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

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Standard

Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise. / Ingold, S.; Dørum, G.; Hanson, E.; Ballard, D.; Berti, A.; Gettings, K. B.; Giangasparo, F.; Kampmann, M. L.; Laurent, F. X.; Morling, N.; Parson, W.; Steffen, C. R.; Ulus, A.; van den Berge, M.; van der Gaag, K. J.; Verdoliva, V.; Xavier, C.; Ballantyne, J.; Haas, C.

In: Forensic Science International: Genetics, Vol. 45, 102208, 03.2020, p. 1-11.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Ingold, S, Dørum, G, Hanson, E, Ballard, D, Berti, A, Gettings, KB, Giangasparo, F, Kampmann, ML, Laurent, FX, Morling, N, Parson, W, Steffen, CR, Ulus, A, van den Berge, M, van der Gaag, KJ, Verdoliva, V, Xavier, C, Ballantyne, J & Haas, C 2020, 'Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise', Forensic Science International: Genetics, vol. 45, 102208, pp. 1-11. https://doi.org/10.1016/j.fsigen.2019.102208

APA

Ingold, S., Dørum, G., Hanson, E., Ballard, D., Berti, A., Gettings, K. B., Giangasparo, F., Kampmann, M. L., Laurent, F. X., Morling, N., Parson, W., Steffen, C. R., Ulus, A., van den Berge, M., van der Gaag, K. J., Verdoliva, V., Xavier, C., Ballantyne, J., & Haas, C. (2020). Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise. Forensic Science International: Genetics, 45, 1-11. [102208]. https://doi.org/10.1016/j.fsigen.2019.102208

Vancouver

Ingold S, Dørum G, Hanson E, Ballard D, Berti A, Gettings KB et al. Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise. Forensic Science International: Genetics. 2020 Mar;45:1-11. 102208. https://doi.org/10.1016/j.fsigen.2019.102208

Author

Ingold, S. ; Dørum, G. ; Hanson, E. ; Ballard, D. ; Berti, A. ; Gettings, K. B. ; Giangasparo, F. ; Kampmann, M. L. ; Laurent, F. X. ; Morling, N. ; Parson, W. ; Steffen, C. R. ; Ulus, A. ; van den Berge, M. ; van der Gaag, K. J. ; Verdoliva, V. ; Xavier, C. ; Ballantyne, J. ; Haas, C. / Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise. In: Forensic Science International: Genetics. 2020 ; Vol. 45. pp. 1-11.

Bibtex

@article{72d0416731af4709a1220ace38bc6829,
title = "Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise",
abstract = "In a previous EUROFORGEN/EDNAP collaborative exercise, we tested two assays for targeted mRNA massively parallel sequencing for the identification of body fluids/tissues, optimized for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms, respectively. The task of the second EUROFORGEN/EDNAP collaborative exercise was to analyze dried body fluid stains with two different multiplexes, the former Illumina 33plex mRNA panel for body fluid/tissue identification and a 35plex cSNP panel for assignment of body fluids/tissues to donors that was introduced in a proof-of-concept study recently. The coding region SNPs (cSNPs) are located within the body fluid specific mRNA transcripts and represent a direct link between the body fluid and the donor. We predicted the origin of the stains using a partial least squares discriminant analysis (PLS-DA) model, where most of the single source samples were correctly predicted. The mixed body fluid stains showed poorer results, however, at least one component was predicted correctly in most stains. The cSNP data demonstrated that coding region SNPs can give valuable information on linking body fluids/tissues with donors in mixed body fluid stains. However, due to the unfavorable performance of some cSNPs, the interpretation remains challenging. As a consequence, additional markers are needed to increase the discrimination power in each body fluid/tissue category.",
keywords = "body fluid identification, coding region SNPs (cSNPs), Forensic science, linear discriminant analysis (LDA), massively parallel sequencing (MPS), mRNA profiling, partial least squares (PLS)",
author = "S. Ingold and G. D{\o}rum and E. Hanson and D. Ballard and A. Berti and Gettings, {K. B.} and F. Giangasparo and Kampmann, {M. L.} and Laurent, {F. X.} and N. Morling and W. Parson and Steffen, {C. R.} and A. Ulus and {van den Berge}, M. and {van der Gaag}, {K. J.} and V. Verdoliva and C. Xavier and J. Ballantyne and C. Haas",
year = "2020",
month = mar,
doi = "10.1016/j.fsigen.2019.102208",
language = "English",
volume = "45",
pages = "1--11",
journal = "Forensic Science International: Genetics",
issn = "1872-4973",
publisher = "Elsevier",

