Forensic validation of the SNPforID 52-plex assay.
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.
Musgrave-Brown
Esther
E
Centre for Haematology, ICMS, Barts & the London, Queen Mary's School of Medicine & Dentistry, London, United Kingdom. e.musgrave-brown@qmul.ac.uk
Ballard
David
D
Balogh
Kinga
K
Bender
Klaus
K
Berger
Burkhard
B
Bogus
Magdalena
M
Børsting
Claus
C
Brion
María
M
Fondevila
Manuel
M
Harrison
Cheryl
C
Oguzturun
Ceylan
C
Parson
Walther
W
Phillips
Chris
C
Proff
Carsten
C
Ramos-Luis
Eva
E
Sanchez
Juan J
JJ
Sánchez Diz
Paula
P
Sobrino Rey
Bea
B
Stradmann-Bellinghausen
Beate
B
Thacker
Catherine
C
Carracedo
Angel
A
Morling
Niels
N
Scheithauer
Richard
R
Schneider
Peter M
PM
Syndercombe Court
Denise
D
D000483:Alleles; D000704:Analysis of Variance; D003299:Cooperative Behavior; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D016172:DNA Fingerprinting / Q000379:methods / Q000592:standards / Q000706:statistics & numerical data; D005060:Europe; D053803:Forensic Genetics / Q000379:methods* / Q000592:standards / Q000706:statistics & numerical data; D005838:Genotype; D006801:Humans; D007753:Laboratories; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity
D004247:DNA