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.

Y-STR data of the Yfiler Plus panel in population of north-eastern Poland. / Dane populacyjne dla markerów zestawu Yfiler Plus w populacji Polski pólnocno-wschodniej.

Background: The use of new high-resolution and forensic identification capabilities for population studies offered by new multiplex methods (such as Yfiler Plus) is crucial in forensic genetics cases. The development of haplotype frequency databases is essential to take full advantage of the new Y chromosome determination capabilities. Purpose: Development of the haplotype database of the Yfiler Plus kit for a population-based sample of 534 males from northeastern Poland and calculation of suitability parameters for forensic genetics studies. Materials and methods: The study was conducted on a population sample of 534 unrelated males from the area of northeastern Poland using the Yfiler Plus panel of 27 markers located on the Y chromosome. Results: Four haplotypes appeared twice. The Discrimination Capacity (DC) of the entire set was 0.9925. The highest Gene Diversity (GD) value was calculated for DYS518 (0.86) belonging to the fast-mutation markers, while the lowest GD was calculated for DYS392 (0.42). Conclusion: The results indicate the need for further research and observation of changes, both in different regions of Poland and across Europe.

Analysis of paternity exclusions in the material collected by the Department of Forensic Medicine, Medical University of Bialystok in 2008-2017.

AIM OF THE STUDY: Analysis of frequency and structure of paternity exclusions in the material collected by the Department of Forensic Medicine, Medical University of Bialystok in 2008-2017. MATERIAL AND METHODS: The paper is based on paternity test reports involving alleged father-child-mother trios. In a total of reviewed 958 cases, 187 exclusions were identified. The analysis was carried out on the basis of the results of DNA tests. DNA extraction was performed using QIAamp DNA Mini Kit (Qiagen) and DNA quantitation using Quantifiler Human DNA Quantification Kit and 7500 Real-Time PCR System (Applied Biosystems). AmpFLSTR Identifiler PCR Amplification Kit and a PCR System 9700 thermal cycler (Applied Biosystems) were used for DNA amplification. RESULTS: Over the analyzed period, the number of paternity tests was nearly halved, whereas the percentage of exclusions in individual years varied significantly (33.9-13.3%), with the average of 26.3%. The highest efficiency of exclusions was observed for D18S51 (0.7166) and FGA (0.7059), and the least effective system was TPOX (0.3048). CONCLUSIONS: The applied set of markers has been demonstrated to be an efficient tool in genetic paternity tests in the context of the recommended rules of exclusion.

Application of massively parallel sequencing (MPS) in paternity testing - case report.

Aim of the study: We present the application of massively parallel sequencing (MPS) to extend the scope of analysis in a disputed paternity case. Material and methods: A standard paternity test comprising 16 autosomal STRs was performed by capillary electrophoresis (CE) using 3130xl Genetic Analyzer. Additionally, MPS was performed with ForenSeq DNA Signature Prep Kit and Illumina MiSeq FGx™ Forensic Genomics System. Paternity index (PI) was calculated using DNAStat v.2.1 software. Results>: CE revealed two mismatches, at D21S11 and VWA, between the putative father and the child. Based on MPS results, the mismatches were analyzed and a nonconsensus sequence of allele 14 at the VWA locus in the mother - child pair was identified. Different sequence variants were also detected in 16-16 homozygote alleles at the D3S1358 locus in the child. Conclusions: MPS helped to formulate a definite conclusion regarding the paternity of the defendant and provided full information on intra-allelic polymorphism.

Genetic variation of 15 autosomal STRs in a population sample of Bedouins residing in the area of the Fourth Nile Cataract, Sudan.

ABSTRACT: The purpose of the paper was to report allelic frequencies of 15 autosomal STR markers (AmpFlSTR NGM PCR Amplification Kit) for Bedouin inhabitants in the area of the Fourth Nile Cataract in Sudan, and compute commonly used population and forensic biostatistical parameters. Buccal swabs were collected from 117 unrelated individuals. DNA was extracted using DNA QIAamp® DNA Mini Kit, and quantitated with Quantifiler Human Quantification Kit in a 7500 Real-Time PCR System. Amplification of 15 AmpFlSTR NGM PCR Kit loci was performed in PCR System 9700. Electrophoresis and typing were performed in 3130 Genetic Analyzer. Arlequin v3.5 software and PowerStats v1.2 spreadsheet were used for statistical calculations. The STR frequency distributions showed no deviations from HWE. The combined values of Matching Probability and Power of Exclusion are 1.77 × 10-18 and 0.9999996, respectively. The average observed heterozygosity over 15 loci is 0.8069. Five different allelic microvariants were found. A significant linkage disequilibrium was observed in five pairs of loci. A 15 STR population database has been established for Sudanese Bedouins. The systems studied have been shown to be useful tool for personal identification in this population.