}

RIS

TY - JOUR

T1 - Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise

AU - Ingold, S.

AU - Dørum, G.

AU - Hanson, E.

AU - Ballard, D.

AU - Berti, A.

AU - Gettings, K. B.

AU - Giangasparo, F.

AU - Kampmann, M. L.

AU - Laurent, F. X.

AU - Morling, N.

AU - Parson, W.

AU - Steffen, C. R.

AU - Ulus, A.

AU - van den Berge, M.

AU - van der Gaag, K. J.

AU - Verdoliva, V.

AU - Xavier, C.

AU - Ballantyne, J.

AU - Haas, C.

PY - 2020/3

Y1 - 2020/3

N2 - In a previous EUROFORGEN/EDNAP collaborative exercise, we tested two assays for targeted mRNA massively parallel sequencing for the identification of body fluids/tissues, optimized for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms, respectively. The task of the second EUROFORGEN/EDNAP collaborative exercise was to analyze dried body fluid stains with two different multiplexes, the former Illumina 33plex mRNA panel for body fluid/tissue identification and a 35plex cSNP panel for assignment of body fluids/tissues to donors that was introduced in a proof-of-concept study recently. The coding region SNPs (cSNPs) are located within the body fluid specific mRNA transcripts and represent a direct link between the body fluid and the donor. We predicted the origin of the stains using a partial least squares discriminant analysis (PLS-DA) model, where most of the single source samples were correctly predicted. The mixed body fluid stains showed poorer results, however, at least one component was predicted correctly in most stains. The cSNP data demonstrated that coding region SNPs can give valuable information on linking body fluids/tissues with donors in mixed body fluid stains. However, due to the unfavorable performance of some cSNPs, the interpretation remains challenging. As a consequence, additional markers are needed to increase the discrimination power in each body fluid/tissue category.

AB - In a previous EUROFORGEN/EDNAP collaborative exercise, we tested two assays for targeted mRNA massively parallel sequencing for the identification of body fluids/tissues, optimized for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms, respectively. The task of the second EUROFORGEN/EDNAP collaborative exercise was to analyze dried body fluid stains with two different multiplexes, the former Illumina 33plex mRNA panel for body fluid/tissue identification and a 35plex cSNP panel for assignment of body fluids/tissues to donors that was introduced in a proof-of-concept study recently. The coding region SNPs (cSNPs) are located within the body fluid specific mRNA transcripts and represent a direct link between the body fluid and the donor. We predicted the origin of the stains using a partial least squares discriminant analysis (PLS-DA) model, where most of the single source samples were correctly predicted. The mixed body fluid stains showed poorer results, however, at least one component was predicted correctly in most stains. The cSNP data demonstrated that coding region SNPs can give valuable information on linking body fluids/tissues with donors in mixed body fluid stains. However, due to the unfavorable performance of some cSNPs, the interpretation remains challenging. As a consequence, additional markers are needed to increase the discrimination power in each body fluid/tissue category.

KW - body fluid identification

KW - coding region SNPs (cSNPs)

KW - Forensic science

KW - linear discriminant analysis (LDA)

KW - massively parallel sequencing (MPS)

KW - mRNA profiling

KW - partial least squares (PLS)

U2 - 10.1016/j.fsigen.2019.102208

DO - 10.1016/j.fsigen.2019.102208

M3 - Journal article

C2 - 31869731

AN - SCOPUS:85076864541

VL - 45

SP - 1

EP - 11

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

SN - 1872-4973

M1 - 102208

ER -

ID: 234076852