Tomasz Grzybowski

• Nicolaus Copernicus University

One of the central dogmas of the Catholic Church is the belief in the Eucharistic presence of Jesus Christ, which requires no scientific confirmation because it concerns a supernatural reality. Since the early Middle Ages, however, instances have been recorded improperly referred to as Eucharistic miracles, which believers consider eyewitness testi...

The purpose of this paper is to formulate recommendations for the disclosure of biological traces in the laboratory and the handling of forensic evidence submitted for identification tests, recommended by the Polish Speaking Working Group of the International Society for Forensic Genetics. The paper organizes the knowledge of the most relevant stag...

Introduction: Massively parallel sequencing of mitogenomes usually requires prior amplification. The PCR step may influence the quality of the data obtained, especially when low-level heteroplasmy detection is applied. Aim: The aim of this study was to compare the reliability of two different DNA polymerases in detecting homoplasmic and heteroplasm...

Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suit...

Objectives Epigenetic dynamics has been indicated to play a role in allergy development. The environmental stimuli have been shown to influence the methylation processes. This study investigated the differences in CpGs methylation rate of immune-attached genes between healthy and allergic infants. The research was aimed at finding evidence for the...

The significance of mtDNA heteroplasmy in forensic and medical genetics has increased recently because massively parallel sequencing (MPS) technologies enable more accurate and precise detection of minority nucleotide variants. Recent reports have shown that detection of low-level substitutions may depend on library preparation or sequencing protoc...

Although infection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) does not appear to be as serious a threat to public health as it was in 2020–2021, the increased transmissibility of multiple Omicron descendants may constitute a continuous challenge for health care systems, and reliable detection of new variants is still imperati...

Genetic markers for the prediction of biogeographical ancestry have proved to be effective tools for law enforcement agencies for many years now. In this study, we attempted to assess the potential of insertion-deletion markers (InDel) and microsatellites (STRs) as subsidiary polymorphisms for inference of Slavic population ancestry. For that purpo...

Human facial morphology is a combination of many complex traits and is determined by a large number of genes and enhancers. Here, we report a Copy Number Variation (CNV) study of enhancer hs1431 in populations of Central European and South Siberian ancestry. Central European samples included 97 Poles, while South Siberian samples included 78 Buryat...

Genetic prediction of different hair phenotypes can help reconstruct the physical appearance of an individual whose biological sample is analyzed in criminal and identification cases. Up to date, forensic prediction models for hair colour, hair shape, hair loss and hair greying have been developed, but studies investigating predictability of hair t...

Increasing understanding of human genome variability allows for better use of the predictive potential of DNA. An obvious direct application is the prediction of the physical phenotypes. Significant success has been achieved, especially in predicting pigmentation characteristics, but the inference of some phenotypes is still challenging. In search...

The child microbiome, including gut and skin communities, is shaped by a multitude of factors, and breastfeeding is one of the most essential. Food allergy (FA) and atopic dermatitis (AD) are among the most common diseases in pediatrics, with the prevalence of each up to 6% and 20%, respectively. Therefore, we aimed at finding differences between t...

The gut microbiota in patients with food allergy, and the skin microbiota in atopic dermatitis patients differ from those of healthy people. We hypothesize that relationships may exist between gut and skin microbiota in patients with allergies. The aim of this study was to determine the possible relationship between gut and skin microbiota in patie...

The wild boar Sus scrofa is one of the widely spread ungulate species in Europe, yet the origin and genetic structure of the population inhabiting Central and Eastern Europe are not well recognized. We analysed 101 newly obtained sequences of complete mtDNA genomes and 548 D-loop sequences of the species and combined them with previously published...

Introduction: Lupus erythematosus (LE) is an autoimmune disease with a strong influence of genetic and environmental factors. C-C motif chemokine receptor 5 (CCR5) gene expression may affect the development and intensity of LE. Aim: To evaluate the possible association between the 32bp deletion in rs333 locus located within the CCR5 gene and the...

Food allergy (FA) affects 4-10% of children, especially children with atopic dermatitis (AD). During infancy the gut microbiome may determine both the course of FA and tolerance to food allergens. Analogically, the skin microbiome changes in the course of AD. Most studies have associated FA with a lower abundance and diversity of Lactobacillales an...

Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack o...

Abstract Background Greying of the hair is an obvious sign of human aging. In addition to age, sex- and ancestry-specific patterns of hair greying are also observed and the progression of greying may be affected by environmental factors. However, little is known about the genetic control of this process. This study aimed to assess the potential of...

