.020. View

18.

Hanson E, Ingold S, Haas C, Ballantyne J . Messenger RNA biomarker signatures for forensic body fluid identification revealed by targeted RNA sequencing. Forensic Sci Int Genet. 2018; 34:206-221. DOI: 10.1016/j.fsigen.2018.02.020. View

19.

van den Berge M, Bhoelai B, Harteveld J, Matai A, Sijen T . Advancing forensic RNA typing: On non-target secretions, a nasal mucosa marker, a differential co-extraction protocol and the sensitivity of DNA and RNA profiling. Forensic Sci Int Genet. 2015; 20:119-129. DOI: 10.1016/j.fsigen.2015.10.011. View

20.

Zhang X, Li J, Liu J, Wang J, Liu Z, Liu Y . Identification of the vaginal secretion donor in mixture stains using polymorphic cSNPs on mRNA biomarkers. Forensic Sci Int Genet. 2022; 59:102703. DOI: 10.1016/j.fsigen.2022.102703. View