A5058863957- Monoclonal and Polyclonal Antibodies Research
- Multiple Myeloma Research and Treatments
- Immunodeficiency and Autoimmune Disorders
- Chronic Lymphocytic Leukemia Research
- Genetic and phenotypic traits in livestock
- Blood groups and transfusion
- Gene expression and cancer classification
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Biosimilars and Bioanalytical Methods
- Genetic Associations and Epidemiology
- Milk Quality and Mastitis in Dairy Cows
- Adipose Tissue and Metabolism
- RNA and protein synthesis mechanisms
- interferon and immune responses
- RNA modifications and cancer
- Machine Learning in Bioinformatics
- Cancer-related molecular mechanisms research
- SARS-CoV-2 and COVID-19 Research
- Adrenal and Paraganglionic Tumors
- Microbial Metabolic Engineering and Bioproduction
- Cancer, Hypoxia, and Metabolism
- Hormonal Regulation and Hypertension
- vaccines and immunoinformatics approaches
- Molecular Biology Techniques and Applications
Wroclaw University of Environmental and Life Sciences
2020-2024
Poznan University of Medical Sciences
2024
Abstract BCMA-targeted bispecific antibodies (BiAb) are efficacious in relapsed/refractory multiple myeloma; however, serious infections have emerged as important toxicities. In this retrospective study, we characterized all and their risk factors, evaluated the impact of infection prophylaxis patients treated with BiAbs. Among 37 patients, 15 (41%) experienced a grade 3–5 infection, two infection-related deaths during deep remissions. Most (84%) occurred disease The cumulative probability...
Undoubtedly, genetic factors play an important role in susceptibility and resistance to COVID-19. In this study, we conducted the GWAS analysis. Out of 15,489,173 SNPs, identified 18,191 significant SNPs for severe 11,799 resistant phenotype, showing that a great number loci were different COVID-19 representations. The majority variants synonymous (60.56% severe, 58.46% phenotype) or located introns (55.77% 59.83% phenotype). We most outcome (in AJAP1 intron) COVID FIG4 intron). found no...
The serious drawback underlying the biological annotation of whole-genome sequence data is p >> n problem, which means that number polymorphic variants (p) much larger than available phenotypic records (n). We propose a way to circumvent problem by combining LASSO logistic regression with deep learning classify cows as susceptible or resistant mastitis, based on single nucleotide polymorphism (SNP) genotypes. Among several architectures, one 204,642 SNPs was selected best. This...
Abstract This study compared computational approaches to parallelization of an SNP calling workflow. The data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. pipeline consisted quality control, alignment reference genome, post-alignment, and calling. Three were compared: (i) a plain Bash script in which for each cow was executed as separate processes invoked at same time, (ii) wrapped single Nextflow process (iii) component defined process. results...
COVID-19 infections pose a serious global health concern so it is crucial to identify the biomarkers for susceptibility and resistance against this disease that could help in rapid risk assessment reliable decisions being made on patients' treatment their potential hospitalisation. Several studies investigated factors associated with severe outcomes can be either environmental, population based, or genetic. It was demonstrated genetics of host plays an important role various immune responses...
Abstract A critical step in the analysis of whole genome sequencing data is variant calling. Despite its importance, calling prone to errors. Our study investigated association between incorrect single nucleotide polymorphism (SNP) calls and quality metrics context. In our study, SNPs were defined 20 Holstein–Friesian cows by comparing their genotypes identified with IlluminaNovaSeq6000 EuroGMD50K genotyping microarray. The dataset was divided into correct SNP set (666 333 SNPs) (4 557...
Abstract A downside of next-generation sequencing technology is the high technical error rate. We built a tool, which uses array-based genotype information to classify sequencing–based SNPs into correct and incorrect calls. The deep learning algorithms were implemented via Keras. Several tested: (i) basic, naïve algorithm, (ii) algorithm modified by pre-imposing different weights on SNP class in calculating loss metric (iii)–(v) random re-sampling (with replacement) match 30%/60%/100% number...
Abstract The most serious drawback underlying the biological annotation of Whole Genome Sequence data is p>>n problem, meaning that number polymorphic variants (p) much larger than available phenotypic records (n). Therefore, major aim study was to propose a way circumvent problem by combining LASSO logistic regression model with Deep Learning (DL). That illustrated practical classification cows into mastitis-susceptible or mastitis-resistant, based on genotypes Single Nucleotide...
