Biology subjects

Popov, I.

Publications and source records attributed to Popov, I..

4 recordsLinked to original sources

bioRxiv2025

WxS-QC - a quality control pipeline for human Whole-Genome and Whole Exome sequencing cohorts

MotivationWhole-exome (WES) and whole-genome (WGS) sequencing are rapidly becoming preferred methods for population-scale analysis of the human genetic landscape. However, there are currently no standardized quality control (QC) pipelines for human WES and WGS datasets. Moveover, there are no open datasets that can be used to test QC pipelines, because most projects (like 1000 genomes and gnomAD) publish only post-QC results. ResultsWe present WxS-QC, a powerful, scalable, and convenient pipeline for the QC of human WGS and WES cohorts, developed at the Wellcome Sanger Institute (WSI). Our pipeline is based on a deep refactoring of the gnomAD quality control pipeline code and is aligned with current best practices in WGS/WES cohort data QC. It offers a set of novel QC techniques, automatic export of resulting graphs and summary tables, excellent performance and scalability, and incorporates comprehensive documentation. To test our pipeline and similar solutions, we also assembled an open dataset with all required metadata. Availability and implementationThe pipeline code is written in Python using the Hail library and is freely available under the BSD-3 license here: https://github.com/wtsi-hgi/wxs-qc. It can run in any UNIX-like environment and has been able to efficiently process cohorts of up to 200,000 whole-exome samples with the potential to handle bigger datasets, depending on the available hardware. The detailed description of the pipeline, resources and test data is available in the pipeline documentation: https://github.com/wtsi-hgi/wxs-qc/blob/main/README.md The open test dataset is available to download from https://wxs-qc-data.cog.sanger.ac.uk/wxs-qc_public_dataset_v3.tar. An example of test dataset analysis is available in the supplementary materials.

bioinformatics↗

bioRxiv2023

Prickle and Ror modulate Dishevelled-Vangl interaction to regulate non-canonical Wnt signaling during convergent extension

Convergent extension (CE) is a fundamental morphogenetic process where oriented cell behaviors lead to polarized extension of diverse tissues. In vertebrates, regulation of CE requires both non-canonical Wnt, its co-receptor Ror, and several "core members" of the planar cell polarity (PCP) pathway. PCP was originally identified as a mechanism to coordinate the cellular polarity in the plane of static epithelium, where core proteins Frizzled (Fz)/ Dishevelled (Dvl) and Van Gogh-like (Vangl)/ Prickle (Pk) partition to opposing cell cortex. But how core PCP proteins interact with each other to mediate non-canonical Wnt/ Ror signaling during CE is not clear. We found previously that during CE, Vangl cell-autonomously recruits Dvl to the plasma membrane and keeps Dvl inactive. In this study, we show that non-canonical Wnt induces Dvl to transition from Vangl to Fz. Pk inhibits the transition, and functionally synergize with Vangl to suppress Dvl during CE. Conversely, Ror is required for the transition, and functionally antagonizes Vangl. Biochemically, Vangl interacts directly with both Ror and Dvl. Ror and Dvl do not bind directly, but can be cofractionated with Vangl. Collectively, we propose that Pk assists Vangl to function as an unconventional adaptor that brings Dvl and Ror into a complex to serves two functions: 1) simultaneously preventing both Dvl and Ror from ectopically activating non-canonical Wnt signaling; and 2) relaying Dvl to Fz for signaling activation upon non-canonical Wnt induced dimerization of Fz and Ror.

developmental biology↗

bioRxiv2019

Allele frequency distribution of SNPs associated with levels of Vitamin D-binding protein and 25-hydroxyvitamin D

Haplotypes defined by rs7041/rs4588 in GC gene modulate 25-hydroxyvitamin D (25(OH)D) and vitamin D-binding protein (DBP) levels. To investigate the distributions of GC polymorphisms, the rs7041 and rs4588 allele and haplotypes frequencies were analyzed in samples from different Eurasian regions. The GC1S haplotype associated with high level of serum 25(OH)D had the maximum frequency in European populations (except Finish population). Such frequency distributions may be a result of adaptation to low solar insolation rate. Besides, there was a strong trend of increasing GC1F haplotype frequency from Europe (10-15%) to Siberia and Easter Asia (40-45%).

genetics↗

bioRxiv2018

Novel autoregulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay

Nonsense-mediated decay (NMD) is a eukaryotic mRNA surveillance system that selectively degrades transcripts with premature termination codons (PTC). Many RNA-binding proteins (RBP) regulate their expression levels by a negative feedback loop, in which RBP binds its own pre-mRNA and causes alternative splicing to introduce a PTC. We present a bioinformatic framework to identify novel such autoregulatory feedback loops by combining eCLIP assays for a large panel of RBPs with the data on shRNA inactivation of NMD pathway, and shRNA-depletion of RBPs followed by RNA-seq. We show that RBPs frequently bind their own pre-mRNAs and respond prominently to NMD pathway disruption. Poison and essential exons, i.e., exons that trigger NMD when included in the mRNA or skipped, respectively, respond oppositely to the inactivation of NMD pathway and to the depletion of their host genes, which allows identification of novel autoregulatory mechanisms for a number of human RBPs. For example, SRSF7 binds its own pre-mRNA and facilitates the inclusion of two poison exons; SFPQ binding promotes switching to an alternative distal 3-UTR that is targeted by NMD; RPS3 activates a poison 5-splice site in its pre-mRNA that leads to a frame shift; U2AF1 binding activates one of its two mutually exclusive exons, leading to NMD; TBRG4 is regulated by cluster splicing of its two essential exons. Our results indicate that autoregulatory negative feedback loop of alternative splicing and NMD is a generic form of post-transcriptional control of gene expression.

bioinformatics↗