Mapping Of Variants Research Articles

Single cell variant to enhancer to gene map for coronary artery disease.

Although genome wide association studies (GWAS) in large populations have identified hundreds of variants associated with common diseases such as coronary artery disease (CAD), most disease-associated variants lie within non-coding regions of the genome, rendering it difficult to determine the downstream causal gene and cell type. Here, we performed paired single nucleus gene expression and chromatin accessibility profiling from 44 human coronary arteries. To link disease variants to molecular traits, we developed a meta-map of 88 samples and discovered 11,182 single-cell chromatin accessibility quantitative trait loci (caQTLs). Heritability enrichment analysis and disease variant mapping demonstrated that smooth muscle cells (SMCs) harbor the greatest genetic risk for CAD. To capture the continuum of SMC cell states in disease, we used dynamic single cell caQTL modeling for the first time in tissue to uncover QTLs whose effects are modified by cell state and expand our insight into genetic regulation of heterogenous cell populations. Notably, we identified a variant in the COL4A1 / COL4A2 CAD GWAS locus which becomes a caQTL as SMCs de-differentiate by changing a transcription factor binding site for EGR1/2. To unbiasedly prioritize functional candidate genes, we built a genome-wide single cell variant to enhancer to gene (scV2E2G) map for human CAD to link disease variants to causal genes in cell types. Using this approach, we found several hundred genes predicted to be linked to disease variants in different cell types. Next, we performed genome-wide Hi-C in 16 human coronary arteries to build tissue specific maps of chromatin conformation and link disease variants to integrated chromatin hubs and distal target genes. Using this approach, we show that rs4887091 within the ADAMTS7 CAD GWAS locus modulates function of a super chromatin interactome through a change in a CTCF binding site. Finally, we used CRISPR interference to validate a distal gene, AMOTL2 , liked to a CAD GWAS locus. Collectively we provide a disease-agnostic framework to translate human genetic findings to identify pathologic cell states and genes driving disease, producing a comprehensive scV2E2G map with genetic and tissue level convergence for future mechanistic and therapeutic studies.

Towards functional maps of non-coding variants in cancer.

Large scale cancer genomic studies in patients have unveiled millions of non-coding variants. While a handful have been shown to drive cancer development, the vast majority have unknown function. This review describes the challenges of functionally annotating non-coding cancer variants and understanding how they contribute to cancer. We summarize recently developed high-throughput technologies to address these challenges. Finally, we outline future prospects for non-coding cancer genetics to help catalyze personalized cancer therapy.

Optical genome mapping of structural variants in Parkinson’s disease-related induced pluripotent stem cells

BackgroundCertain structural variants (SVs) including large-scale genetic copy number variants, as well as copy number-neutral inversions and translocations may not all be resolved by chromosome karyotype studies. The identification of genetic risk factors for Parkinson’s disease (PD) has been primarily focused on the gene-disruptive single nucleotide variants. In contrast, larger SVs, which may significantly influence human phenotypes, have been largely underexplored. Optical genomic mapping (OGM) represents a novel approach that offers greater sensitivity and resolution for detecting SVs. In this study, we used induced pluripotent stem cell (iPSC) lines of patients with PD-linked SNCA and PRKN variants as a proof of concept to (i) show the detection of pathogenic SVs in PD with OGM and (ii) provide a comprehensive screening of genetic abnormalities in iPSCs.ResultsOGM detected SNCA gene triplication and duplication in patient-derived iPSC lines, which were not identified by long-read sequencing. Additionally, various exon deletions were confirmed by OGM in the PRKN gene of iPSCs, of which exon 3–5 and exon 2 deletions were unable to phase with conventional multiplex-ligation-dependent probe amplification. In terms of chromosomal abnormalities in iPSCs, no gene fusions, no aneuploidy but two balanced inter-chromosomal translocations were detected in one line that were absent in the parental fibroblasts and not identified by routine single nucleotide variant karyotyping.ConclusionsIn summary, OGM can detect pathogenic SVs in PD-linked genes as well as reveal genomic abnormalities for iPSCs that were not identified by other techniques, which is supportive for OGM’s future use in gene discovery and iPSC line screening.

