Anette Kalnapenkis
A5006101846- Genetic Associations and Epidemiology
- Genetic Mapping and Diversity in Plants and Animals
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Genetics and Neurodevelopmental Disorders
- Inflammasome and immune disorders
- Cognitive Abilities and Testing
- Autism Spectrum Disorder Research
- Epigenetics and DNA Methylation
- Health, Environment, Cognitive Aging
- Genetic and phenotypic traits in livestock
- RNA Research and Splicing
- COVID-19 Clinical Research Studies
- Galectins and Cancer Biology
- Gene expression and cancer classification
- Cancer Immunotherapy and Biomarkers
- Ovarian function and disorders
- Single-cell and spatial transcriptomics
- interferon and immune responses
- Genomics and Chromatin Dynamics
- Genetic Syndromes and Imprinting
- Birth, Development, and Health
- PARP inhibition in cancer therapy
- Genomic variations and chromosomal abnormalities
- Attention Deficit Hyperactivity Disorder
University of Tartu
2018-2024
University of Cambridge
2023
British Heart Foundation
2023
Summary While many disease-associated variants have been identified through genome-wide association studies, their downstream molecular consequences remain unclear. To identify these effects, we performed cis- and trans-expression quantitative trait locus (eQTL) analysis in blood from 31,684 individuals the eQTLGen Consortium. We observed that cis -eQTLs can be detected for 88% of studied genes, but they a different genetic architecture compared to variants, limiting our ability use pinpoint...
Circulating proteins have important functions in inflammation and a broad range of diseases. To identify genetic influences on inflammation-related proteins, we conducted genome-wide protein quantitative trait locus (pQTL) study 91 plasma measured using the Olink Target platform 14,824 participants. We identified 180 pQTLs (59 cis, 121 trans). Integration pQTL data with eQTL disease association studies provided insight into pathogenesis, implicating lymphotoxin-α multiple sclerosis. Using...
Abstract Genome-wide association studies (GWAS) have identified thousands of variants associated with complex traits, but their biological interpretation often remains unclear. Most these overlap expression QTLs, indicating potential involvement in regulation gene expression. Here, we propose a transcriptome-wide summary statistics-based Mendelian Randomization approach (TWMR) that uses multiple SNPs as instruments and traits exposures, simultaneously. Applied to 43 human phenotypes, it...
Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level datasets. The development of methods that can harness is valuable enable in broader settings enhance power due increased sample size. Thus, we develop a framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) adapts multiple polygenic risk score (PRS) estimate weights from conducts an omnibus TWAS. We show practical powerful tool by both...
The proteome holds great potential as an intermediate layer between the genome and phenome. Previous protein quantitative trait locus studies have focused mainly on describing effects of common genetic variations proteome. Here, we assessed impact rare well copy number variants (CNVs) 326 plasma proteins measured in up to 500 individuals. We identified 184 cis 94 trans signals for 157 traits, which were further fine-mapped credible sets 101 87 151 proteins. Rare variation contributed levels...
Abstract Genotype‐stratified variance of a quantitative trait could differ in the presence gene–gene or gene–environment interactions. Genetic markers associated with phenotypic are thus considered promising candidates for follow‐up interaction joint location‐scale analyses. However, as studies main effects, X‐chromosome is routinely excluded from “whole‐genome” scans due to analytical challenges. Specifically, males carry only one copy X‐chromosome, inherent sex‐genotype dependency bias...
Abstract We performed the largest genome-wide meta-analysis (GWAMA) (Max N=26,494) of levels 184 cardiovascular-related plasma protein to date and reported 592 independent loci (pQTL) associated with level at least one (1308 significant associations, median 6 per protein). estimated that only between 8-37% testable pQTL overlap established expression quantitative trait (eQTL) using multiple methods, while 132 out 1064 lead variants show evidence for transcription factor binding, found 75%...
Severe COVID-19 is characterised by immunopathology and epithelial injury. Proteomic studies have identified circulating proteins that are biomarkers of severe COVID-19, but cannot distinguish correlation from causation. To address this, we performed Mendelian randomisation (MR) to identify mediate COVID-19. Using protein quantitative trait loci (pQTL) data the SCALLOP consortium, involving meta-analysis up 26,494 individuals, genome-wide association Host Genetics Initiative, MR for 157...
Abstract Genotype-stratified variance of a quantitative trait could differ in the presence gene-gene or gene-environment interactions. Genetic markers associated with phenotypic are thus considered promising candidates for follow-up interaction joint location-scale analyses. However, as studies main effects, X-chromosome is routinely excluded from ‘whole-genome’ scans due to analytical challenges. Specifically, males carry only one copy X-chromosome, inherent sex-genotype dependency bias...
ABSTRACT Circulating proteins play key roles in inflammation and a broad range of diseases. To identify genetic influences on inflammation-related proteins, we conducted genome-wide protein quantitative trait locus (pQTL) study 91 plasma measured using the Olink Target platform 15,150 participants. We identified 180 pQTLs, which 50 were novel. Integration pQTL data with eQTL disease GWAS provided insights into pathogenesis, implicating lymphotoxin-alpha (LTA) multiple sclerosis. Using...
Abstract The proteome holds great potential as an intermediate layer between the genome and phenome. Previous protein quantitative trait locus studies have focused mainly on describing effects of common genetic variations proteome. Here, we assessed impact rare well copy number variants (CNVs) 326 plasma proteins measured in up to 500 individuals. We identified 184 cis 94 trans signals for 157 traits, which were further fine-mapped credible sets 101 87 151 proteins. Rare variation...