Forensic validation of the SNPforID 52-plex assay

Esther Musgrave-Brown; David Ballard; Kinga Balogh; Klaus Bender; Burkhard Berger; Magdalena Bogus; Claus Børsting; María Brion; Manuel Fondevila; Cheryl Harrison; Ceylan Oguzturun; Walther Parson; Chris Phillips; Carsten Proff; Eva Ramos-Luis; Juan Jose Sanchez Sanchez; Paula Sánchez Diz; Bea Sobrino Rey; Beate Stradmann-Bellinghausen; Catherine Thacker; Angel Carracedo; Niels Morling; Richard Scheithauer; Peter M Schneider; Denise Syndercombe-Court

doi:10.1016/j.fsigen.2007.01.004

Forensic validation of the SNPforID 52-plex assay

Esther Musgrave-Brown, David Ballard, Kinga Balogh, Klaus Bender, Burkhard Berger, Magdalena Bogus, Claus Børsting, María Brion, Manuel Fondevila, Cheryl Harrison, Ceylan Oguzturun, Walther Parson, Chris Phillips, Carsten Proff, Eva Ramos-Luis, Juan Jose Sanchez Sanchez, Paula Sánchez Diz, Bea Sobrino Rey, Beate Stradmann-Bellinghausen, Catherine ThackerAngel Carracedo, Niels Morling, Richard Scheithauer, Peter M Schneider, Denise Syndercombe-Court

Section of Forensic Genetics

70 Citations (Scopus)

Abstract

The advantages of single nucleotide polymorphism (SNP) typing in forensic genetics are well known and include a wider choice of high-throughput typing platforms, lower mutation rates, and improved analysis of degraded samples. However, if SNPs are to become a realistic supplement to current short tandem repeat (STR) typing methods, they must be shown to successfully and reliably analyse the challenging samples commonly encountered in casework situations. The European SNPforID consortium, supported by the EU GROWTH programme, has developed a multiplex of 52 SNPs for forensic analysis, with the amplification of all 52 loci in a single reaction followed by two single base extension (SBE) reactions which are detected with capillary electrophoresis. In order to validate this assay, a variety of DNA extracts were chosen to represent problems such as low copy number and degradation that are commonly seen in forensic casework. A total of 40 extracts were used in the study, each of which was sent to two of the five participating laboratories for typing in duplicate or triplicate. Laboratories were instructed to carry out their analyses as if they were dealing with normal casework samples. Results were reported back to the coordinating laboratory and compared with those obtained from traditional STR typing of the same extracts using Powerplex 16 (Promega). These results indicate that, although the ability to successfully type good quality, low copy number extracts is lower, the 52-plex SNP assay performed better than STR typing on degraded samples, and also on samples that were both degraded and of limited quantity, suggesting that SNP analysis can provide advantages over STR analysis in forensically relevant circumstances. However, there were also additional problems arising from contamination and primer quality issues and these are discussed.

Original language	English
Journal	Forensic science international. Genetics
Volume	1
Issue number	2
Pages (from-to)	186-90
Number of pages	4
DOIs	https://doi.org/10.1016/j.fsigen.2007.01.004
Publication status	Published - 2007

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10.1016/j.fsigen.2007.01.004

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Musgrave-Brown, E., Ballard, D., Balogh, K., Bender, K., Berger, B., Bogus, M., Børsting, C., Brion, M., Fondevila, M., Harrison, C., Oguzturun, C., Parson, W., Phillips, C., Proff, C., Ramos-Luis, E., Sanchez Sanchez, J. J., Sánchez Diz, P., Sobrino Rey, B., Stradmann-Bellinghausen, B., ... Syndercombe-Court, D. (2007). Forensic validation of the SNPforID 52-plex assay. Forensic science international. Genetics, 1(2), 186-90. https://doi.org/10.1016/j.fsigen.2007.01.004

Musgrave-Brown, E, Ballard, D, Balogh, K, Bender, K, Berger, B, Bogus, M, Børsting, C, Brion, M, Fondevila, M, Harrison, C, Oguzturun, C, Parson, W, Phillips, C, Proff, C, Ramos-Luis, E, Sanchez Sanchez, JJ, Sánchez Diz, P, Sobrino Rey, B, Stradmann-Bellinghausen, B, Thacker, C, Carracedo, A, Morling, N, Scheithauer, R, Schneider, PM & Syndercombe-Court, D 2007, 'Forensic validation of the SNPforID 52-plex assay', Forensic science international. Genetics, vol. 1, no. 2, pp. 186-90. https://doi.org/10.1016/j.fsigen.2007.01.004

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title = "Forensic validation of the SNPforID 52-plex assay",

abstract = "The advantages of single nucleotide polymorphism (SNP) typing in forensic genetics are well known and include a wider choice of high-throughput typing platforms, lower mutation rates, and improved analysis of degraded samples. However, if SNPs are to become a realistic supplement to current short tandem repeat (STR) typing methods, they must be shown to successfully and reliably analyse the challenging samples commonly encountered in casework situations. The European SNPforID consortium, supported by the EU GROWTH programme, has developed a multiplex of 52 SNPs for forensic analysis, with the amplification of all 52 loci in a single reaction followed by two single base extension (SBE) reactions which are detected with capillary electrophoresis. In order to validate this assay, a variety of DNA extracts were chosen to represent problems such as low copy number and degradation that are commonly seen in forensic casework. A total of 40 extracts were used in the study, each of which was sent to two of the five participating laboratories for typing in duplicate or triplicate. Laboratories were instructed to carry out their analyses as if they were dealing with normal casework samples. Results were reported back to the coordinating laboratory and compared with those obtained from traditional STR typing of the same extracts using Powerplex 16 (Promega). These results indicate that, although the ability to successfully type good quality, low copy number extracts is lower, the 52-plex SNP assay performed better than STR typing on degraded samples, and also on samples that were both degraded and of limited quantity, suggesting that SNP analysis can provide advantages over STR analysis in forensically relevant circumstances. However, there were also additional problems arising from contamination and primer quality issues and these are discussed.",

