haploR: an R package for querying web-based annotation tools

Zhbannikov, Ilya Y.; Arbeev, Konstantin G.; Ukraintseva, Svetlana V.; Yashin, Anatoliy I.

doi:10.12688/f1000research.10742.2

Cited by 27 publications

(22 citation statements)

References 4 publications

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“…We used HaploReg v4 48 to construct two data sets including information for GWAS SNPs (index SNPs) and SNPs in high LD with the index SNPs. This information was obtained via haploR package 49 . LD SNPs were selected based on a threshold r 2 > 0.8 and were matched by population with index SNPs.…”

Section: Methodsmentioning

confidence: 99%

Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits

Salnikova

Khadzhieva

Kolobkov

et al. 2020

Sci Rep

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Dysregulation in cytokine production has been linked to the pathogenesis of various immune-mediated traits, in which genetic variability contributes to the etiopathogenesis. GWA studies have identified many genetic variants in or near cytokine genes, nonetheless, the translation of these findings into knowledge of functional determinants of complex traits remains a fundamental challenge. In this study we aimed at collection, analysis and interpretation of data on cytokines focused on their tissue-specific expression, eQTLs and GWAS traits. Using GO annotations, we generated a list of 314 cytokines and analyzed them with the GTEx resource. Cytokines were highly tissue-specific, 82.3% of cytokines had Tau expression metrics ≥ 0.8. In total, 3077 associations for 1760 unique SNPs in or near 244 cytokines were mapped in the NHGRI-EBI GWAS Catalog. According to the Experimental Factor Ontology resource, the largest numbers of disease associations were related to ‘Inflammatory disease’, ‘Immune system disease’ and ‘Asthma’. The GTEx-based analysis revealed that among GWAS SNPs, 1142 SNPs had eQTL effects and influenced expression levels of 999 eGenes, among them 178 cytokines. Several types of enrichment analysis showed that it was cytokines expression variability that fundamentally contributed to the molecular origins of considered immune-mediated conditions.

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Section: Methodsmentioning

confidence: 99%

Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits

Salnikova

Khadzhieva

Kolobkov

et al. 2020

Sci Rep

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“…The details of post-GWAS analyses including functional annotation, prioritization, and interpretation of GWAS results based on functional mapping are included in Additional file 2 [33][34][35][36][37][38][39][40][41].…”

Section: Post-gwas Analyses and Data Visualizationmentioning

confidence: 99%

GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network

Namjou

Lingren

Huang

et al. 2019

BMC Med

126

129

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Background: Non-alcoholic fatty liver disease (NAFLD) is a common chronic liver illness with a genetically heterogeneous background that can be accompanied by considerable morbidity and attendant health care costs. The pathogenesis and progression of NAFLD is complex with many unanswered questions. We conducted genome-wide association studies (GWASs) using both adult and pediatric participants from the Electronic Medical Records and Genomics (eMERGE) Network to identify novel genetic contributors to this condition. Methods: First, a natural language processing (NLP) algorithm was developed, tested, and deployed at each site to identify 1106 NAFLD cases and 8571 controls and histological data from liver tissue in 235 available participants. These include 1242 pediatric participants (396 cases, 846 controls). The algorithm included billing codes, text queries, laboratory values, and medication records. Next, GWASs were performed on NAFLD cases and controls and case-only analyses using histologic scores and liver function tests adjusting for age, sex, site, ancestry, PC, and body mass index (BMI). Results: Consistent with previous results, a robust association was detected for the PNPLA3 gene cluster in participants with European ancestry. At the PNPLA3-SAMM50 region, three SNPs, rs738409, rs738408, and rs3747207, showed strongest association (best SNP rs738409 p = 1.70 × 10 − 20). This effect was consistent in both pediatric (p = 9.92 × 10 − 6) and adult (p = 9.73 × 10 − 15) cohorts. Additionally, this variant was also associated with disease severity and NAFLD Activity Score (NAS) (p = 3.94 × 10 − 8 , beta = 0.85). PheWAS analysis link this locus to a spectrum of liver diseases beyond NAFLD with a novel negative correlation with gout (p = 1.09 × 10 − 4). We also identified novel loci for NAFLD disease severity, including one novel locus for NAS score near IL17RA (rs5748926, p = 3.80 × 10 − 8), and another near ZFP90-CDH1 for fibrosis (rs698718, p = 2.74 × 10 − 11). Post-GWAS and gene-based analyses identified more than 300 genes that were used for functional and pathway enrichment analyses.

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“…PolyFun, PAINTOR+). API access to a large compendium of genome-wide annotations and epigenomic data is provided, including: tissue and/or cell type/line-specific chromatin marks from Roadmap (Bernstein et al, 2010;Satterlee et al, 2019), ENCODE (Jou et al, 2019), genic annotations through biomaRt (Durinck et al, 2009),HaploReg (Zhbannikov et al, 2017;Ward and Kellis, 2012), cell-type-specific epigenomic datasets (Nott et al, 2019;Corces et al), and hundreds of additional annotations through the R package XGR (http://xgr.r-forge.r-project.org/) (Fang et al, 2016). catalogueR, another R package developed by our group, provides rapid API access to full summary statistics from 110 uniformly reprocessed QTL datasets (across 20 studies) with parallelized Tabix queries.…”

Section: Genome-wide Annotationsmentioning

confidence: 99%

echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline

Schilder

Humphrey

Raj

2020

Preprint

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echolocatoR integrates a diverse suite of statistical and functional fine-mapping tools in order to identify, test enrichment in, and visualize high-confidence causal consensus variants in any phenotype. It requires minimal input from users (a summary statistics file), can be run in a single R function, and provides extensive access to relevant datasets (e.g. reference linkage disequilibrium (LD) panels, quantitative trait loci (QTL) datasets, genome-wide annotations, cell type-specific epigenomics, thereby enabling rapid, robust and scalable end-to-end fine-mapping investigations.

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haploR: an R package for querying web-based annotation tools

Cited by 27 publications

References 4 publications

Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits

Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits

GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network

echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline

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