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.

The influence of renal function on the association of rs854560 polymorphism of paraoxonase 1 gene with long-term prognosis in patients after myocardial infarction.

Paraoxonase 1 (PON1) is an enzyme responsible for the antioxidant properties of high density lipoprotein (HDL). The activity of PON1 is decreased in patients with coronary artery disease, myocardial infarction or chronic kidney disease. rs662 and rs854560 are single nucleotide polymorphisms (SNPs) associated with PON1 activity and 10-year cardiovascular mortality of patients with stable coronary artery disease. We investigated the association of rs662 and rs854560 SNPs of the PON1 gene with 5-year mortality in patients with ST-elevation myocardial infarction (STEMI) treated invasively. We analyzed the data of consecutive patients with STEMI treated with primary PCI. Genotyping was performed with the TaqMan method. The analyzed end-point was total 5-year mortality. Additional subgroup analysis was performed for survival of patients depending on their eGFR. The study group comprised 634 patients (mean age 62.3 ± 11.85 years; 25.2% of women, n = 160; PCI successful in 92.3%, n = 585). No clinically relevant differences in baseline characteristics were found between the genotypes. No association between either genotype and 5-year mortality was found: p = 0.4 for the rs662 SNP, p = 0.73 for the rs854560 one (log-rank test). However, in a subgroup of patients with eGFR below median value (78.6 ml/min/1.73m2) the rs854560 AA homozygotes had a significantly lower probability of survival (p = 0.047, log-rank test). The AA genotype of the rs854560 SNPs of the PON1 gene is associated with increased mortality in patients after myocardial infarction in the subpopulation of patients with lowered eGFR. This phenomenon may be explained by potentially lower PON1 activity in kidney disease.

The 9p21 polymorphism is linked with atrial fibrillation during acute phase of ST-segment elevation myocardial infarction.

The aim of the study was to find whether patients carrying polymorphic allele of the rs10757278 polymorphism from 9p21 locus have changed risk of arrhythmia (atrial fibrillation, AF; sustained ventricular tachycardia or ventricular fibrillation, sVT/VF) during acute phase of myocardial infarction. Retrospective analysis of data collected prospectively from two independent centers was performed. The clinical data were pooled from two independent cardiac registries: (1) the Warsaw ACS genetic registry (STEMI and NSTEMI/UA patients hospitalized in the years 2008-2011; only STEMI patients were analyzed); (2) the Bialystok STEMI genetic registry (STEMI patients hospitalized in years 2001-2005, who survived the first 48 h from hospital admission). Data regarding sVT/VF and AF within first 24 h were analyzed. The patients were genotyped with rs10757278 polymorphism. 1083 patients were included in the analysis; 62 (5.7 %) patients had sVT/VF during acute phase and 78 (7.2 %) patients had AF, 46 (4.2 %) patients had new-onset AF. Minor allele frequency in all patients with AF was significantly different from those without AF (0.40 vs 0.51, p = 0.0096). When only new-onset AF was analyzed, the trend was the same, with significant protective effect in recessive model [OR 0.41 (95 % CI 0.17-0.97), p = 0.025]. The effect was independent of age and GRACE score. No relationship was found between sVT/VF and rs10757278. Patients with STEMI, who survived until hospitalization with polymorphic allele of 9p21 rs10757278 SNP have less AF during acute phase of STEMI. SNP rs10757278 is not linked with sVT/VF in acute phase of STEMI.

Typeability of DNA in Touch Traces Deposited on Paper and Optical Data Discs.