author = "Esther Musgrave-Brown and David Ballard and Kinga Balogh and Klaus Bender and Burkhard Berger and Magdalena Bogus and Claus B{\o}rsting and Mar{\'i}a Brion and Manuel Fondevila and Cheryl Harrison and Ceylan Oguzturun and Walther Parson and Chris Phillips and Carsten Proff and Eva Ramos-Luis and {Sanchez Sanchez}, {Juan Jose} and {S{\'a}nchez Diz}, Paula and {Sobrino Rey}, Bea and Beate Stradmann-Bellinghausen and Catherine Thacker and Angel Carracedo and Niels Morling and Richard Scheithauer and Schneider, {Peter M} and Denise Syndercombe-Court",

note = "Keywords: Alleles; Analysis of Variance; Cooperative Behavior; DNA; DNA Fingerprinting; Europe; Forensic Genetics; Genotype; Humans; Laboratories; Microsatellite Repeats; Polymorphism, Single Nucleotide; Sensitivity and Specificity",

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doi = "10.1016/j.fsigen.2007.01.004",

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T1 - Forensic validation of the SNPforID 52-plex assay

AU - Musgrave-Brown, Esther

AU - Ballard, David

AU - Balogh, Kinga

AU - Bender, Klaus

AU - Berger, Burkhard

AU - Bogus, Magdalena

AU - Børsting, Claus

AU - Brion, María

AU - Fondevila, Manuel

AU - Harrison, Cheryl

AU - Oguzturun, Ceylan

AU - Parson, Walther

AU - Phillips, Chris

AU - Proff, Carsten

AU - Ramos-Luis, Eva

AU - Sanchez Sanchez, Juan Jose

AU - Sánchez Diz, Paula

AU - Sobrino Rey, Bea

AU - Stradmann-Bellinghausen, Beate

AU - Thacker, Catherine

AU - Carracedo, Angel

AU - Morling, Niels

AU - Scheithauer, Richard

AU - Schneider, Peter M

AU - Syndercombe-Court, Denise

N1 - Keywords: Alleles; Analysis of Variance; Cooperative Behavior; DNA; DNA Fingerprinting; Europe; Forensic Genetics; Genotype; Humans; Laboratories; Microsatellite Repeats; Polymorphism, Single Nucleotide; Sensitivity and Specificity

PY - 2007

Y1 - 2007

N2 - The advantages of single nucleotide polymorphism (SNP) typing in forensic genetics are well known and include a wider choice of high-throughput typing platforms, lower mutation rates, and improved analysis of degraded samples. However, if SNPs are to become a realistic supplement to current short tandem repeat (STR) typing methods, they must be shown to successfully and reliably analyse the challenging samples commonly encountered in casework situations. The European SNPforID consortium, supported by the EU GROWTH programme, has developed a multiplex of 52 SNPs for forensic analysis, with the amplification of all 52 loci in a single reaction followed by two single base extension (SBE) reactions which are detected with capillary electrophoresis. In order to validate this assay, a variety of DNA extracts were chosen to represent problems such as low copy number and degradation that are commonly seen in forensic casework. A total of 40 extracts were used in the study, each of which was sent to two of the five participating laboratories for typing in duplicate or triplicate. Laboratories were instructed to carry out their analyses as if they were dealing with normal casework samples. Results were reported back to the coordinating laboratory and compared with those obtained from traditional STR typing of the same extracts using Powerplex 16 (Promega). These results indicate that, although the ability to successfully type good quality, low copy number extracts is lower, the 52-plex SNP assay performed better than STR typing on degraded samples, and also on samples that were both degraded and of limited quantity, suggesting that SNP analysis can provide advantages over STR analysis in forensically relevant circumstances. However, there were also additional problems arising from contamination and primer quality issues and these are discussed.

AB - The advantages of single nucleotide polymorphism (SNP) typing in forensic genetics are well known and include a wider choice of high-throughput typing platforms, lower mutation rates, and improved analysis of degraded samples. However, if SNPs are to become a realistic supplement to current short tandem repeat (STR) typing methods, they must be shown to successfully and reliably analyse the challenging samples commonly encountered in casework situations. The European SNPforID consortium, supported by the EU GROWTH programme, has developed a multiplex of 52 SNPs for forensic analysis, with the amplification of all 52 loci in a single reaction followed by two single base extension (SBE) reactions which are detected with capillary electrophoresis. In order to validate this assay, a variety of DNA extracts were chosen to represent problems such as low copy number and degradation that are commonly seen in forensic casework. A total of 40 extracts were used in the study, each of which was sent to two of the five participating laboratories for typing in duplicate or triplicate. Laboratories were instructed to carry out their analyses as if they were dealing with normal casework samples. Results were reported back to the coordinating laboratory and compared with those obtained from traditional STR typing of the same extracts using Powerplex 16 (Promega). These results indicate that, although the ability to successfully type good quality, low copy number extracts is lower, the 52-plex SNP assay performed better than STR typing on degraded samples, and also on samples that were both degraded and of limited quantity, suggesting that SNP analysis can provide advantages over STR analysis in forensically relevant circumstances. However, there were also additional problems arising from contamination and primer quality issues and these are discussed.

U2 - 10.1016/j.fsigen.2007.01.004

DO - 10.1016/j.fsigen.2007.01.004

M3 - Journal article

C2 - 19083753

SN - 1872-4973

VL - 1

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EP - 190

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

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ER -