Malgorzata Skawronska

Population genetics of 15 STR loci in the population of Podlasie (NE Poland)

Allele frequencies for 15 STR loci included in AmpFlSTR Profiler and AmpFlSTR SGM Plus kits were determined in a sample of 413 unrelated individuals living in the region of Podlasie (NE Poland)

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.

X-chromosomal polymorphism data for the ethnic minority of Polish Tatars and the religious minority of Old Believers residing in northeastern Poland

Population samples of 420 unrelated individuals of the ethnic minority of Polish Tatars and the religious minority of Old Believers residing in northeastern Poland were tested for four X-chromosomal STR frequencies by multiplex PCR and subsequent automated fluorescent detection (ABI 310) using a commercially available kit Mentype Argus X-UL. Kinship tests revealed a typical X-linked inheritance with no mutation. Significant differences in allele frequency distributions confirm previous findings regarding genetic variation among ethnic groups residing in northeastern Poland.

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.

Evaluation of Apoptosis Markers in Conjunctival and Eyelid Benign and Malignant Tumors

Abstract: The balance between cell proliferation and programmed cell death plays a crucial role in malignant development. Bcl‐2 family proteins, including proapoptosis protein Bak and antiapoptosis protein Bcl‐2, regulate the apoptotic process. Mutation of the p53 gene, which results in P53 protein accumulation, was observed in many types of human cancer. The aim of our study was to evaluate immunohistochemical Bcl‐2, Bak, and P53 protein expression and the relation between these proteins in conjunctival and eyelid benign and malignant tumors. We examined a series of 42 papillomas (CEP), 12 squamous cell cancers (SCC), and 19 cases of basal cell cancer (BCC). The age in the CEP group ranged from 18–94 years, and in the SCC and BCC groups from 42–87 years. Staining patterns were correlated with sex, age, and tumor localization. P53 protein‐positive immunostaining was observed in 71% of cases, Bcl‐2 in 83.9%, and Bak in 74.2 cases in the SCC and BCC groups. In the CEP group, P53 overexpression was observed in 90.5% of cases, Bcl‐2 in 71.4%, and Bak in 76.2%. No statistically significant correlation was found between examined protein expression and sex, age, and tumor localization. An inverse correlation was observed between P53 and Bak protein expression in the CEP group. No statistically significance correlation was noted between Bcl‐2 and P53 and Bcl‐2 and Bak protein expression in both examined groups. The obtained data suggests that P53 and Bcl‐2 protein expression coupled with decreasing Bak expression are associated with apoptosis and proliferation as well as malignant progression in conjunctival and eyelid tumors.

The rs1801133 polymorphism of methylenetetrahydrofolate reductase gene- the association with 5-year survival in patients with ST-elevation myocardial infarction.

PURPOSE Methylenetetrahydrofolate reductase (MTHFR) is an enzyme involved in endothelial nitric oxide synthase (eNOS) coupling and homocysteine metabolism. The rs1801133 polymorphism of the MTHFR gene affects risk of coronary artery disease. We assessed its influence on 5-year survival of patients with ST-elevation acute myocardial infarction (STEMI). MATERIAL/METHODS The study group comprised consecutive patients with STEMI. Genotyping was performed with a TaqMan SNP Genotyping Assay using the ABI 7500 Real Time PCR System (Applied Biosystems). The analyzed end-point was all-cause 5-year survival. RESULTS The study group comprised 637 patients (mean age 62.3 ± 11.9 years; 25.1% females, n=160; 5-year mortality 16.3%, n=104). The percentages of TT, CT and CC genotypes were: 10.8 (n=69), 39.7 (n=253) and 49.45 (n=315), respectively. No significant differences in clinical characteristics were identified between the genotypes (p>0.05 for all parameters). Eleven (15.9%) TT homozygotes, 40 (15.8%) heterozygotes and 53 (16.8%) CC homozygotes died during follow up (p=0.99 log-rank test). TT homozygotes presented only weak and insignificant tendency towards higher mortality rates in subgroups of patients ≤75 years old (15.6 vs. 11.54%, p=0.35) or with intermediate risk according to the GRACE risk score (13.3% vs. 8.76%, p=0.42). CONCLUSIONS The rs1801133 polymorphism did not show significant association with 5-year survival.

Polymorphism of 11 non-CODIS STRs in a population sample of religious minority of Old Believers residing in northeastern Poland

PURPOSE The objective of this paper was to provide a database of 11 short tandem repeat (STR) markers not included in the Combined DNA Index System (non-CODIS) for a population sample of Old Believers (n=120) living in northeastern Poland. MATERIAL AND METHODS Deoxyribonucleic acid (DNA) was extracted using Chelex-100 procedure. Genetic profiles were obtained using Mentype Chimera Kit (AG Biotype) and ABI 310 Genetic Analyzer. The statistical tests were performed using GDA v1.1 and PowerStats v1.2 software. RESULTS The genotype frequency distributions showed no deviations from Hardy-Weinberg equilibrium (HWE) except for D5S2500 and D3S1744. The departures appeared statistically insignificant when the Bonferroni correction was used for the number of analysed loci. Significant differences between the Old Believers and Polish Caucasians were found at D7S1517, D8S1132, D2S1360, D5S2500, D6S474, D4S2366 and D3S1744. The combined values of matching probability (MP) and mean exclusion chance (MEC) are 8.35×10-15 and 0.999998, respectively. CONCLUSIONS A DNA database was established that may be used for the purpose of genetic profile comparison in criminal cases and chimerism monitoring after bone marrow transplantation. Significant differences revealed between the autochthonous Poles and the Old Believers by using RxC test and FST estimate support the idea of genetic isolation of this religious minority. Genetic polymorphisms analysed using statistical methods may be informative in differentiation of populations and ethnic groups in northeastern Poland.

Loss of heterozygosity (LOH)--implications for human genetic identification.

The aim of this study was assessment of possible effects of loss of heterozygosity on human genetic identification of histolopathogical tissue sections. DNA templates were extracted from tumour tissue specimens excised from oncological patients and from reference blood samples. AmpFlSTR Identifiler PCR Amplification Kit and ABI 310 Genetic Analyzer (Applera) were used to obtain genetic profiles. Frequency of LOH was calculated for respective samples. Fishers exact test was performed for statistical analysis. Forty-two percent of the 101 cancer cases analysed were found to possess alterations of the microsatellites manifesting with allelic loss. The most frequently altered loci were D3S1358 and D18S51. The alteration was detected in 47% of cases with larynx carcinoma, 44% of cases with uveal melanoma, 60% of cases with cervical cancers, one case of liposarcoma G3 and one case od neurofibrosarcoma. No LOH was found in liposarcoma G1, dermatofibrosarcoma and cystosarcoma protuberans in either primary or recurrent tumours. In benign tumours (lipoma and fibroma) LOH was also absent. During genotyping of DNA extracted from histopathological tissue sections caution should be taken when non-match or exclusion based on few discrepancies is concluded.

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.

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.