536. TUMOR-INFORMED “LIQUID BIOPSY” FOR ESOPHAGEAL ADENOCARCINOMA FROM MATCHED CANCER ORGANOID CULTURE

Abstract Background The absence of recurrent mutations in esophageal adenocarcinoma (EAC) poses a challenge in detecting circulating tumor DNA (ctDNA) in plasma and may hinder the advancement of liquid biopsy methods. To address this, we cultured patient-derived EAC organoids (PDOs), speculating that they could serve as a guide for identifying ctDNA in the patient's blood samples. This approach aims to leverage organoids as a potential tool to overcome the complexity of identifying ctDNA in EAC, offering a promising avenue for refining liquid biopsy strategies in clinical practice. Methods PDOs were generated from EAC tumor tissue in Matrigel domes and expanded in suspension culture. To isolate mononucleosomes (147 bp), chromatin from PDOs was extracted and digested with micrococcal nuclease (MNase). Fragments larger than 147 bp were removed through size selection. MNase-sequencing was performed to generate a mutation map with preferential coverage of nucleosome-protected DNA for each sample. Matched whole genome sequencing of the tumor for each respective PDO sample was used as a control. Primers were designed for the identified mutations in nucleosome-protected DNA and used to amplify patient cfDNA for sequencing. Results DNA from five different PDOs were collected and MNase digested. MNase concentration and digestion time were optimized for each sample. MNase digestion produced mononucleosomes of approximately 147 bp for all samples. MNase-sequencing identified 24 mutations in peaks (mononucleosomes) in 24 genes, including known oncogenes. Among these were 16 missense, 2 frameshift, and 1 nonsense mutations, and 5 mutations in splice regions. To date, amplicons of expected size were detected by PCR for six genes using either total PDO DNA or normal cell-free DNA, confirming the detectability of these genes. PCR amplification using patient ctDNA and next-generation sequencing is ongoing. Conclusion These findings show that we are able to isolate and detect somatic mutations in nucleosomes from different PDOs, allowing us to generate a nucleosome SNV map for each sample. Preliminary data indicate these regions can be PCR amplified from normal cfDNA. Amplification and sequence verification of mutated regions from corresponding patient blood ctDNA is ongoing. The mapping of patient-specific variants will enable the development of targeted personalized PCR panels, aiding in recurrence prediction and enhancing drug screening accuracy. This advancement holds promise for early cancer detection and improving prognoses for individuals with EAC by addressing gaps in recurrence prediction.

3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity.

The prevalence of childhood obesity is increasing worldwide, along with the associated common comorbidities of type 2 diabetes and cardiovascular disease in later life. Motivated by evidence for a strong genetic component, our prior genome-wide association study (GWAS) efforts for childhood obesity revealed 19 independent signals for the trait; however, the mechanism of action of these loci remains to be elucidated. To molecularly characterize these childhood obesity loci we sought to determine the underlying causal variants and the corresponding effector genes within diverse cellular contexts. Integrating childhood obesity GWAS summary statistics with our existing 3D genomic datasets for 57 human cell types, consisting of high-resolution promoter-focused Capture-C/Hi-C, ATAC-seq, and RNA-seq, we applied stratified LD score regression and calculated the proportion of genome-wide SNP heritability attributable to cell type-specific features, revealing pancreatic alpha cell enrichment as the most statistically significant. Subsequent chromatin contact-based fine-mapping was carried out for genome-wide significant childhood obesity loci and their linkage disequilibrium proxies to implicate effector genes, yielded the most abundant number of candidate variants and target genes at the BDNF, ADCY3, TMEM18 and FTO loci in skeletal muscle myotubes and the pancreatic beta-cell line, EndoC-BH1. One novel implicated effector gene, ALKAL2 - an inflammation-responsive gene in nerve nociceptors - was observed at the key TMEM18 locus across multiple immune cell types. Interestingly, this observation was also supported through colocalization analysis using expression quantitative trait loci (eQTL) derived from the Genotype-Tissue Expression (GTEx) dataset, supporting an inflammatory and neurologic component to the pathogenesis of childhood obesity. Our comprehensive appraisal of 3D genomic datasets generated in a myriad of different cell types provides genomic insights into pediatric obesity pathogenesis.

Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome

Heparan sulfate (HS) is degraded in lysosome by a series of glycosidases. Before the glycosidases can act, the terminal glucosamine of HS must be acetylated by the integral lysosomal membrane enzyme heparan-α-glucosaminide N-acetyltransferase (HGSNAT). Mutations of HGSNAT cause HS accumulation and consequently mucopolysaccharidosis IIIC, a devastating lysosomal storage disease characterized by progressive neurological deterioration and early death where no treatment is available. HGSNAT catalyzes a unique transmembrane acetylation reaction where the acetyl group of cytosolic acetyl-CoA is transported across the lysosomal membrane and attached to HS in one reaction. However, the reaction mechanism remains elusive. Here we report six cryo-EM structures of HGSNAT along the reaction pathway. These structures reveal a dimer arrangement and a unique structural fold, which enables the elucidation of the reaction mechanism. We find that a central pore within each monomer traverses the membrane and controls access of cytosolic acetyl-CoA to the active site at its luminal mouth where glucosamine binds. A histidine-aspartic acid catalytic dyad catalyzes the transfer reaction via a ternary complex mechanism. Furthermore, the structures allow the mapping of disease-causing variants and reveal their potential impact on the function, thus creating a framework to guide structure-based drug discovery efforts.

High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology

BackgroundKCNE1 encodes a 129-residue cardiac potassium channel (IKs) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical consequences and thus limited clinical utility.MethodsIn this study, we leveraged the power of variant effect mapping, which couples saturation mutagenesis with high-throughput sequencing, to ascertain the function of thousands of protein-coding KCNE1 variants.ResultsWe comprehensively assayed KCNE1 variant cell surface expression (2554/2709 possible single-amino-acid variants) and function (2534 variants). Our study identified 470 loss- or partial loss-of-surface expression and 574 loss- or partial loss-of-function variants. Of the 574 loss- or partial loss-of-function variants, 152 (26.5%) had reduced cell surface expression, indicating that most functionally deleterious variants affect channel gating. Nonsense variants at residues 56–104 generally had WT-like trafficking scores but decreased functional scores, indicating that the latter half of the protein is dispensable for protein trafficking but essential for channel function. 22 of the 30 KCNE1 residues (73%) highly intolerant of variation (with > 70% loss-of-function variants) were in predicted close contact with binding partners KCNQ1 or calmodulin. Our functional assay data were consistent with gold standard electrophysiological data (ρ = − 0.64), population and patient cohorts (32/38 presumed benign or pathogenic variants with consistent scores), and computational predictors (ρ = − 0.62). Our data provide moderate-strength evidence for the American College of Medical Genetics/Association of Molecular Pathology functional criteria for benign and pathogenic variants.ConclusionsComprehensive variant effect maps of KCNE1 can both provide insight into IKs channel biology and help reclassify variants of uncertain significance.

3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures.

The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional context to genetic coding variants. However, mapping genes to proteins is a tedious and error-prone task due to inconsistencies in data formats. Over the past two decades, numerous tools and databases have been developed to automatically map annotated positions and variants to protein structures. However, most of these tools are web-based and not well-suited for large-scale genomic data analysis. To address this issue, we introduce 3Dmapper, a stand-alone command-line tool developed in Python and R. It systematically maps annotated protein positions and variants to protein structures, providing a solution that is both efficient and reliable. https://github.com/vicruiser/3Dmapper.

Applying data science methodologies with artificial intelligence variant reinterpretation to map and estimate genetic disorder prevalence utilizing clinical data.

