Development and validation of the EUROFORGEN NAME (North African and Middle Eastern) ancestry panel.

Inference of biogeographic origin is an important factor in clinical, population and forensic genetics. The information provided by AIMs (Ancestry Informative Markers) can allow the differentiation of major continental population groups, and several AIM panels have been developed for this purpose. However, from these major population groups, Eurasia covers a wide area between two continents that is difficult to differentiate genetically. These populations display a gradual genetic cline from West Europe to South Asia in terms of allele frequency distribution. Although differences have been reported between Europe and South Asia, Middle East populations continue to be a target of further investigations due to the lack of genetic variability, therefore hampering their genetic differentiation from neighboring populations. In the present study, a custom-built ancestry panel was developed to analyze North African and Middle Eastern populations, designated the 'NAME' panel. The NAME panel contains 111 SNPs that have patterns of allele frequency differentiation that can distinguish individuals originating in North Africa and the Middle East when combined with a previous set of 126 Global AIM-SNPs.

Inference of biogeographical ancestry across central regions of Eurasia.

The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.

Evaluation of reliability on STR typing at leukemic patients used for forensic purposes.

Over the past decades, main advances in the field of molecular biology, coupled with benefits in genomic technologies, have led to detailed molecular investigations in the genetic diversity generated by researchers. Short tandem repeat (STR) loci are polymorphic loci found throughout all eukaryotic genome. DNA profiling identification, parental testing and kinship analysis by analysis of STR loci have been widely used in forensic sciences since 1993. Malignant tissues may sometimes be the source of biological material for forensic analysis, including identification of individuals or paternity testing. There are a number of studies on microsatellite instability in different types of tumors by comparing the STR profiles of malignant and healthy tissues on the same individuals. Defects in DNA repair pathways (non-repair or mis-repair) and metabolism lead to an accumulation of microsatellite alterations in genomic DNA of various cancer types that result genomic instabilities on forensic analyses. Common forms of genomic instability are loss of heterozygosity (LOH) and microsatellite instability (MSI). In this study, the applicability of autosomal STR markers, which are routinely used in forensic analysis, were investigated in order to detect genotypes in blood samples collected from leukemic patients to estimate the reliability of the results when malignant tissues are used as a source of forensic individual identification. Specimens were collected from 90 acute and 10 chronic leukemia volunteers with oral swabs as well as their paired peripheral blood samples from the Oncology Centre of the Department of Hematology at Istanbul University, during the years 2010-2011. Specimens were tested and compared with 16 somatic STR loci (CSFIPO, THO1, TPOX, vWA, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11 and FGA) widely used in forensic identification and kinship. Only two STR instabilities were encountered among 100 specimens. An MSI in the FGA loci and a LOH in the D2S1338 loci were determined in two individuals separately. Our results demonstrate that the use of the biological samples from leukemia patients in forensic identification and kinship testing is questionable, especially if known microsatellite instability is available. Genetic instabilities may alter the STR polymorphism, leading to potential errors on forensic identification of individuals. Therefore, typing of autosomal STRs from leukemia patients should be performed with both healthy and malignant tissue samples of individual as references.

Population genetics of 17 Y-STR markers in Turkish Cypriots from Cyprus.

