Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1051104 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27176476_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 1 of 1 |
Similar Datasets
Project description:Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase and decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression
2023-11-06 | GSE246139 | GEO
Project description:Multiplexed Assays of Variant Effects (MAVE) of PALB2 single nucleotide variants in exon 10.
| PRJNA1073543 | ENA
Project description:satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect
| PRJNA828159 | ENA
Project description:Inherited variants in the LDL receptor (LDLR) gene are the most common cause of familial hypercholesterolemia (FH), significantly increasing coronary artery disease risk. Early identification of pathogenic LDLR variants enables prompt intervention with lipid-lowering therapies; however, most LDLR variants observed in the population have uncertain or absent clinical classifications, limiting the clinical utility of genetic testing for definitive FH diagnosis, cascade testing of at-risk relatives, and timely lipid-lowering intervention. We developed an innovative, activity-normalized prime editing screening pipeline to measure the impact of 5,184 LDLR coding variants on LDL-cholesterol (LDL-C) uptake. Through pairing a genotypic outcome reporter with every prime editing guide RNA (pegRNA), we adjust phenotypic measurements to account for variable editing efficiency. Further, we use a statistical estimation approach that leverages measurements for all missense variants at a given position to denoise the resulting scores. We show that prime editing-mediated reporter editing correlates with endogenous variant installation frequency, allowing activity normalization to improve imputation of LDLR variant effect. Our optimized prime editing assay identifies a broad, continuous spectrum of variant functional effects. We achieve robust separation of pathogenic vs. benign ClinVar variants and concordance between experimentally derived functional scores and LDL-C levels measured in UK Biobank participants. Further, we calibrate the strength of this functional evidence to align with the ACMG/AMP variant interpretation guidelines. By integrating additional sources of evidence, a majority of currently unclassified rare LDLR variants appear to meet computational evidence thresholds for reclassification and can be prioritized for expert review. We use the broad coverage of this screen to gain insight into how apolipoproteins bind to LDLR. In particular, we identify and characterize rare LDLR variants that enhance LDL-C uptake through increased interaction with apolipoprotein B. Finally, we compare prime editing-based functional scores with those derived from recent base editing and cDNA-based LDLR variant screens, and find that all approaches show robust correlation with clinically observed LDL-C levels and computational scores, while prime editing identifies splice-altering coding variants that are not modeled by cDNA screening. Altogether, our approach demonstrates the power of prime editing to significantly improve understanding of how variants in LDLR impact function and contribute to FH.
2026-04-30 | GSE329001 | GEO
Project description:Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression
| PRJNA1031631 | ENA
Project description:Multiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal disease mechanisms. To date, MAVEs have focussed on a single mutation type - amino acid (AA) substitutions - despite the diversity of coding variants that cause disease. Here we use Deep Indel Mutagenesis (DIM) to generate the first comprehensive atlas of diverse variant effects for a disease protein, amyloid beta (Aß) that aggregates in Alzheimer’s disease (AD) and is mutated in familial AD (fAD). The atlas identifies known fAD variants and many mutations beyond substitutions that accelerate Aß aggregation. Truncations, substitutions, insertions, single- and multi-AA deletions differ in their propensity to enhance or impair aggregation, but likely pathogenic variants from all classes are strongly enriched in the polar N-terminus of Aß. This first comparative atlas for any disease gene highlights the importance of including diverse mutation types in MAVEs and provides important mechanistic insights into amyloid nucleation.
2022-10-27 | GSE193837 | GEO
Project description:Delineating functionally normal variants from functionally abnormal variants in tumor suppressor proteins is critical for cancer surveillance, prognosis, and treatment options. BRCA1 is a protein that has many variants of uncertain significance which are not yet classified as functionally normal or abnormal. In vitro functional assays can be used to identify the functional impact of a variant when the variant has not yet been categorized through clinical observation. Here we employ a homology-directed repair (HDR) reporter assay to evaluate over 300 missense and nonsense BRCA1 variants between amino acid residues 1280 and 1576, which encompasses the coiled-coil and serine cluster domains. Functionally abnormal variants tended to cluster in residues known to interact with PALB2, which is critical for homology-directed repair. Multiplexed results were confirmed by singleton assay and by ClinVar database variant interpretations. Comparison of multiplexed results to designated benign or likely benign or pathogenic or likely pathogenic variants in the ClinVar database yielded 100% specificity and 100% sensitivity of the multiplexed assay. Clinicians can reference the results of this functional assay for help in guiding cancer treatment and surveillance options. These results are the first to evaluate this domain of BRCA1 using a multiplexed approach and indicate the importance of this domain in the DNA repair process.
2023-10-13 | GSE237142 | GEO
Project description:Despite widespread advances in DNA sequencing in the past decade, the functional consequences of most rare genetic variants remain poorly understood, severely limiting our ability to connect variants to their consequences on protein function, identify biochemical mechanisms by which variation causes disease, and interpret variant pathogenicity. Multiplexed Assays of Variant Effect (MAVEs), which can measure the function of tens of thousands variants, are beginning to address this problem. However, existing MAVEs cannot be applied to the approximately 10% of human genes encoding secreted proteins, about a quarter of which are associated with disease. We developed a flexible and scalable human cell surface display method, Multiplexed Surface Tethering of Extracellular Proteins (MultiSTEP), that can simultaneously measure the functional effects of tens of thousands of variants in secreted proteins. We used MultiSTEP to study the consequences of missense variation in coagulation factor IX (FIX), a vitamin K-dependent plasma serine protease where variation can cause FIX deficiency and the bleeding disorder hemophilia B. We used a panel of antibodies to detect FIX secretion or FIX post-translational modification, measuring a total of 45,024 effects for 9,007 variants. 43.8% of all possible F9 missense variants impact FIX secretion, post-translational modification or both. We also identify new signals of functional constraint on secretion including within the signal peptide, folded domains, and for nearly all variants that caused gain or loss of cysteine. FIX secretion scores correlate strongly with FIX levels in patient plasma and also reveal that most F9 missense variants causing severe hemophilia do so by profoundly impacting secretion. We integrate the secretion and post-translational modification data to develop a F9 variant classifier that can identify loss of function variants with high specificity. We use the resulting classifications to reinterpret and upgrade 62 of 97 F9 variants of uncertain significance (VUS) in the MyLifeOurFuture hemophilia genotyping project to likely pathogenic. Lastly, we show that MultiSTEP can be applied to a wide variety of secreted proteins, ranging from small signaling proteins like insulin to large proteins like factor VIII. Thus, we establish a multiplexed, multimodal, and generalizable method for systematically assessing variant effects for secreted proteins at scale, paving the way for improved understanding of biochemical mechanisms of disease and clinical variant interpretation.
2025-01-14 | GSE242805 | GEO
Project description:To validate a high-throughput screening data in human cells using Multiplexed Assays for Variant Effects (MAVE), we performed a high-throughput deep mutational scanning of single nucleotide changes in exon 10 encoding p.G1000 to p.I1037 of the WD40 domain of PALB2 using a cell survival assay in haploid human HAP1 cells. We obtained MAVE scores for 276 single-nucleotide variants, leading to 9 nonsense and 68 synonymous changes, as well as 199 amino acid substitutions. Both variant groups showed an asymmetric distribution that is skewed towards low MAVE scores of nonsense and damaging variants, respectively. These MAVE data included scores for 218 unique single-nucleotide variants, leading to 9 nonsense changes and 209 amino acid substitutions. We observed a good and significant correlation between the outcomes from the MAVE and high-throughput screens (n=179, r=-0,6439, p<0.0001), indicating concordance between the outcomes of high-throughput analysis of PALB2 variants in human and mouse cells.
2024-02-08 | GSE255117 | GEO