Data science methodologies can be utilized to ascertain and analyze clinical genetic data that is often unstructured and rarely used outside of patient encounters. Genetic variants from all genetic testing resulting to a large pediatric healthcare system for a 5-year period were obtained and reinterpreted utilizing the previously validated Franklin© Artificial Intelligence (AI). Using PowerBI©, the data were further matched to patients in the electronic healthcare record to associate with demographic data to generate a variant data table and mapped by ZIP codes. Three thousand and sixty-five variants were identified and 98% were matched to patients with geographic data. Franklin© changed the interpretation for 24% of variants. One hundred and fifty-six clinically actionable variant reinterpretations were made. A total of 739 Mendelian genetic disorders were identified with disorder prevalence estimation. Mapping of variants demonstrated hot-spots for pathogenic genetic variation such as PEX6-associated Zellweger Spectrum Disorder. Seven patients were identified with Bardet-Biedl syndrome and seven patients with Rett syndrome amenable to newly FDA-approved therapeutics. Utilizing readily available software we developed a database and Exploratory Data Analysis (EDA) methodology enabling us to systematically reinterpret variants, estimate variant prevalence, identify conditions amenable to new treatments, and localize geographies enriched for pathogenic variants.

Evaluation of anatomical variants and pathological findings of the maxillary sinus prior to sinus floor elevation: A Cone Beam CT retrospective study in 660 patients.

Maxillary sinuses may present a wide spectrum of anatomical variations and pathological lesions whose recognition is mandatory for the clinician, especially prior to any surgical intervention in the area, such as in cases of sinus floor elevation. The goal of this study was the evaluation, mapping and prevalence of sinus anatomical variants and pathoses in Cone Beam Computed Tomography (CBCT) scans of dental patients. 660 CBCT examinations of adult patients involving both sinuses were obtained (between 2017 and 2023) and analyzed. The following anatomic variants and pathologic findings were evaluated: antral septa (AS), posterior superior alveolar artery (PSAA), sinus hypoplasia, sinusitis, odontogenic cysts, retention cysts, antroliths, and various less common lesions (e.g.: benign fibro-osseous dysplastic lesions, neoplasms etc.). Investigation of the association of the findings with patients' age and gender was performed using the Chi-square test (X2), Fisher's exact test, t-test, and ANOVA (P<0.05). Differences in prevalence between findings, based on their location (right and/or left sinus), were investigated using z-test and t-test. AS were found in 38.6%, and PSAA was identifiable in 90.2% (mean distance from the sinus floor=6.44 mm) of the patients respectively. 3% of patients had hypoplasia, 15.6% sinusitis, 2.7% odontogenic cysts, 16.1% retention cysts, 8.6% antroliths, and 1.7% uncommon lesions (e.g. malignant neoplasms and fibrous dysplasia). A statistically significant association was found between gender and PSAA diameter, PSAA distance from the sinus floor, hypoplasia, sinusitis, and retention cysts, as well as a statistically significant association between age and PSSA diameter and sinusitis. The prevalence of various anatomical variants and pathologic findings of the maxillary sinus did not differ based on their location. However, some of these findings appear to be related to either gender or age. CBCT is a valuable diagnostic tool to identify various anatomical variants and pathological findings of the maxillary sinus. Key words:Sinus, anatomy, pathology, CBCT.

Expanded utility of the R package, qgg, with applications within genomic medicine.

Here, we present an expanded utility of the R package qgg for genetic analyses of complex traits and diseases. One of the major updates of the package is, that it now includes Bayesian linear regression modeling procedures, which provide a unified framework for mapping of genetic variants, estimation of heritability and genomic prediction from either individual level data or from genome-wide association study summary data. With this release, the qgg package now provides a wealth of the commonly used methods in analysis of complex traits and diseases, without the need to switch between software and data formats. The methodologies are implemented in the publicly available R software package, qgg, using fast and memory efficient algorithms in C++ and is available on CRAN or as a developer version at our GitHub page (https://github.com/psoerensen/qgg). Notes on the implemented statistical genetic models, tutorials and example scripts are available at our GitHub page https://psoerensen.github.io/qgg/.

