Forensic application of Y chromosome SNPs in inconclusive cases

Biallelic markers, Single Nucleotide Polymorphisms (SNPs), are nowadays a powerful tool in the analysis of degraded samples. Namely, Y chromosome SNPs allow to determine the gender of the analyzed sample and to establish its haplogroup, making possible to attribute the ethnicity of male individuals. The aim of this study is to obtain Y-SNPs in forensic samples without STRs results, checking methodologies previously used.     

Successful STR and SNP typing of FTA Card samples with low amounts of DNA after DNA extraction using a Qiagen BioRobot EZ1 Workstation

FTA Cards (GE Healthcare) have been used for more than 4 years in Denmark for the collection of buccal cells as reference samples in crime cases. Semi-automated protocols for STR typing of DNA on punches of FTA Cards are routinely used. In average, full STR profiles were generated from approximately 95% of the FTA Cards with a standard punching protocol, while partial or no STR profile were obtained from 5% of the samples. Here, the Qiagen BioRobot^® EZ1 Workstation (Qiagen) and the EZ1 DNA Investigator Kit (Qiagen) was used to extract DNA from 29 FTA Cards from which a complete STR profile was not generated with the standard punching protocol. All 29 samples were successfully typed with the AmpF?STR^® Identifiler™ PCR Amplification Kit (Applied Biosystems) and with the SNPforID 49plex SNP assay. The lowest amount of DNA that resulted in complete STR and SNP profiles was 80 pg. The STR and SNP profiles were identical to those generated from another sample collected from each of the 29 individuals.     

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.     

Performance of the SNPforID 52 SNP-plex assay in paternity testing

The performance of a multiplex assay with 52 autosomal single nucleotide polymorphisms (SNPs) developed for human identification was tested on 124 mother–child–father trios. The typical paternity indices (PIs) were 10⁵–10⁶ for the trios and 10³–10⁴ for the child–father duos. Using the SNP profiles from the randomly selected trios and 700 previously typed individuals, a total of 83,096 comparisons between mother, child and an unrelated man were performed. On average, 9–10 mismatches per comparison were detected. Four mismatches were genetic inconsistencies and 5–6 mismatches were opposite homozygosities. In only two of the 83,096 comparisons did an unrelated man match perfectly to a mother–child duo, and in both cases the PI of the true father was much higher than the PI of the unrelated man. The trios were also typed for 15 short tandem repeats (STRs) and seven variable number of tandem repeats (VNTRs). The typical PIs based on 15 STRs or seven VNTRs were 5–50 times higher than the typical PIs based on 52 SNPs. Six mutations in tandem repeats were detected among the randomly selected trios. In contrast, there was not found any mutations in the SNP loci. The results showed that the 52 SNP-plex assay is a very useful alternative to currently used methods in relationship testing. The usefulness of SNP markers with low mutation rates in paternity and immigration casework is discussed.     

The genetics of eye colours in an Italian population measured with an objective method for eye colour quantification

Brown and blue eye colours are primarily explained by the single nucleotide polymorphism (SNP) HERC2 rs12913832. However, the genetics of eye colours that appear to be neither blue nor brown are not well understood. In this study, 230 unrelated Italian individuals were typed for 32 SNP loci in pigmentary genes. High resolution digital images of the participants’ eyes were taken and the iris region was successfully extracted with the use of the custom designed software Digital Iris Analysis Tool (DIAT) from 218 of the 230 (95%) images. The software counted the numbers of blue and brown pixels in the iris region and calculated a Pixel Index of the Eye (PIE-score) that described the eye colours quantitatively. The PIE-score ranged from −1 to 1 (brown to blue). We investigated the association of the PIE-scores extracted from the eye images with the genotypes of the 32 pigmentary SNPs. We observed a statistically significant association between the PIE-scores and the SNP loci rs12913832, rs4778241, rs7495174 in the HERC2/OCA2 region and the locus rs16891982 in SLC45A2.     

Anatomy of a Scottish Revolution: The Potential of Postnationalist Scotland and the Future of the United Kingdom

Scottish politics isn't about some remote northern politics but go to the heart of the nature, character and power dimensions of the UK and British state. Scotland has been dramatically changed by the scale of the SNP landslide victory in the 2011 Scottish Parliament elections. Scottish society, identity and culture along with the politics of unionism and nationalism have all changed and will change further. The old fashioned politics of devolution are dead, but what comes next and what are the consequences for Scottish independence? What has to be challenged are old‐fashioned out‐of‐date views of the SNP, and the unreconstructed nationalism of the British state.     

A New Method for Human ABO Genotyping Using a Universal Reporter Primer System

Abstract: We developed a new method for forensic ABO genotyping based on a universal reporter primer (URP) system. This allows for the simultaneous detection of six single nucleotide polymorphism (SNP) sites in the ABO gene (nucleotide positions 261, 297, 526, 703, 796, and 803). This URP system provides obvious peaks, ranging from 82 to 151 bp in length. ABO genotypes were classified and successfully genotyped by our method, including minor alleles that may cause a discrepancy between the genetic data and serological phenotypes. Full profiles were identified using as little as 0.1 ng (0.05 ng/reaction) of standard K562 and 9947A DNA. Moreover, the success rate of genotyping from a URP system was much higher than that from a conventional primer extension method in degraded DNA. This method enables simple and rapid detection of multiple SNP sites on human ABO genes and is highly specific and sensitive when using limited and degraded DNA.     

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.     

X染色体上高信息量SNP位点及其法医学价值

人类X染色体长154.8Mb,其上密布SNP位点,蕴涵着大量的信息。用于法医学鉴定的X-SNP标记多态性好、突变率低。本研究从Hapmap、NCBI的数据库中筛选了167个高信息量SNP位点,这些位点的等位基因在北京汉族人群中的分布频率均高于0.3,通过高通量、高灵敏度的检测方法可对各个X-SNP位点进行分型验证,通过正确的统计学分析可得到其法医学多态性参数。X-SNP位点具有一些常染色体遗传标记无法比拟的优点,作为常规STR基因座的补充,能用于解决特殊的亲子鉴定案,性别鉴定和混合斑鉴定。     

单核苷酸多态性及其检测方法

单核苷酸多态性（single nucleotide polymorphisms，SNPs），作为第三代遗传标记，已经广泛应用于基因作图、遗传性和遗传相关性疾病的诊断、群体遗传学、药学研究和法医学等领域。SNP的检测方法多种多样．本文简要介绍SNP的特点和几种检测方法。