Y chromosome typing has been performed in forensic genetic practice for more than 20 years. The latest recommendations of the DNA Commission of the International Society of Forensic Genetics (ISFG) concerning the application of Y-chromosomal markers in forensic genetics were published in 2006. The aim of this report is to recapitulate, systematise...

Background There are several subtypes of Lupus Erythematosus (LE), which may be limited to the skin (eg. Discoid Lupus Erythematosus , DLE) or involve multiple organ dysfunctions ( Systemic Lupus Erythematosus , SLE). LE is an autoimmune disease that is influenced by genetic and environmental factors. Despite some genetic changes between DLE and SL...

The available literature on traces characterised by a suboptimal amount of DNA, as well as expert research practice, show the complex nature of LT-DNA traces: from their detection and collection, through genetic analysis, up to the interpretation of final results. The aims of this paper are to systematise the current state of knowledge on handling...

Purpose: To evaluate CLU polymorphisms in patients with pseudoexfoliation syndrome. Materials and methods: We studied 81 patients (23 males and 58 females, the median age 76 years) and 91 control subjects (27 males and 64 females, the median age 75 years). Genotypes of the CLU polymorphisms (SNPs), rs3087554 and rs2279590, were determined using...

Freckles or ephelides are hyperpigmented spots observed on skin surface mainly in European and Asian populations. Easy recognition and external visibility make prediction of ephelides, the potentially useful target in the field of forensic DNA phenotyping. Prediction of freckles would be a step forward in sketching the physical appearance of unknow...

Background p53 is a tumour suppressor protein that is involved in many cancer‐related processes. Growing evidence suggests that p53 also plays an important role in mtDNA maintenance. Somatic mitogenome mutations are frequently observed in colorectal cancer cells. Thus, it was important to verify whether somatic mtDNA changes are associated with TP5...

Considering the possibility of a common genetic background of vertigo and epilepsy, we genotyped an affected group of individuals with vertigo and an unaffected group, by studying 26 single-nucleotide polymorphisms (SNPs) in 14 genes which were previously reported to be of particular importance for epilepsy. Significant differences were found betwe...

Complete mitochondrial genomics is an effective tool for studying the demographic history of human populations, but there is still a deficit of mitogenomic data in European populations. In this paper, we present results of study of variability of 80 complete mitochondrial genomes in two Hungarian populations from eastern part of Hungary (Szeged and...

Purpose To evaluate the expression profiles of the VEGFα and TGFβ in the ERMs and ILMs in retinal disorders. Methods In this nonrandomized prospective study, 75 patients (34 females and 41 males) referred to pars plana vitrectomy (PPV) due to different retinal diseases were enrolled to the study. The samples of ERMs and ILMs collected during PPV w...

So far, a reliable spectrum of mitochondrial DNA mutations in colorectal cancer cells is still unknown, and neither is their significance in carcinogenesis. Indeed, it remains debatable whether mtDNA mutations are “drivers” or “passengers” of colorectal carcinogenesis. Thus, we analyzed 200 mitogenomes from normal and cancer tissues of 100 colorect...

Introduction: To date, several nuclear DNA variants have been shown to be associated with increased risk of developing colorectal cancer. Despite the fact that mitochondria play an important role in carcinogenesis, little is known about inherited mitochondrial DNA mutations that could be involved in this disease. Thus, potential associations betwe...

Although mitochondrial DNA (mtDNA) testing has been used in forensic genetics only since the mid-1990s, forensic DNA laboratories have been recently increasing the range of mtDNA sequencing, employing new analytical approaches and methods of data analysis. Therefore, it seems fitting to gather and systematize existing recommendations in the field o...

This study aimed to find novel genetic variants of susceptibility to aspąergillosis in paediatric patients with haematological malignancies. Complete sequences of fifteen genes of human innate immunity (CCL2, CCR2, CD209, CLEC6A, CLEC7A and ten TLR genes) were studied in 40 patients diagnosed with haematological disorders (20 unaffected and 20 affe...

The ε4 allele of the apolipoprotein E (APOE) gene is known as a risk factor for dementia. How APOE ε polymorphism affects cognitive performance in nondemented aging subjects remains less clear. In this study, the relationship between APOE status and cognitive performance across various cognitive domains in adults aged 55 to 75 years ( n = 74) witho...

Introduction: Many studies have shown that some SNPs might be a risk factor for systemic lupus erythematosus (SLE), but little is known about potential susceptibility loci of the skin types of the disease. Discoid lupus erythematosus (DLE) is the most common form of the cutaneous lupus erythematosus. Nevertheless, a genetic contribution to DLE is n...

Complete mtDNA genome sequencing improves molecular resolution for distinguishing variation between individuals and populations, but there is still deficiency of mitogenomic population data. To overcome this limitation, we used Sanger-based protocol to generate complete mtDNA sequences of 376 Russian individuals from six populations of European par...

Background: Available mitochondrial (mtDNA) data demonstrate genetic differentiation among South Slavs inhabiting the Balkan Peninsula. However, their resolution is insufficient to elucidate the female-specific aspects of the genetic history of South Slavs, including the genetic impact of various migrations which were rather common within the Balka...

The authors obtained Y-STR haplotypes of 496 Polish males using new Yfiler® Plus PCR Amplification Kit (ThermoFisher Scientific) containing seven rapidly mutating markers. Standard diversity and forensic indices were calculated for individual loci and full haplotypes and subsequently compared with minimal haplotype and standard Yfiler® marker sets....

Introduction Toll-like receptor 7 (TLR7) is an important molecule involved in the development of autoimmunity and the response to different pathogens. Several polymorphisms within the TLR7 gene were previously found to be associated with systemic lupus erythematosus (SLE). However, none of those studies investigated the TLR7 promoter flanking varia...

Examination of bovine pituitary gland transcriptome by strand-specific RNA-seq allows detection of putative single nucleotide polymorphisms (SNPs) within potential candidate genes (CGs) or QTLs regions as well as to understand the genomics variations that contribute to economic trait. Here we report a breed-specific model to successfully perform th...

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-1 of Hereford cattle aged 6 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-2 of Hereford cattle aged 6 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-6 of Hereford cattle aged 12 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-3 of Hereford cattle aged 9 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-4 of Hereford cattle aged 9 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-5 of Hereford cattle aged 12 months.(XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-7 of Polish Red cattle aged 6 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-9 of Polish Red cattle aged 9 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-8 of Polish Red cattle aged 6 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-10 of Polish Red cattle aged 9 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-11 of Polish Red cattle aged 12 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-12 of Polish Red cattle aged 12 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-13 of Polish HF cattle aged 6 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-14 of Polish HF cattle aged 6 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-17 of Polish HF cattle aged 12 months. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-15 of Polish HF cattle aged 9 months. (XLSX)

Analysis of breed-specific SNP-db using the SNP filtering criteria of a minimum10 SNP reads per base with an accuracy ≥ 90%. (XLSX)

Analysis of breed-specific SNP-db using the SNP filtering criteria of a minimum10 SNP reads per base with an accuracy = 100%. (XLSX)

Screening of SNP type and occurrence in the experimental breed-specific SNPdb. (XLSX)

Identification of unique SNPs using 90% and 100% SNP filtering in Polish Red cattle. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-16 of Polish HF cattle aged 9 months. (XLSX)

Identification of unique SNPs using 90% and 100% SNP filtering in Hereford cattle. (XLSX)

Identification of unique SNPs using 90% and 100% SNP filtering in Polish HF cattle. (XLSX)

RNA-seq SNP-db of bovine pituitary gland tissue of young bull-18 of Polish HF cattle aged 12 months. (XLSX)

Construction of filtered/trimmed breed-specific SNP-db of bovine pituitary gland transcriptome. (XLSX)

Identification de novo SNPs in Hereford, Polish Red and Polish HF cattle using 90% and 100% SNP filtering criteria. (XLSX)

Domesticated species are often composed of distinct populations differing in the character and strength of artificial and natural selection pressures, providing a valuable model to study adaptation. In contrast to pure-breed dogs that constitute artificially maintained inbred lines, free-ranging dogs are typically free-breeding, i.e., unrestrained...

Y chromosome microsatellite (Y-STR) diversity has been studied in different Mongolic-speaking populations from South Siberia, Mongolia, North-East China and East Europe. The results obtained indicate that the Mongolic-speaking populations clustered into two groups, with one group including populations from eastern part of South Siberia and Central...

Aim of the study : In recent years, RNA analysis has been increasingly used in clinical and forensic genetics. Nevertheless, a major limitation of RNA-based applications is very low RNA stability in biological material, due to the RNAse activity. This highlights the need for improving the methods of RNA collection and storage. Technological approac...

Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and...

Mitochondrial DNA polymerase gamma (POLG) is the only DNA polymerase involved in maintaining the mitochondrial genome. Recent studies demonstrated an association of CAG repeat polymorphism in the second exon of POLG gene with the risk of cancer. We investigated the CAG repeat variability in the POLG gene in tumor and non-tumor tissues from colorect...

Cattle provide a wide range of products and services to humans; thus the significance of conservation of livestock genetic resources is evident. We analyzed the genetic variability of five Y-chromosomal microsatellites in 395 bulls representing six cattle breeds (Polish Red, Polish Whitebacks, Polish Red-and-White, Polish Black-and-White, Polish Ho...

To contribute to the complete mitogenome database of the species Canis lupus familiaris and shed more light on its origin, we have sequenced mitochondrial genomes of 120 modern dogs from worldwide populations. Together with all the previously published mitogenome sequences of acceptable quality, we have reconstructed a global phylogenetic tree of 5...

Background. Recent studies suggest that polymorphisms of genes involved in the clopidogrel metabo- lism may be associated with an impaired drug bioactivation and possibly with unfavourable clinical out- comes. The aim of this study was to assess the effect of selected genetic polymorphisms on adenosine diphosphate-induced platelet aggregation (ADP-...

Mitochondrial DNA was found to be highly mutated in colorectal cancer cells. One of the key molecules involved in the maintenance of the mitochondrial genome is the nuclear-encoded polymerase gamma. The aim of our study was to determine if there is a link between polymorphisms within the polymerase gamma gene (POLG) and somatic mutations within the...

Alcohol abuse is one of the most significant factors in the development of liver fibrosis. The pathomechanism of liver fibrosis is the same regardless of its etiology. Fibrosis is a sign of an imbalance between the synthesis of the extracellular matrix components and their degradation. Among the many cytokines that affect hepatic stellate cell acti...

Tobacco smoking continues to be a leading cause of disease and mortality. Recent research has confirmed the important role of nicotinic acetylcholine receptor (nAChR) gene cluster on chromosome 15q 24-25 in nicotine dependence and smoking. In this study we tested the association of smoking initiation, age at onset of daily smoking, and heaviness of...

A Late Viking-Age Elite Cemetary in Central Poland: Bodzia is one of the most fascinating archaeological discoveries of the post-war period in Poland. It is one of the few cemeteries in Poland from the time of the origins of the Polish state. The unique character of this discovery is mainly due to the fact that a small, elite population was buried...

As microsatellites located on Y chromosome mutate with different rates, they may be exploited in evolutionary studies, genealogical testing of a variety of populations and even, as proven recently, aid individual identification. Currently available commercial Y-STR kits encompass mostly low to moderately mutating loci, making them a perfect choice...

Abstract Mitochondrial DNA (mtDNA) heteroplasmy has been widely described from clinical, evolutionary and analytical points of view. Historically, the majority of studies have been based on Sanger sequencing. However, next-generation sequencing technologies are now being used for heteroplasmy analysis. Ultra-deep sequencing approaches provide incre...

Background Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected pre...

During every criminal investigation, it is vital to extract as much information as possible from every piece of evidence. When it comes to DNA testing, simple short tandem repeat (STR) typing may soon become a relic because it is now possible to genotype more characteristics. Ancestry informative markers are receiving attention from the forensic co...

Several clinical and genetic variables are associated with influencing high on treatment platelet reactivity (HTPR). The aim of the study was to propose a path model explaining a concurrent impact among variables influencing HTPR and ischemic events. In this prospective cohort study polymorphisms of CYP2C19*2, CYP2C19*17, ABCB1, PON1 alleles and pl...

Background. Endothelial cells play a crucial role in the angiogenesis which is initiated by vascular endothelial growth factor (VEGF). Low level laser therapy (LLLT) stimulates repair processes which are based on the formation of new blood vessels. Aim. The aim of this study was to evaluate the impact of LLLT on VEGF gene expression in endothelial...

The Mongolic-speaking Kalmyks currently inhabiting the steppes of the Volga region have Central Asian ancestry and are organized into the tribal groups. The genetic relationships among these tribes and their origin have remained obscure. We analyzed 17 short tandem repeat and 44 binary polymorphisms of Y-chromosome in 426 individuals mainly from th...