Mapping of Anatomic Variants of the Proximal Vertebral Artery in Relation to Embryology.

Variations in the origins and courses of the vertebral arteries are relatively rare but may be clinically meaningful. We hypothesize a relationship between variant origins of the vertebral arteries and their levels of entry to the foramina transversaria. In this retrospective study of CT angiograms, we document the frequency and types of vertebral artery variants, correlating origins with levels of entry to the foramina transversaria. Vertebral artery variants were observed in 18.7% of a sample of 460 CT angiograms of the neck. Right-sided variants were less common than left (44.2% versus 68.6%, with 12.8% bilateral) and more common than previously thought. The most common variant on both sides was a variant origin proximal to the normal vertebral artery origin and entry at C5. Most right vertebral arteries originating within 2 cm of the origin of the right subclavian artery and left vertebral arteries originating between the left common carotid and subclavian arteries were "high-entry" variants. Most "low-entry" variants, entering at C7, took origin from the arch just distal to the left subclavian artery or at a common origin with the costocervical trunk. Multiple origins or accessory vertebral arteries were also described, and each moiety followed the same rules described for single origins. A map of vertebral artery origins mirrored the map of aortic arch embryology. Vertebral artery variants follow certain well-defined patterns that correlate with the embryology of the aortic arch and great vessels.

Genome-wide mapping of regulatory variants for temperature- and salinity-adaptive genes reveals genetic basis of genotype-by-environment interaction in Crassostrea ariakensis

Regulatory variants in gene expression serve as bridges linking genetic variation and phenotypic plasticity. Environmental conditions typically influence the effects of regulatory variants on phenotypic plasticity; however, such genotype-by-environment interactions (G × E) are poorly understood. This study aimed to investigate the genetic basis of G × E in estuarine oyster (Crassostrea ariakensis), which is an important model animal for studying environmental adaption owing to its high plasticity and large intraspecific divergence. Genome-wide mapping of expression quantitative trait loci (eQTLs) for 23 environmental adaptive genes was performed for 256 estuarine oysters. We identified 1194 eQTL single nucleotide polymorphisms (eSNPs), including 433 cis-eSNPs in four genes and 722 trans-eSNPs in eight genes. The expression variation explanation of cis-eSNPs (9.95%) was significantly higher than that of trans-eSNPs (9.15%). We specifically showed cis- and trans-eSNPs with high linkage disequilibrium (LD) for Traf7, Slc6a5, Ggt, and Dap3. For example, we identified a cis-regulatory LD block containing 68 cis-eSNP and a trans-regulatory LD block, including 20 trans-eSNPs in Traf7. A high proportion (85%) of 40 vital eSNPs exhibited significant G × E effects. We identified crossing and nonparallel interactions of G × E, with the tag cis-eSNPs of Baat and Slc6a5 as representatives. Our results indicated that cis-eQTLs are highly conserved. This study provides insights into the understanding of adaptive evolutionary mechanisms and phenotypic response prediction to variable environments, as well as the genetic improvement for superior adaptive traits for genetic resource conservation and aquaculture.

Reconstructing the landscape of gut microbial species across 29,000 diverse individuals.

The human gut microbiome has been linked to health and disease. Investigation of the human microbiome has largely employed 16S amplicon sequencing, with limited ability to distinguish microbes at the species level. Herein, we describe the development of Reference-based Exact Mapping (RExMap) of microbial amplicon variants that enables mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures ∼75% of microbial species identified by whole-genome shotgun sequencing, despite hundreds-fold less sequencing depth. RExMap re-analysis of existing 16S data from 29,349 individuals across 16regions from around the world reveals a detailed landscape of gut microbial species across populations and geography. Moreover, RExMap identifies a core set of fifteen gut microbes shared by humans. Core microbes are established soon after birth and closely associate with BMI across multiple independent studies. RExMap and the human microbiome dataset are presented as resources with which to explore the role of the human microbiome.

