Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations.

The EUROFORGEN NAME panel is a regional ancestry panel designed to differentiate individuals from the Middle East, North Africa, and Europe. The first version of the panel was developed for the MassARRAY system and included 111 SNPs. Here, a custom AmpliSeq EUROFORGEN NAME panel with 102 of the original 111 loci was used to sequence 1098 individuals from 14 populations from Europe, the Middle East, North Africa, North-East Africa, and South-Central Asia. These samples were also sequenced with a global ancestry panel, the Precision ID Ancestry Panel. The GenoGeographer software was used to assign the AIM profiles to reference populations and calculate the weight of the evidence as likelihood ratios. The combination of the EUROFORGEN NAME and Precision ID Ancestry panels led to fewer ambiguous assignments, especially for individuals from the Middle East and South-Central Asia. The likelihood ratios showed that North African individuals could be separated from European and Middle Eastern individuals using the Precision ID Ancestry Panel. The separation improved with the addition of the EUROFORGEN NAME panel. The analyses also showed that the separation of Middle Eastern populations from European and South-Central Asian populations was challenging even when both panels were applied.

Analysis of Uyghur and Kazakh populations using the Precision ID Ancestry Panel.

Autosomal ancestry informative markers (AIMs) are important markers for inferring ancestry of humans. In the present study, we typed 105 Uyghurs and 94 Kazakhs with the Precision ID Ancestry Panel that amplifies 165 autosomal AIMs. No statistically significant deviation from Hardy-Weinberg equilibrium and no linkage disequilibrium between loci was observed after Bonferroni correction. STRUCTURE and PCA analyses showed that Uyghurs and Kazakhs appeared as admixed individuals of primarily European and East Asian ancestry and were clearly differentiated from Europeans, Middle Easterners, South/Central Asians, and East Asians. However, it was not possible to differentiate the two populations from each other and they were also difficult to differentiate from Greenlanders, a population with European/Inuit admixture. GenoGeographer was used to evaluate the weight of the evidence. Initially, the results showed that the majority of AIM profiles from Uyghur and Kazakh individuals were not represented by any of the 36 reference populations of the GenoGeographer database. Consequently, it was not reasonable to infer the ancestry of these individuals. A randomly selected subset of the studied populations (75 Uyghur and 75 Kazakh individuals) was used to construct two new reference populations for GenoGeographer, and ancestry prediction was performed on the remaining test individuals. A total of 42 out of 49 test individuals were represented by at least one population after the introduction of Uyghur and Kazakh reference populations. Likelihood ratios ≥106 were obtained when the alternative hypothesis was that the individual belonged to the South/Central Asian, East Asian, Middle Eastern, European, or the admixed Greenlandic population.

Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel.

The CEPH human genome diversity cell line panel (CEPH-HGDP) of 51 globally distributed populations was used to analyze patterns of variability in 20 core human identification STRs. The markers typed comprised the 15 STRs of Identifiler, one of the most widely used forensic STR multiplexes, plus five recently introduced European Standard Set (ESS) STRs: D1S1656, D2S441, D10S1248, D12S391 and D22S1045. From the genotypes obtained for the ESS STRs we identified rare, intermediate or off-ladder alleles that had not been previously reported for these loci. Examples of novel ESS STR alleles found were characterized by sequence analysis. This revealed extensive repeat structure variation in three ESS STRs, with D12S391 showing particularly high variability for tandem runs of AGAT and AGAC repeat units. The global geographic distribution of the CEPH panel samples gave an opportunity to study in detail the extent of substructure shown by the 20 STRs amongst populations and between their parent population groups. An assessment was made of the forensic informativeness of the new ESS STRs compared to the loci they will replace: CSF1PO, D5S818, D7S820, D13S317 and TPOX, with results showing a clear enhancement of discrimination power using multiplexes that genotype the new ESS loci. We also measured the ability of Identifiler and ESS STRs to infer the ancestry of the CEPH-HGDP samples and demonstrate that forensic STRs in large multiplexes have the potential to differentiate the major population groups but only with sufficient reliability when used with other ancestry-informative markers such as single nucleotide polymorphisms. Finally we checked for possible association by linkage between the two ESS multiplex STRs closely positioned on chromosome-12: vWA and D12S391 by examining paired genotypes from the complete CEPH data set.

Association between use of asthma drugs and prevalence of demarcated opacities in permanent first molars in 6-to-8-year-old Danish children.

OBJECTIVES: Demarcated opacities in permanent first molars are common developmental tooth defects, characterized by areas with insufficient mineralization of the enamel. The defects present clinically as a continuum from creamy-white demarcated opacities, yellowish-brown demarcated opacities to macroscopic loss of tooth substance. The etiology is sparsely elucidated, but asthma drugs have been suspected to increase the prevalence. The aim of this study was to examine the prevalence of demarcated opacities in permanent first molars among 6-to-8-year-old children with prescriptions and without prescriptions for asthma drugs. METHODS: In a cross-sectional study in two Danish municipalities, all children aged 6-8 years (n = 891) were included. A total of 745 (83.6%) went through a dental examination during which demarcated opacities and tooth substance loss due to these were recorded. The analyses were restricted to 647 children in whom all four permanent first molars had erupted. Data on use of asthma drugs from birth until the time of the dental examination were obtained from a population-based pharmaco-epidemiological prescription database. RESULTS: Among 47 children with prescriptions for both inhaled beta(2)-agonists and inhaled corticosteroids before the age of 3 years, 15 (31.9%) had demarcated opacities of any type, and six children (12.8%) had opacity-related loss of tooth substance. Among 264 children with no prescriptions for either inhaled or oral asthma drugs from birth until the date of the dental examination, 96 (36.4%) had demarcated opacities of any type, and 13 (4.9%) had opacity-related loss of tooth substance. The odds ratio (OR) of any demarcated opacity, and of opacity-related loss of tooth substance in children with prescriptions for both inhaled beta(2)-agonists and inhaled corticosteroids before the age of 3 years was 0.82 (95% CI: 0.39-1.65), and 2.42 (95% CI: 0.70-7.43). CONCLUSIONS: Children with prescriptions for inhaled asthma drugs before the age of 3 years did not have an overall increased risk of demarcated opacities in first permanent molar but they seemed to have an increased risk of the severe demarcated opacities, i.e. opacities resulting in macroscopic loss of tooth substance, and possibly a need for restorative care.

Seasonal changes in climatic parameters and their relationship with the incidence of pneumococcal bacteraemia in Denmark.

The seasonal variation in the incidence of invasive pneumococcal disease is well recognized, but little is known about its relationship with actual changes in climatic parameters. In this 8-year longitudinal population-based study in Denmark, a harmonic sinusoidal regression model was used to examine whether preceding changes in climatic parameters corresponded with subsequent variations in the incidence of pneumococcal bacteraemia, independently of seasonal variation. The study shows that changes in temperature can be used to closely predict peaks in the incidence of pneumococcal bacteraemia with a time-lag of 16 days (95% CI 14-18 days), independently of a strong seasonal pattern.