Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise

Ingold, Sabrina; Dørum, Guro; Hanson, Erin; Ballard, David J.; Berti, Andrea; Gettings, Katherine B.; Giangasparo, Federica; Kampmann, Marie-Louise; Laurent, François-Xavier; Morling, Niels; Parson, Walther; Steffen, Carolyn R.; Ulus, A.; Berge, M. van den; Gaag, Kristiaan J. van der; Verdoliva, Vincenzo; Xavier, Catarina; Ballantyne, Jack; Haas, Cordula

doi:10.1016/j.fsigen.2019.102208

Cited by 30 publications

(9 citation statements)

References 26 publications

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“…Although all 158 samples were collected from skin or from fabric that was in close contact with skin, only 7% (11) of the samples gave a positive result for skin. This low rate was in accordance with the findings of previous studies [ 12 , 20 ] which showed that low RNA yields were often recovered from skin samples.…”

Section: Discussionsupporting

confidence: 93%

“…The advantage of MPS is that, in addition to detecting mRNA markers, the nucleotide sequence of the RNA transcript is also achieved. The detection of coding region SNPs (cSNPs) within the mRNA transcript has been introduced as a promising approach to associate a body fluid with a donor [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 ]. Comparison of cSNP genotypes within a body fluid-specific transcript to the corresponding genomic cSNP genotypes in reference samples from donors, may be used to associate a donor with a given body fluid.…”

Section: Introductionmentioning

confidence: 99%

“…Comparison of cSNP genotypes within a body fluid-specific transcript to the corresponding genomic cSNP genotypes in reference samples from donors, may be used to associate a donor with a given body fluid. However, previous studies have suggested that more markers for some body fluids, including vaginal mucosa, are needed to improve the discriminatory power of cSNPs [ 12 , 17 ]. In a recent study by Hanson et al [ 20 ], a dual-functional mRNA sequencing panel (“BFID-cSNP-6F assay”) was demonstrated, including 23 mRNA biomarkers covering six body fluids/cell types (blood, semen, saliva, vaginal mucosa, menstrual blood and skin) and 46 cSNPs.…”

Section: Introductionmentioning

confidence: 99%

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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

Johannessen

Hanson

Gill

et al. 2023

Genes

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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.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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

Johannessen

Hanson

Gill

et al. 2023

Genes

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“…For cSNPs in the same amplimer, phased haplotypes can also be retrieved, which means they can be regarded as a microhaplotype. In addition, this cSNP panel was tested in a collaborative exercise within the EUROFORGEN and EDNAP laboratories [80]. Recently, an MPS assay on the Ion S5 system comprising a set of 21 cSNPs in body fluid specific mRNA transcripts (7 blood, 8 semen, 6 saliva) was reported [50] Information on the age of a trace, or more precisely, the time since deposition (TsD) is crucial for evaluating the relevance of evidence in the investigative process.…”

Section: Assigning Body Fluids To Donors In Mixed Body Fluid Stainsmentioning

confidence: 99%

Forensic transcriptome analysis using massively parallel sequencing

Haas

Neubauer

Salzmann

et al. 2021

Forensic Science International: Genetics

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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“…PCR is widely used to amplify molecular markers, such as short tandem repeat (STR), single nucleotide polymorphism (SNP), insertion-deletion (InDel) and other molecular markers from forensic samples to solve problems, such as paternity testing, individual identification ( Hammond et al, 1994 ), ancestry inference ( Guo et al, 2020 ), age estimation ( Marquez-Ruiz et al, 2020 ), body fluids identification ( Ingold et al, 2020 ), phenotypic inference ( Chaitanya et al, 2018 ), complicated kinship inference ( Kling and Tillmar, 2019 ), and post-mortem interval estimation ( Tu et al, 2018 ). Traditional PCR reagents are in liquid form and stored at −20°C.…”

Section: Introductionmentioning

confidence: 99%

Validation of a 6-Dye Short Tandem Repeat System: A Dry Kit With Lyophilized Amplification Reagent

Lin

Honglei³

et al. 2021

Front. Genet.

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The SureID®S6 system used a lyophilized pellet as the amplification reagent to enable multiplexing of sex-determining marker Amelogenin, 21 autosomal short tandem repeats (STRs), and one Y-STR. To assess the performance, reliability, and limitation of the dry amplification system, the validation studies including PCR condition, reproducibility, sizing and precision, analytical threshold calculation, sensitivity and stochastic threshold calculation, species specificity, stability, mixture, case sample, and population and concordance were conducted according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) Validation Guidelines. Experimental data suggested that the optimal range of total input DNA was from 125 to 500 pg; the appropriate analytical threshold was 80 relative fluorescence units (RFUs) while the stochastic threshold was 260 RFUs; for the stability studies, SureID®S6 system could resist against less than 500 μmol/L of hematin, 100 ng/μl of humic acid, 4 mM of indigotin, 800 mM of tannic acid, and 800 mM of calcium ion. Population and concordance studies using 500 unrelated individuals showed that the combined probability of discrimination (CPD) and cumulative probability of exclusion (CPE) values were 0.999999999999 and 0.999999998416, respectively. The genotypes for the same sample were concordant with the previously validated HUAXIA™ Platinum kit. The validation results demonstrated that the SureID®S6 system could be used for forensic applifications.

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Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise

Cited by 30 publications

References 26 publications

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

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

Forensic transcriptome analysis using massively parallel sequencing

Validation of a 6-Dye Short Tandem Repeat System: A Dry Kit With Lyophilized Amplification Reagent

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