Биоклиматические варианты оробиома Северо-Восточного Забайкалья

Introduction. The spatial structure of the biota at the regional level of its organization is most closely associated with the climate, expressed primarily through bioclimatic indicators. In the geography of the botanical diversity of Northeastern Transbaikalia, which is characterized by a complex organization of vegetation cover, the influence of a number of important gradients of climatic conditions is expressed. The identification of these gradients was the purpose of this research. Methods and materials of the research. The methodological basis of the research was the ecosystem approach to the identification and evaluation of phytocenotic diversity associated with ecological and geographical factors that determine its spatial differentiation. The geographic and genetic classification of plant communities was used to identify the typological diversity of vegetation. The climatic characteristics of the Northeastern Transbaikalia was given on the basis of key bioclimatic indicators (global model BioClim). The bioclimatic substantiation of the spatial structure was carried out taking into account the principles of identifying the diversity of ecosystems at the regional level. Mapping of the bioclimatic variants of the orobiome was compiled using the clustering of units according to the average values of parameters by the k-means method. Research results and discussion. A joint analysis of vegetation and climate made it possible, for the first time for Northeastern Transbaikalia, to determine the internal structure of ecosystem diversity that develops in the mountains within the framework of an orobiome. It also allowed mapping the spatial organization of ecosystems at the regional level on a climate basis. Using the cluster analysis of climatopes of the main vegetation formations, subdivisions of the orobiome (bioclimatic variants) are proposed. Two variants of the Ist order are expressed through the structure of the vegetation cover of mountain systems: the relatively low Patom highland in the north, and more massive ridges of the strongly dissected North Baikal and Stanovoy highlands in the south. Variants of the IInd order, differing in the degree of continentality and moisture conditions, have specificity in the altitudinal belts and sub-belts of vegetation. Diversity within belts and sub-belts, expressed through the typological diversity of vegetation at the level of formations, classes, and groups of associations, is marked by climatic differences in bioclimatic variants of the IIIrd order. The diversity of climatic conditions that determine the phytocoenotic diversity of Northeastern Transbaikalia is characterized through integral bioclimatic types of orobiome, determined by temperature and moisture supply. Three ombroclimatic types were distinguished by continentality conditions. The influence of the complex orographic structure of a vast mountainous territory, as well as zonal and sectoral patterns in changing climatic conditions, is characterized in their change from continental to extracontinental in according to the degree of climate continentality. The same factors determine the identification of three thermoclimatic types, which are associated with the distinguished altitudinal vegetation belts (mountain tundra, subalpine, mountain taiga). The temperate cold type is expressed in the intermountain depressions and low mountains of the Patom highlands, the cold type is associated with the middle mountains and the lower part of the high mountains (mountain taiga and subalpine belts), and the extra cold type is distinguished in the high mountains of the most massive ridges – Kodar and Kalar. Conclusion. Quantitative interpretation of the climatic conditions of the bioclimatic variants of the orobiome made it possible to give an integral evaluation of the climatic conditionality of the development of basic vegetation formations, the altitudinal belt divisions, and the altitudinal spectra of vegetation in general. The resulting basis can be used for the sustainable development of the region in connection with economic activities in areas adjacent to the Baikal-Amur Railway, for monitoring and forecasting changes in vegetation and ecosystems in general due to climate change and intensification of economic activities in the region.

Exome-wide analysis identify multiple variations in olfactory receptor genes (OR12D2 and OR5V1) associated with autism spectrum disorder in Saudi females.

