Oleksyk, O. T. | bioRxiv Science

bioRxiv2024

PopGenPlayground: a population genomics analysis pipeline

BackgroundPopulation genomic projects are essential in the current drive to map the genome diversity of human populations across the globe. Various barriers persist hindering these efforts, and the lack of bioinformatic expertise and reproducible standardized population-scale analysis is one of the major challenges limiting their discovery potential. Scalable, automated, user-friendly pipelines can help researchers with minimum programming skills to tackle these issues without extensive training. ResultsPopGenPlayground (PGP), is a streamlined, single-command computation pipeline designed for human population genomics analysis based on Snakemake workflow management system. Developed to automate secondary analysis of a previously published national genome project, it leverages the publicly available genomic databases for comparative analysis and annotation of variant calls. ConclusionsPGP presents a multi-platform robust population analysis pipeline, that reduces the time and the expertise levels to perform the main core of population analysis for a national genome project. PGP provides a comprehensive secondary analysis tool and can be used to perform analysis on a personal computer or using a remote high-performance computing platform.

bioinformatics↗

bioRxiv2020

Genome Diversity in Ukraine

The main goal of this collaborative effort is to provide genome wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for the public data release. DNBSEQ-G50 sequences, and genotypes by an Illumina GWAS chip were cross-validated on multiple samples, and additionally referenced to one sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. The genome data has been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, CNVs, SNPs and microsatellites. This study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for historic and medical research in a large understudied population. While most of the common variation is shared with other European populations, this survey of population variation contributes a number of novel SNPs and structural variants that have not been reported in the gnomAD/1KG databases representing global distribution of genomic variation. These endemic variants will become a valuable resource for designing future population and clinical studies, help address questions about ancestry and admixture, and will fill a missing place in the puzzle characterizing human population diversity in Eastern Europe. Our results indicate that genetic diversity of the Ukrainian population is uniquely shaped by the evolutionary and demographic forces, and cannot be ignored in the future genetic and biomedical studies. This data will contribute a wealth of new information bringing forth different risk and/or protective alleles. The newly discovered low frequency and local variants can be added to the current genotyping arrays for genome wide association studies, clinical trials, and in genome assessment of proliferating cancer cells.

genomics↗