SNPs and MALDI-TOF MS: tools for DNA typing in forensic paternity testing and anthropology

DNA markers used for individual identification in forensic sciences are based on repeat sequences in nuclear DNA and the mitochondrial DNA hypervariable regions 1 and 2. An alternative to these markers is the use of single nucleotide polymorphisms (SNPs). These have a particular advantage in the analysis of degraded or poor samples, which are often all that is available in forensics or anthropology. In order to study the potential of SNP analysis in these fields, 41 SNPs were selected on the basis of following criteria: conservation, lack of phenotypic expression, and frequency of occurrence in populations. Thirty-six autosomal SNPs were used for genotyping 21 inclusionary and 3 exclusionary paternity cases. The behavior of 5 X-chromosome SNPs was analyzed in a French representative population. Our approach to SNP typing is a multiplex PCR based amplification followed by simultaneous detection by primer extension (PEX) analyzed by Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). The selected autosomal SNPs showed independent inheritance and gave clear results in paternity investigation. All X-SNPs were useful as both paternity and identification markers. PEX and MALDI-TOF MS, with their high sensitivity, precision and speed, gave a powerful method for forensic and anthropological exploitation of biallelic markers.     

A fatality involving metaxalone

A case is presented of a 54-year-old white female found dead in a secured apartment. Postmortem toxicologic analysis of the heart blood identified acetaminophen (97 mg/L), citalopram (0.4 mg/L), gabapentin (24 mg/L) and metaxalone (21 mg/L). The metaxalone concentration is within the range of previously reported fatalities involving metaxalone. The medical examiner ruled that the cause of death was metaxalone and gabapentin intoxication and the manner of death was suicide.     

Human Y-specific STR haplotypes in the Western Croatian population sample

Nine Y-chromosome STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385 and YCAII) were analysed in a sample of 101 unrelated males from Croatia. Allelic frequencies and gene diversities for each Y-STR locus and haplotype diversity were determined. Ninety-one different haplotypes were obtained from 101 unrelated males and 84 haplotypes were unique. Three most common haplotypes were shared by 3% of the sample, one of them was not found in the online Y-STR Haplotype Reference Database (http://www.ystr.org/).     

STR-genotyping from human medieval tooth and bone samples

We extracted the DNA contained in samples of bones and teeth from 10 skeletons excavated from the Gravette site (400-1000 AD, south of France). Ancient DNA was analysed by autosomal short tandem repeats (STRs). The DNA present in these ancient remains appeared very degraded, but nevertheless, better conserved in tooth than in bone samples. Moreover, we showed that the DNA extracted from ancient dental pulp was not exempt from polymerase chain reaction (PCR) inhibitors, which could result from extreme DNA fragmentation. An adapted protocol with a supplementary step of purification removed this inhibition.     

Raman spectroscopy and the forensic analysis of black/grey and blue cotton fibres Part 1: investigation of the effects of varying laser wavelength

Raman spectroscopy was investigated to determine the optimal conditions, mainly laser wavelength/s, for the analysis of the commonly encountered black/grey and blue cotton fibres dyed with reactive dyes. In this first part, a single blue cotton fibre, its three dye components, and an undyed cotton fibre were analysed with five different laser wavelengths from two different Raman microprobe spectrometers. The quality of the spectra, fibre degradation and speed of acquisition were used to determine that, under the conditions used, the 785 and 830 nm lasers gave superior results. The 632.8 nm laser wavelengths provided good results with little acquisition time and no spectral degradation. Results indicate that, at least, the major dye component could be identified using Raman spectroscopy.     

Genetic data for the 13 CODIS STR loci in Singapore Chinese

Allele frequencies for the 13 CODIS STR loci included in the AmpFISTR Profiler Plus and AmpFISTR Cofiler kits (Applied Biosystems, Foster City, USA) were determined in a sample of 209 unrelated Chinese in Singapore. The combined random match probability for the 13 loci is about 6.6 x10(-15) and the overall probability of excluding paternity is 0.9999899. The results demonstrate that the loci are useful for forensic human identification and parentage testing for the Chinese population in Singapore.