Autism Spectrum Disorder (ASD) is a multifactorial, neurodevelopmental disorder, characterized by deficits in communication, restricted and repetitive behaviors. ASD is highly heritable in Saudi Arabia; indecencies of affected individuals are increasing. To identify the most significant genes and SNPs associated with the increased risk of ASD in Saudi females to give an insight for early diagnosis. Pilot case-control study mostly emphasized on the significant SNPs and haplotypes contributing to Saudi females with ASD patients (n = 22) compared to controls (n = 51) without ASD. With the use of allelic association analysis tools, 243,345 SNPs were studied systematically and classified according to their significant association. The significant SNPs and their genes were selected for further investigation for mapping of ASD candidate causal variants and functional impact. In females, five risk SNPs at p ≤ 2.32 × 10-05 was identified in association with autism. The most significant exonic variants at chromosome 6p22.1 with olfactory receptor genes (OR12D2 and OR5V1) clustered with high linkage disequilibrium through haplotyping analysis. Comparison between highly associated genes (56 genes) of male and female autistic patients with female autistic samples revealed that 39 genes are unique biomarkers for Saudi females with ASD. Multiple variations in olfactory receptor genes (OR5V1 and OR12D2) and single variations on SPHK1, PLCL2, AKAP9 and LOC107984893 genes are contributing to ASD in females of Arab origin. Accumulation of these multiple predisposed coding SNPs can increase the possibility of developing ASD in Saudi females.

P898 Uncovering of tissue-associated risk factors that lead to different genetic risk profiles across Inflammatory Bowel Disease patients

Abstract Background Polygenic risk scores (PRSs) are emerging as a tool of choice to summarize the risk of disease in each individual. The calculation of PRSs is based on genetic variants and effect sizes obtained from large studies using many different cohorts of patients. In inflammatory bowel disease (IBD), GWAS meta-analysis based on over 75.000 IBD patients from different multi-ethnic cohorts has discovered around 300 independent associated variants. This information can be used to estimate genetic risk and detect individuals with several higher odds of developing the disease during their lifetime. However, PRSs usually do not incorporate functional information about causal variants, and the potential for heterogeneity in effect sizes among subgroups of individuals is disregarded entirely. Hence, PRSs might be ill-suited to capture subcomponents of genetic risk that may account for key differences among specific etiological profiles of patients. Fine mapping of GWAS causal variants show an enrichment in variants associated with changes in gene expression in specific tissues, suggesting that risk of complex diseases is led by an accumulation of variants that change the transcriptome towards a pathogenic profile. To explore the biological nature of IBD risk we propose a tissue transcriptional risk (t-TRS) score Methods We perform Transcription Wide Association studies (TWAS) based on gene expression prediction models in nine IBD relevant tissues and a meta-analysis of European IBD GWAS. We next estimated the t-TRS of people from UK biobank and compared its prediction performance against PRS measuring the area under the curve (AUC) Results We performed nine TWAS studies and obtained 636 genes that are genome wide significant in at least one tissue. Although eQTL weights are shared across tissues, we observe a high number of tissue specific signals, specifically in terminal ileum and lymphocytes. Pathway enrichment analysis on the 600-gene set showed enrichment of immune functions like “Signaling by interleukins” and “Antigen presentation”. We also show the predicting value of t-TRS is better than the PRS in all tissues. In addition, clustering of individuals according with t-TRS yield 3 subgroups of patients Conclusion Functionally informed genetic predictors allow not only to better stratify patients, but also to discover which are the biological pathways that accumulate risk variants in subgroups of IBD patients

A fine mapping of single nucleotide variants and haplotype analysis of IL13 gene in patients with Leishmania guyanensis-cutaneous leishmaniasis and plasma cytokines IL-4, IL-5, and IL-13.

Leishmaniasis continues to pose a substantial health burden in 97 countries worldwide. The progression and outcome of Leishmania infection are influenced by various factors, including the cytokine milieu, the skin microbiota at the infection site, the specific Leishmania species involved, the genetic background of the host, and the parasite load. In endemic regions to leishmaniasis, only a fraction of individuals infected actually develops the disease. Overexpression of IL-13 in naturally resistant C57BL/6 mice renders them susceptible to L. major infection. Haplotypes constructed from several single nucleotide variant (SNV) along a chromosome fragment may provide insight into any SNV near the fragment that may be genuinely associated with a phenotype in genetic association studies. We investigated nine SNVs (SNV1rs1881457A>C, SNV2rs1295687C>G, SNV3rs2069744C>T, SNV4rs2069747C>T, SNV5rs20541A>G, SNV6rs1295685A>G, SNV7rs848A>C, SNV8rs2069750G >C, and SNV9rs847T>C) spanning the entire IL13 gene in patients with L. guyanensis cutaneous leishmaniasis (Lg-CL). Our analysis did not reveal any significant association between the SNVs and susceptibility/protection against Lg-CL development. However, haplotype analysis, excluding SNV4rs2069747 and SNV8rs2069750 due to low minor allele frequency, revealed that carriers of the haplotype CCCTAAC had a 93% reduced likelihood developing Lg-CL. Similarly, the haplotypes ACCCGCT (ORadj=0.02 [95% CI 0.00-0.07]; p-value, 6.0×10-19) and AGCTAAC (ORadj=0.00[95% CI 0.00-0.00]; p-value 2.7×10-12) appeared to provide protection against the development of Lg-CL. Conversely, carriers of haplotype ACCTGCC have 190% increased likelihood of developing Lg-CL (ORadj=2.9 [95%CI 1.68-5.2]; p-value, 2.5×10-6). Similarly, haplotype ACCCAAT (ORadj=2.7 [95%CI 1.5-4.7]; p-value, 3.2×10-5) and haplotype AGCCGCC are associated with susceptibility to the development of Lg-CL (ORadj=1.7[95%CI 1.04-2.8]; p-value, 0.01). In our investigation, we also found a correlation between the genotypes of rs2069744, rs20541, rs1295685, rs847, and rs848 and plasma IL-5 levels among Lg-Cl patients. Furthermore, rs20541 showed a correlation with plasma IL-13 levels among Lg-Cl patients, while rs2069744 and rs848 showed a correlation with plasma IL-4 levels among the same group. Overall, our study identifies three haplotypes of IL13 associated with resistance to disease development and three haplotypes linked to susceptibility. These findings suggest the possibility of a variant outside the gene region that may contribute, in conjunction with other genes, to differences in susceptibility and partially to the pathology.

Integrated genomic, phenomic, functional and structural mapping of variants in thyroid hormone transporter MCT8

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)

RNA editing underlies genetic risk of common inflammatory diseases.

A major challenge in human genetics is to identify the molecular mechanisms of trait-associated and disease-associated variants. To achieve this, quantitative trait locus (QTL) mapping of genetic variants with intermediate molecular phenotypes such as gene expression and splicing have been widely adopted1,2. However, despite successes, the molecular basis for a considerable fraction of trait-associated and disease-associated variants remains unclear3,4. Here we show that ADAR-mediated adenosine-to-inosine RNA editing, a post-transcriptional event vital for suppressing cellular double-stranded RNA (dsRNA)-mediated innate immune interferon responses5-11, is an important potential mechanism underlying genetic variants associated with common inflammatory diseases. We identified and characterized 30,319 cis-RNA editing QTLs (edQTLs) across 49 human tissues. These edQTLs were significantly enriched in genome-wide association study signals for autoimmune and immune-mediated diseases. Colocalization analysis of edQTLs with disease risk loci further pinpointed key, putatively immunogenic dsRNAs formed by expected inverted repeat Alu elements as well as unexpected, highly over-represented cis-natural antisense transcripts. Furthermore, inflammatory disease risk variants, in aggregate, were associated with reduced editing of nearby dsRNAs and induced interferon responses in inflammatory diseases. This unique directional effect agrees with the established mechanism that lack of RNA editing by ADAR1 leads to the specific activation of the dsRNA sensor MDA5 and subsequent interferon responses and inflammation7-9. Our findings implicate cellular dsRNA editing and sensing as a previously underappreciated mechanism of common inflammatory diseases.