Journal ArticleDOI
Forensic typing of autosomal SNPs with a 29 SNP-multiplex—Results of a collaborative EDNAP exercise
Juan J. Sanchez,Claus Børsting,Kinga Balogh,Burkhard Berger,Magdalena Bogus,John M. Butler,Angel Carracedo,D. Syndercombe Court,L.A. Dixon,B Filipović,Marcos F. Fondevila,Peter Gill,C. Harrison,Carsten Hohoff,René Huel,Bertrand Ludes,Walther Parson,Thomas J. Parsons,E. Petkovski,Christopher Phillips,H. Schmitter,Peter M. Schneider,Peter M. Vallone,Niels Morling +23 more
TLDR
The results of the collaborative exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases demonstrate that SNP typing with SBE, capillary electrophoresis and multicolour detection methods can be developed for forensic genetics.Abstract:
We report the results of an inter-laboratory exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases. The European DNA Profiling Group (EDNAP), a working group under the International Society for Forensic Genetics (ISFG), organised the exercise. A total of 11 European and one US forensic genetic laboratories tested a subset of a 52 SNP-multiplex PCR kit developed by the SNPforID consortium. The 52 SNP-multiplex kit amplifies 52 DNA fragments with 52 autosomal SNP loci in one multiplex PCR. The 52 SNPs are detected in two separate single base extension (SBE) multiplex reactions with 29 and 23 SNPs, respectively, using SNaPshot kit, capillary electrophoresis and multicolour fluorescence detection. For practical reasons, only the 29 SBE multiplex reaction was carried out by the participating laboratories. A total of 11 bloodstains on FTA cards including a sample of poor quality and a negative control were sent to the laboratories together with the essential reagents for the initial multiplex PCR and the multiplex SBE reaction. The total SNP locus dropout rate was 2.8% and more than 50% of the dropouts were observed with the poor quality sample. The overall rate of discrepant SNP allele assignments was 2.0%. Two laboratories reported 60% of all the discrepancies. Two laboratories reported all 29 SNP alleles in all 10 positive samples correctly. The results of the collaborative exercise were surprisingly good and demonstrate that SNP typing with SBE, capillary electrophoresis and multicolour detection methods can be developed for forensic genetics.read more
Citations
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Journal ArticleDOI
Binary probes for nucleic acid analysis.
TL;DR: The introduction of real-time detection approaches, such as molecular beacon probes, has enabled fast assays, in which the fluorescence change is detected immediately after probe hybridization, thus avoiding the need to separate the probe-analyte hybrid from the excess of the unbound probe.
Journal ArticleDOI
Performance of a next generation sequencing SNP assay on degraded DNA.
TL;DR: The performance of a next generation sequencing SNP assay and CE-based STR, mini-STR, and InDel assays was evaluated with a series of fragmented, size-selected samples, indicating the potential advantage of NGS SNP assays for forensic analysis of degraded DNA samples.
Journal ArticleDOI
Performance of the SNPforID 52 SNP-plex assay in paternity testing
Claus Børsting,Juan J. Sanchez,Hanna E. Hansen,Anders J. Hansen,Hanne Q. Bruun,Niels Morling +5 more
TL;DR: The results showed that the 52 SNP-plex assay is a very useful alternative to currently used methods in relationship testing and the usefulness of SNP markers with low mutation rates in paternity and immigration casework is discussed.
Journal ArticleDOI
Evaluation of the Ion Torrent™ HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing.
TL;DR: The Ion PGM™ is a very promising platform for forensic genetics, however, the secondary sequence analysis software made wrong genotype calls from correctly sequenced alleles and these types of errors must be corrected before the platform can be used in case work.
Reference EntryDOI
Single Nucleotide Polymorphism
TL;DR: This chapter makes a short introduction to NGS and explains how NGS may combine analysis of the traditional forensic genetic markers with analysis of SNPs to allow acquisition of more information from the sample materials and open up for new possibilities as well as new challenges.
References
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Journal ArticleDOI
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
Ravi Sachidanandam,David Weissman,Steven Schmidt,Jerzy M. Kakol,Lincoln Stein,Gabor T. Marth,Steve Sherry,James C. Mullikin,Beverley J. Mortimore,David Willey,Sarah E. Hunt,Charlotte G. Cole,Penny Coggill,Catherine M. Rice,Zemin Ning,Jane Rogers,David R. Bentley,Pui-Yan Kwok,Elaine R. Mardis,Raymond T. Yeh,Brian Schultz,Lisa Cook,Ruth Davenport,Michael Dante,Lucinda Fulton,LaDeana W. Hillier,Robert H. Waterston,John Douglas Mcpherson,Brian Gilman,Stephen F. Schaffner,William J. Van Etten,David Reich,John M. Higgins,Mark J. Daly,Brendan Blumenstiel,Jennifer Baldwin,Nicole Stange-Thomann,Michael C. Zody,Lauren Linton,Eric S. Lander,David Altshuler +40 more
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The development of reduced size STR amplicons as tools for analysis of degraded DNA.
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Journal ArticleDOI
A multiplex assay with 52 single nucleotide polymorphisms for human identification
Juan J. Sanchez,Christopher Phillips,Claus Børsting,Kinga Balogh,Magdalena Bogus,Manuel Fondevila,C. Harrison,E. Musgrave-Brown,Antonio Salas,Denise Syndercombe-Court,Peter M. Schneider,Angel Carracedo,Niels Morling +12 more
TL;DR: A highly sensitive and reproducible SNP‐typing method is established with amplification of all 52 DNA fragments in one PCR reaction followed by detection of the SNPs with two single base extension reactions analysed using CE.
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