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3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk
[article]
2020
bioRxiv
pre-print
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Genome-wide association and fine-mapping studies have enabled the discovery of single nucleotide polymorphisms (SNPs) and other variants that are significantly associated with many autoimmune diseases ...
We identified 7,900 candidate variants and 3,245 candidate target genes, generating a list of potential sites for future T1D or autoimmune research. ...
Filtered variants disrupt Transcription Factor Binding Sites (TFBS) including a
FOXP3-like binding site Fundamental to understanding the function of specific disease associated variants is the identification ...
doi:10.1101/2020.09.04.279554
fatcat:2cc3vyffb5gsti4nljf643maqq
GWAS genetic variant data and their integration in the context of network biology
2016
Journal of Systems and Integrative Neuroscience
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Regardless of the success of Genome Wide Association Studies (GWAS) to identify genetic variants associated with human diseases, investigating the molecular mechanisms and disease-associated genes linked ...
to those genetic variants, is a very complex task. ...
DNA hyper-methylation near transcription start sites (TSS) of tumour suppressor genes associates with their silencing [68] . ...
doi:10.15761/jsin.1000135
fatcat:xhvcgelncne7tgywvom35mupny
Merging data from genetic and epigenetic approaches to better understand autistic spectrum disorder
2016
Epigenomics
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Herein, we discuss recent developments in the research of ASD with a focus on epigenetic pathways as a complement to current genetic screening. ...
Mutations impact the expression of large numbers of genes and also have downstream consequences depending on specific pathways associated with the mutation. ...
start sites [41] . ...
doi:10.2217/epi.15.92
pmid:26551091
pmcid:PMC4864049
fatcat:6nyrl2vwvjb5lb2y3aka3ywqxu
A Preliminary Study to Investigate the Genetic Background of Longevity Based on Whole-Genome Sequence Data of Two Methuselah Dogs
2020
Frontiers in Genetics
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We hypothesize a possible link between extreme longevity and the regulation of gene transcription/translation, which hypothesis should be further investigated in the future. ...
animals - across 472 genes. ...
We also thank Ilona Kádárné, Pegazus Lovarda Sárrétudvari and Henriette Merza, