STR data for the AmpFlSTR Profiler Plus loci from Greece

Allele frequencies for the nine STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) were estimated from a sample of 143 unrelated individuals living in different regions of Greece.     

Population genetics of the D1S1656, D12S391, and D18S535 loci in Asturias (North Spain)

Allele and genotype frequencies for three recently described short tandem repeat loci D1S1656, D12S391, and D18S535 were determined in a population sample from Asturias (North Spain). The loci were amplified using a fluorescence based PCR method and were typed automatically. No deviation from Hardy-Weinberg expectations were observed. The three loci proved to be highly discriminating and the allele frequencies observed are similar to those of the other European populations that have been typed for these loci to date.     

Alternative primers for DYS391 typing: advantages of their application to forensic genetics

The amplification of the STR DYS391, using the primers described in the Genome Data Base (GDB: G00-365-251), shows not only an additional band to the Y-specific one in males with a size range of 26 bp less than those of DYS391 locus alleles, but also a polymorphic pattern in females in the same size range as the additional band observed in males. The DYS391 pattern in families reflects a Y-specific linked locus and also a polymorphic X locus with an X-linked pattern of inheritance. A first screening in the X homologous locus allowed the identification of five different alleles. Allele frequencies were explored in different population groups for both the Y locus and the homologous locus in the X chromosome showing a similar allele distribution pattern in the X and Y homologous loci. An alternative reverse primer was designed to amplify the Y-chromosome specific STR in order to improve the specificity and applicability of this system to forensic genetics. Comparative results of the amplification with the new and the previously described primers proved that with this new primer there is a substantial increase in the specificity of the amplification. Moreover, a smaller fragment is amplified with a size out of the range of the alleles of the other Y-STRs usually used in forensic applications, therefore simplifying its inclusion in multiplex systems.     

Nine autosomal STRs genotype profiles in a sample from Córdoba (Argentina)

Nine STRs loci have been typed in a sample from Córdoba (Argentina).     

Y-chromosome STR haplotypes in Córdoba (Argentina)

Eight Y-chromosome STRs were investigated in a male population sample from Córdoba region (Argentina). Complete Y-chromosomal STRs haplotypes were obtained in 100 individuals, among which 91 different haplotypes were observed. The most common haplotype was shared by 4% of the sample, while 86 haplotypes were unique. The gene diversity was 0.9875 and the discrimination capacity was 0.8600. The combined polymorphism provides a powerful discrimination tool for routine forensic applications.     

The use of the LightCycler for the detection of Y chromosome SNPs

A novel methodology based on PCR monitoring on-line with fluorescent formats using the LightCycler for Y chromosome SNP typing is proposed. The main advantages of the system are the time necessary for the analysis (which is around 20 min), the robustness and the accuracy of the method and especially its sensitivity, which permits the detection of the male component in male-female mixtures up to 1:300 for some of the SNPs.Singleplexes of four different SNPs (M9, sY81, SRY-1532 and SRY-2627) as well as two duplexes (M9 and sY81 on the one hand and SRY-1532 and SRY-2627 on the other) were efficiently implemented. A simultaneous amplification and analysis of the four SNPs is also possible. It seems difficult with the current methodology to implement more than a quadruplex.     

Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs

Tests that infer the ancestral origin of a DNA sample have considerable potential in the development of forensic tools that can help to guide crime investigation. We have developed a single-tube 34-plex SNP assay for the assignment of ancestral origin by choosing ancestry-informative markers (AIMs) exhibiting highly contrasting allele frequency distributions between the three major population-groups. To predict ancestral origin from the profiles obtained, a classification algorithm was developed based on maximum likelihood. Sampling of two populations each from African, European and East Asian groups provided training sets for the algorithm and this was tested using the CEPH Human Genome Diversity Panel. We detected negligible theoretical and practical error for assignments to one of the three groups analyzed with consistently high classification probabilities, even when using reduced subsets of SNPs. This study shows that by choosing SNPs exhibiting marked allele frequency differences between population-groups a practical forensic test for assigning the most likely ancestry can be achieved from a single multiplexed assay.     

Chimpanzee homologous of human Y specific STRs. A comparative study and a proposal for nomenclature

Eleven Y specific microsatellites, previously studied in humans, were typed for fragment length and sequenced in chimpanzees (Pan troglodytes).The primers described by Ayub et al. (Nucleic Acids Res. 28, 2000, 2) for amplifying DYS434, DYS435, DYS436, DYS437, DYS438, DYS439 and those described by White et al. (Genomics, 57, 1999, 433) for GATA A10, A7.1, A7.2, C4, and H4, were used to amplify DNA samples from chimpanzees.Primers described for Y GATA A4 were found to amplify the same region as reported for DYS439. Moreover, the GATA A4 forward primer only matches the repeat flanking region in 14 of the 28bp, being responsible for a very weak amplification. Therefore, this system was not included in this study.The analysis of the repeat and sequence structure observed in chimpanzee and human Y chromosomes allowed evolutionary comparisons as well as the basis for improving Y STR nomenclature and therefore, a unified nomenclature for these novel STRs is proposed to the scientific community following ISFG recommendations.     

Case report: Identification of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur

Applying two extraction protocols to isolate DNA from a charred femur recovered after a major forest fire, a range of established and recently developed forensic marker sets that included mini-STRs and SNPs were used to type the sample and confirm identity by comparison to a claimed daughter of the deceased. Identification of the remains suggested that the individual had been dead for 10 years and the DNA was therefore likely to be severely degraded from the combined effects of decomposition and exposure to very high temperatures. We used new marker sets specifically developed to analyze degraded DNA comprising both reduced-length amplicon STR sets and autosomal SNP multiplexes, giving an opportunity to assess the ability of each approach to successfully type highly degraded material from a challenging case. The results also suggest a modified ancient DNA extraction procedure offers improved typing success from degraded skeletal material.     

Challenging DNA: Assessment of a range of genotyping approaches for highly degraded forensic samples

It is common in forensic casework to encounter highly degraded DNA samples from a variety of sources. In this category bone and teeth samples are often the principal source of evidential material for criminal investigations or identification of long-deceased individuals. In these circumstances standard STRs are prone to fail due to their long amplicon sizes (since DNA becomes progressively more fragmented as it degrades). To successfully resolve such cases alternative markers can be used and until recently the only other tool available was mitochondrial DNA, which despite being more resistant to degradation, is much less informative. A rapidly developing approach to analyzing degraded DNA is the typing of loci from short-amplicon PCR products based on markers such as mini-STRs and autosomal SNPs. We have performed an analysis of several cases with naturally degraded DNA using established STRs plus mini-STRs and autosomal SNPs in order to make an objective comparison of the performance of each method using challenging DNA. The main aim was to establish the benefits and drawbacks of each marker set to help the practitioner choose the DNA analysis method most suited to the circumstances of each case.