Effect of soil and water environment on typeability of PowerPlex Y (Promega) in selected tissue samples.

In cases of decomposed bodies Y chromosomal STR markers may be useful in identification of a male relative. The authors assessed typeability PowerPlex Y (Promega) loci in tissue material stored in water and soil environment. Tissue material was collected during autopsies of five persons aged 20-30 years with time of death determined within the limit of 14 hours. Heart muscle, liver and lung specimens were stored in pond water, sea water, sand and peat soil. DNA was extracted by organic method from tissue samples collected in 7-day intervals. Liver specimens were typeable in all PowerPlex Y loci within 100 days of storage in pond water with gradual decline at DYS392 in sea water. Heart muscle specimens stored in pond water exhibited allelic loss at DYS19, DYS385, DYS389II and DYS392, while all loci were typeable in sea water stored samples. For lung specimens allelic loss was noted throughout the profile. Storage of liver specimens in peat soil for more than 14 days resulted in allelic drop-out, and after 21 days no profiles were typeable. Heart muscle specimens were typeable in all PowerPlex Y systems after 35-day storage in sand, while allelic drop-out and subsequent lack of profiles were noted after 14 and 35 days respectively. Lung specimens stored in garden soil exhibited allelic drop-out and subsequent lack of profiles after 7 and 21 days, respectively. All PowerPlex Y loci were typeable in the latter material in sand up to day 35 with gradual decline of longer amplicons (DYS19, DYS385, DYS389II and DYS392)

Population genetics of 30 INDELs in populations of Poland and Taiwan

The Investigator DIPplex(®) kit (Qiagen) contain components for the simultaneous amplification and analysis of 30 biallelic autosomal INDELs and amelogenin. The objective of this study was to estimate the diversity of the 30 markers in Polish (N(P) = 122) and Taiwanese (N(T) = 126) population samples and to evaluate their usefulness in forensic genetics. All amplicon lengths were shorter than 160 base pairs. The DIPplex genotype distributions showed no significant deviation from Hardy–Weinberg rule expectations (Bonferroni corrected) except for DLH39 in the Taiwanese population. Among the Poles and the Taiwanese the mean observed heterozygosity values are 0.4385 and 0.4079, and the combined matching probability values are 7.98 × 10(−14) and 1.22 × 10(−11), respectively. The investigated marker set has been confirmed as a potential extension to standard short tandem repeat-based kits or a separate informative system for individual identification and kinship analysis. Eight INDELs have been selected as possible ancestry informative single-nucleotide polymorphisms for further analyses

A hunter-gatherer-farmer population model: Lie symmetries, exact solutions and their interpretation

The Lie symmetry classification of the known three-component reaction-diffusion system modelling the spread of an initially localized population of farmers into a region occupied by hunter-gatherers is derived. The Lie symmetries obtained for reducing the system in question to systems of ODEs and constructing exact solutions are applied. Several exact solutions of traveling front type are found, their properties are identified and biological interpretation is discussed

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.Peer reviewe

The rs2228145 polymorphism in the interleukin-6 receptor and its association with long-term prognosis after myocardial infarction in a pilot study

Introduction : Interleukin-6 (IL-6) is a cytokine with a complex function that is described as both pro- and anti-inflammatory. One factor that influences its function is the rs2228145 A/C single nucleotide polymorphism (SNP) of the IL-6 receptor (IL6R) gene. C allele carriers have a decreased inflammatory response and decreased prevalence of ischemic heart disease. The aim of the study was to investigate the association of the rs2228145 SNP of the IL6R gene with long-term total mortality in patients with ST-elevation myocardial infarction (STEMI) treated invasively. Material and methods : We analyzed the data of consecutive patients with ST elevation myocardial infarction (STEMI) treated with primary percutaneous coronary intervention (PCI). Genotyping was performed with the TaqMan method. The analyzed end-point was total long-term mortality (median: 2875 days). Results: The registry comprised 553 patients (mean age: 62.4 ±11.9 years; 25.6% females, n = 142; TIMI 3 obtained in 91.7% of patients, n = 507). No significant differences in baseline characteristics were found between the genotypes. During long-term follow-up 171 (30.9%) patients died. There was non-significantly higher mortality in the rs2228145 AA homozygotes compared to C allele carriers (OR = 1.34, 95% CI: 0.93–1.93, p = 0.1). Conclusions : The rs2228145 polymorphism of IL6R was not significantly associated with long-term mortality after STEMI. However, AA homozygotes (high-risk genotype for ischemic heart disease) showed a trend towards adverse outcome compared to C allele carriers. The observed trend is promising, but it requires independent replication studies

Population Genetic Data of 30 Insertion-Deletion Markers in the Polish Population

(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included in the Investigator DIPplex kit (Qiagen) were obtained in a sample of 631 unrelated Polish individuals. Allelic frequency data were compared with those reported for selected populations (3) Results: All the loci conformed with Hardy-Weinberg equilibrium after applying a Bonferroni correction and no pair-wise significant linkage disequilibrium was detected. (4) Conclusions: DIPplex Kit differences were high among populations worldwide. The InDel markers are highly discriminating for human identification purposes in the Polish population

Polymorphism of 9p21.3 locus is associated with 5-year survival in high-risk patients with myocardial infarction.

OBJECTIVE: The rs1333049, rs10757278 and rs4977574 are single nucleotide polymorphisms (SNPs) of chromosome 9p21 locus that are associated with prevalence of acute coronary syndromes (ACS). The rs1333049 SNP was also associated with cardiac outcome 6 months post ACS. No data concerning their association with long term prognosis after myocardial infarction is available. The aim of our study was to investigate the association of the 9p21.3 locus with 5-year overall mortality in patients with ST-elevation myocardial infarction (STEMI) treated invasively. MATERIALS AND METHODS: We performed a retrospective analysis of data collected prospectively in a registry of consecutive patients with STEMI treated with primary PCI. Genotyping was performed with a TaqMan method. The analyzed end-point was total 5-year mortality. RESULTS: The study group comprised 589 patients: 25.3% of females (n = 149), mean age 62.4±11.9 years, total 5-year mortality 16.6% (n = 98). When all the study group was analyzed, no significant differences in mortality were found between the genotypes. However, in high-risk patients (Grace risk score ≥155 points, n = 238), low-risk homozygotes had significantly better 5-year survival compared to other genotypes. The hazard ratio associated with high-risk genotype (high-risk homozygote or heterozygote) was: HR = 2.9 (95%CI 1.4-6.1) for the rs4977574 polymorphism, HR = 2.6 (1.25-5.3) for the rs1333049 one and HR = 2.35 (1.2-4.6) for the rs10757278 one (Cox proportional hazards model). CONCLUSIONS: The 9p21.3 locus is associated with 5-year mortality in high-risk patients with STEMI. This finding, due to very high effect size, could potentially be applied into clinical practice, if appropriate methods are elaborated

The rs4977574 polymorphism and 5-year survival.

<p>No significant differences were observed between the genotypes.</p