We analyzed seventeen Y-chromosomal short tandem repeats (STRs) [DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y-GATA-H4, DYS437, DYS438, and DYS448] in 253 unrelated, male individuals from the Turkish Cypriot population of the Eastern Mediterranean island of Cyprus. While 206 out of the 253 haplotypes present in the dataset were unique, there are also 22 haplotypes that were observed in two individuals each, and 1 haplotype that was observed in three individuals. While no locus duplications or null alleles were observed in our dataset, we have detected 43 allelic variants in total, the majority of which (25 out of 253 haplotypes or 9.88%) comprised of .2 intermediate variants at the DYS458 locus (alleles 16.2, 17.2, 18.2, 19.2, and 20.2). For the 229 different haplotypes observed in the Turkish Cypriot dataset, the calculated discrimination capacity (DC) was 0.9051 and the haplotype diversity (HD) was 0.9992. The calculated average gene diversity (GD) values ranged from 0.3828 to 0.9631 for the DYS392 and DYS385a/b loci, respectively. Pairwise genetic distance comparisons of the Turkish Cypriot Y-STR dataset with those from the neighbouring (Turkey, Greece, Israel/Palestinian Authority area, Egypt and Italy) and relatively distant (Lithuania, Taiwan and Australia) countries through the use of analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) analyses confirmed that our data do not deviate significantly from the typical core haplotypes of the Eastern Mediterranean region. The Turkish Cypriot Y-STR haplotype dataset will find an immediate use in the Committee on Missing Persons in Cyprus Project on the "Exhumation, Identification and Return of Remains of Missing Persons" and it is also expected to contribute to the establishment of forensic genetic services in North Cyprus.

Effect of glucocorticoids on nasal polyposis, with detection of inflammatory response by measurement of nitric oxide levels in nasal polyp tissue.

OBJECTIVE: To investigate endoscopic staging, and nitric oxide levels in the polyp tissue, in patients with nasal polyposis undergoing glucocorticoid therapy. METHODS: Nasal polyposis was evaluated using endoscopic staging and measurement of polyp tissue nitric oxide levels (chemiluminescence method). Forty-five nasal polyposis patients received either nasal therapy (n = 15), oral therapy (n = 15) or combined therapy (n = 15). Pre-treatment and post-treatment staging and nitric oxide levels were evaluated. RESULTS: Endoscopic grading indicated significant post-treatment staging improvements in the oral (p = 0.016) and combined (p = 0.016) groups. Post-treatment staging differed significantly between the three groups (p = 0.041), with greater improvements in the oral and combined groups. All groups showed significantly lower post-treatment nitric oxide levels, compared with baseline, but post-treatment levels did not differ significantly between groups. A significant association was found between treatment response and nitric oxide level alteration. CONCLUSION: This study demonstrates the favourable effects of glucocorticoids on nasal polyposis, and alteration in nitric oxide tissue levels post-treatment. Nitric oxide level in nasal polyp tissue could be an indicator of treatment response, and may aid surgical decision-making by detecting cases that probably will not respond to medical treatment.

Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries.

We have selected a set of single nucleotide polymorphisms (SNPs) with the specific aim of differentiating European and South Asian ancestries. The SNPs were combined into a 23-plex SNaPshot primer extension assay: Eurasiaplex, designed to complement an existing 34-plex forensic ancestry test with both marker sets occupying well-spaced genomic positions, enabling their combination as single profile submissions to the Bayesian Snipper forensic ancestry inference system. We analyzed the ability of Eurasiaplex plus 34plex SNPs to assign ancestry to a total 1648 profiles from 16 European, 7 Middle East, 13 Central-South Asian and 21 East Asian populations. Ancestry assignment likelihoods were estimated from Snipper using training sets of five-group data (three Eurasian groups, East Asian and African genotypes) and four-group data (Middle East genotypes removed). Five-group differentiations gave assignment success of 91% for NW European populations, 72% for Middle East populations and 39% for Central-South Asian populations, indicating Middle East individuals are not reliably differentiated from either Europeans or Central-South Asians. Four-group differentiations provided markedly improved assignment success rates of 97% for most continental Europeans tested (excluding Turkish and Adygei at the far eastern edge of Europe) and 95% for Central-South Asians, despite applying a probability threshold for the highest likelihood ratio above '100 times more likely'. As part of the assessment of the sensitivity of Eurasiaplex to analyze challenging forensic material we detail Eurasiaplex and 34-plex SNP typing to infer ancestry of a cranium recovered from the sea, achieving 82% SNP genotype completeness. Therefore, Eurasiaplex provides an informative and forensically robust approach to the differentiation of European and South Asian ancestries amongst Eurasian populations.