Disentangling effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex trait loci
نویسندگان
چکیده
1) Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA. 2) Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA. 3) Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. 4) Current address: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK. 5) Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138, USA. 6) Harvard-MIT Division of Health Sciences and Technology, Boston, MA USA 7) Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA. 8) Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA and Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA. 9) Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK.
منابع مشابه
Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci.
Identifying genomic annotations that differentiate causal from trait-associated variants is essential to fine mapping disease loci. Although many studies have identified non-coding functional annotations that overlap disease-associated variants, these annotations often colocalize, complicating the ability to use these annotations for fine mapping causal variation. We developed a statistical app...
متن کاملDiscovering DNA motifs and genomic variants associated with DNA methylation
DNA methylation plays a crucial role in establishing tissue-specific gene expression. However, our incomplete understanding of the cis elements that regulate DNA methylation prevents us from interpreting the functional effects of non-coding variants. We present CpGenie (http://cpgenie.csail.mit.edu), a deep convolutional neural network that learns a regulatory sequence code of DNA methylation a...
متن کاملExpression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation
Disease-associated loci identified through genome-wide association studies (GWAS) frequently localize to non-coding sequence. We and others have demonstrated strong enrichment of such single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTLs), supporting an important role for regulatory genetic variation in complex disease pathogenesis. Herein we describe our initial ...
متن کاملEffects of Marker Density, Number of Quantitative Trait Loci and Heritability of Trait on Genomic Selection Accuracy
The success of genomic selection mainly depends on the extent of linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), number of QTL and heritability (h2) of the traits. The extent of LD depends on the genetic structure of the population and marker density. This study was conducted to determine the effects of marker density, level of heritability, number of QTL, and to ...
متن کاملA Multiple QTL-Seq Strategy Delineates Potential Genomic Loci Governing Flowering Time in Chickpea
Identification of functionally relevant potential genomic loci using an economical, simpler and user-friendly genomics-assisted breeding strategy is vital for rapid genetic dissection of complex flowering time quantitative trait in chickpea. A high-throughput multiple QTL-seq strategy was employed in two inter (Cicer arietinum desi accession ICC 4958 × C reticulatum wild accession ICC 17160)- a...
متن کامل