BACKGROUND: Nucleated epithelial cells that are transferred by casual touching and handling of objects are the primary source of biological evidence that is found in high-volume crimes. Cellular material associated with touch traces usually contains low levels of DNA template making it challenging to acquire an informative profile. OBJECTIVES: The main purpose of this study was to examine the efficacy of DNA typing in fingerprints deposited on optical data discs and the office paper. MATERIAL AND METHODS: Latent fingerprints were made by 60 subjects of both sexes (30 males and 30 females). A highly effective DNA extraction method with QIAamp DNA Mini Kit (Qiagen) and an increased sensitivity PCR by AmpFlSTR® NGM™ Amplification Kit (Applied Biosystems) carried out at standard 30 cycles and at increased 34 cycles were used. RESULTS: The mean value of total DNA recovery was 0.4 ng from CDs/DVDs and 0.3 ng from the office paper. Amplification of Low Template DNA (LT-DNA) resulted in improved analytical success by increasing the number of PCR cycles from standard 30 to 34. On the other hand, the increased PCR cycles resulted in allele drop-ins showing additional peaks, the majority of which were outside the stutter positions. CONCLUSIONS: Rigorous procedures and interpretation guidelines are required during LT-DNA for producing reliable and reproducible DNA profiles for forensic purposes.

Changes in Surface Charge Density of Blood Cells in Fatal Accidental Hypothermia.

The objective of this research was to evaluate postmortem changes concerning electric charge of human erythrocytes and thrombocytes in fatal accidental hypothermia. The surface charge density values were determined on the basis of the electrophoretic mobility measurements of the cells conducted at various pH values of electrolyte solution. The surface charge of erythrocyte membranes after fatal accidental hypothermia increased compared to the control group within whole range of experimental pH values. Moreover, a slight shift of the isoelectric point of erythrocyte membranes towards high pH values was observed. The surface charge of thrombocyte membranes in fatal accidental hypothermia decreased at low pH compared to the control group. However, at pH range 4-9, the values increased compared to the control group. The isoelectric point of thrombocyte membranes after fatal accidental hypothermia was slightly shifted towards low pH values compared to the control group. The observed changes are probably connected with the partial destruction and functional changes of the blood cell structure.

The rs12526453 Polymorphism in an Intron of the PHACTR1 Gene and Its Association with 5-Year Mortality of Patients with Myocardial Infarction.

OBJECTIVE: The rs12526453 (C/G) is a single nucleotide polymorphism in an intron of the PHACTR1 gene (phosphatase and actin regulator 1). The C allele is associated with increased risk of coronary artery disease in an unknown mechanism. We investigated its association with long-term overall mortality in patients with ST-elevation myocardial infarction (STEMI) treated invasively. METHODS: Two independent groups of patients with STEMI were analyzed: a derivation group (n= 638) and a validation one (n=348). Genotyping was performed with the TaqMan method. The analyzed end-point was total long term mortality. Additionally, transcriptomic analysis was performed in mononuclear blood leukocytes from rs12526453 CC monozygotes or G allele carriers. RESULTS: In the study group (mean age 62.3 ± 11.9 years; 24.9% of females, n=159), percentages of CC, CG, and GG genotypes were 45.3% (n=289), 44.7% (n=285), and 10% (n=64), respectively. In the 5-year follow-up 105 patients died (16.46%). CC homozygotes had significantly lower mortality compared to other genotypes: 13.1% (n=38) vs. 18.3% in G-allele carriers (n=67), (p=0.017, Cox`s F test). In the validation group 47 patients died within 3 years (13.5%). We confirmed lower mortality of CC homozygotes: 10.1 % (n=18) vs. 16.95% in G-allele carriers (n=29), (p=0.031, Cox`s F test). Transcriptomic analysis revealed a markedly higher expression of NLRP-2 in CC homozygotes. CONCLUSIONS: The rs12526453 CC homozygotes (previously associated with increased risk of myocardial infarction) showed, in 2 independent samples, better long-term survival. The finding of such high effect size, after appropriate validation, could potentially be translated into clinical practice.

The rs9982601 polymorphism of the region between the SLC5A3/MRPS6 and KCNE2 genes associated with a prevalence of myocardial infarction and subsequent long-term mortality.

INTRODUCTION:  rs9982601 (C>T) is a polymorphism of the noncoding region between the SLC5A3/MRPS6 and KCNE2 genes. It has been shown to be associated with early-onset myocardial infarction (MI) with T as a risk allele. OBJECTIVES:  The aim of our study was to investigate the association of the rs9982601 polymorphism with long-term overall mortality from MI and prevalence of MI in a Polish population. PATIENTS AND METHODS:  The study involved patients with MI treated invasively. Individuals who underwent paternity testing served as a population group. Genotyping was performed by the TaqMan method. The analyzed endpoint was the overall long-term mortality. RESULTS:  The study group comprised 981 patients (mean age, 62.8 ±12.1 years; 259 women [26.4%]). The percentages of TT, CT, and CC genotypes were 3.1%, 25.6%, and 71.3%, respectively, in the whole group, and 2.4%, 16.8%, and 80.8% (P = 0.01) in the population group (n = 167). During follow-up (median, 1826 days), 157 patients died (16%). No significant differences were observed between the genotypes either in clinical characteristics or in mortality. However, in a subgroup of high-risk patients (GRACE risk score of 155 points or higher, n = 428), low-risk CC homozygotes had a significantly better survival rate compared with the other genotypes (hazard ratio, 0.64; 95% confidence interval, 0.43-0.96; P = 0.03). CONCLUSIONS:  We showed that the rs9982601 polymorphism of the region between SLC5A3/MRPS6 and KCNE2 genes is associated with long-term mortality in high-risk patients after MI. Additionally, our study supports the previous reports on the correlation of this polymorphism with the prevalence of MI.

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

OBJECTIVE: The rs10757278, rs1333049 and rs4977574 are single nucleotide polymorphisms (SNPs) of chromosome 9p21 locus associated with a prevalence of acute coronary syndromes (ACS). Reports concerning their association with long-term outcome after an ACS are equivocal. 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). MATERIALS AND METHODS: We performed a retrospective analysis of data collected prospectively in 2 independent registries of consecutive patients with STEMI (derivation and validation group). Genotyping was performed with the TaqMan method. The analyzed end-point was total mortality. RESULTS: The derivation group comprised 589 patients: 25.3% female (n = 149), mean age 62.4 ± 12.0 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), homozygotes associated with higher risk for ACS had significantly better 5-year survival compared to other genotypes. The hazard ratio associated with the high-risk genotype (a homozygote of high risk for ACS or a heterozygote) was: HR = 2.2 (1.15-4.2) for the rs10757278 polymorphism, HR = 2.7 (95% CI 1.3-5.4) for the rs4977574 one and HR = 2.3 (1.2-4.5) for the rs1333049 one (Cox proportional hazards model). Survival analysis in the validation group (n = 365) showed a clear trend towards better prognosis in GG homozygotes of the rs10757278 SNP, which confirms our initial results (p = 0.09, log-rank test). CONCLUSIONS: The 9p21.3 locus is associated with 5-year mortality in high-risk patients with STEMI. The genotypes associated with higher risk for ACS show a protective effect in terms of further survival (instead of a deteriorating prognosis, as reported previously). This finding, due to the very high size of the effect, could potentially be applied to clinical practice, if appropriate methods are elaborated.

Polish population data on 15 autosomal STRs of AmpFlSTR NGM PCR kit.

The objective of the research was to provide a comprehensive database of autosomal microsatellite loci included in AmpFlSTR NGM PCR kit for a population of Poland considering possible genetic differentiation of a forensic interest. Fifteen STR markers were analyzed in 2041 unrelated individuals residing in eight geographically different regions. All the loci were found to be in Hardy-Weinberg equilibrium. The combined probability of match is 3.52 × 10(-19) and the combined Power of Exclusion is 0.9999998. The F(ST) estimate over all 15 STRs is 0.0051 for the Polish population. We established that a combined NGM database may be employed for a 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.

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.

Fatal drowning as a result of an airplane crash--case report.

An ULM (Ultra Light Motorized) plane Aeroprakt 22-L with two men on board dived unexpectedly into the Dworackie lake near the town of Olecko in Warmia and Mazury district, Northeastern Poland. The pilot and the passenger had multiorgan blunt injuries, including subdural and subarachnoid hemorrhage, fractured ribs, fractured thigh (in one of the deceased) and pulmonary contusions as a result of the impact with the lake. The multiorgan injuries and unconsciousness resulting from head trauma prevented the casualties from saving themselves. The underlying cause of the death was the crash into the lake, however drowning was assessed as the proximate cause of death. The accident was analyzed together with an account prepared by State Commission on Aircraft Accident Investigation and with the Human Factor Analysis and Classification System - HFACS (the standardized method of analysis of flight accidents, the tool originally developed and tested within the U.S. military).