Since global temperature is expected to rise by 2 °C in 2050 heat stress may become the most severe environmental factor. In study, we illustrate application of mixed linear models for analysis whole transcriptome expression livers and adrenal tissues Sprague-Dawley rats obtained a experiment. By applying those models, considered four sources variation transcript expression, comprising transcripts (1), genes (2), Gene Ontology terms (3), Reactome pathways (4) focussed on accounting...
Abstract This study compared computational approaches to parallelisation of an SNP calling workflow. Data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. The pipeline consisted quality control, alignment reference genome, post-alignment, and calling. Three were compared: (i) a plain Bash script in which for each cow was executed as separate processes invoked at same time, (ii) wrapped single Nextflow process, (iii) component defined process. results...
ABSTRACT A critical step in the analysis of WGS data is variant calling. Despite its importance, calling prone to errors. Our study investigated association between incorrect SNP and quality metrics nucleotide context. In our study, SNPs were defined twenty Holstein-Friesian cows by comparing their genotypes identified whole genome sequencing with IlluminaNovaSeq6000 EuroGMD50K genotyping microarray. The set was divided into correct (666,333 SNPs) (4,557 SNPs). training consisted only SNPs,...
ABSTRACT The rapid advancement of high-throughput sequencing technologies has revolutionised genomic research by providing access to large amounts data. However, the most important disadvantage using Whole Genome Sequencing (WGS) data is its statistical nature, so-called p>>n problem. This study aimed compare three approaches feature selection allowing for circumventing problem, among which one a novel modification Supervised Rank Aggregation (SRA). use methods was demonstrated in...
<title>Abstract</title> Paragangliomas (PGLs) are a heterogeneous group of tumors the nonepithelial neuroendocrine type with significant percentage being genetically determined. They can develop from cells parasympathetic as well sympathetic nervous system. Tumors located in head and neck usually have origin, whereas those abdomen origin. The aim this study was to determine whether development PGLs at both locations is associated specific variants genes proven relevance for formation these...
Abstract Although gene panels for complex phenotypes target genes contributing significantly to phenotypic variation, identifying causal mutations remains challenging. We aimed define the process of analysing panel data uncover genomic insights traits with inheritance. The implemented procedure included exploration (i) association between variability and SNPs within genes, (ii) attributed specific variants, (iii) causality potential by context in vicinity associated (iii_a) either through...
Background: Severe outcomes of COVID-19 account for up to 15% all cases. The study aims check if any gene variants related cardiovascular (CVD) and pulmonary diseases (PD) are correlated with a severe outcome in Polish cohort patients. Methods: In this study, subset 747 samples from unrelated individuals collected across Poland 2020 2021 was used whole-genome sequencing performed. Results: GWAS analysis SNPs short indels located genes CVD identified one variant significant the HADHA gene,...
<p>Absolute lymphocyte counts over time in individual patients</p>
<p>Absolute neutrophil counts over time in individual patients</p>
<p>Anonymized patient-level data. Drug names have been de-identified and will be made available upon request once all of the sponsors published results from these trials.</p>
<p>Swimmer’s plot for bacterial grade 1-5 infections during the study period, divided into ‘On-IVIg’ and “Off-IVIg’ periods</p>
<p>Swimmer’s plot for bacterial grade 3-5 infections during the study period, divided into ‘On-IVIg’ and “Off-IVIg’ periods</p>
<p>Swimmer’s plot for all grade 1-5 infections during the study period, divided into ‘On-IVIg’ and “Off-IVIg’ periods</p>
<div>Abstract<p>BCMA-targeted bispecific antibodies (BiAb) are efficacious in relapsed/refractory multiple myeloma; however, serious infections have emerged as important toxicities. In this retrospective study, we characterized all and their risk factors, evaluated the impact of infection prophylaxis patients treated with BCMA-targeted BiAbs. Among 37 patients, 15 (41%) experienced a grade 3–5 infection, two infection-related deaths during deep remissions. Most (84%) occurred...
<p>Swimmer’s plot for bacterial grade 1-5 infections during the study period, divided into ‘On-IVIg’ and “Off-IVIg’ periods</p>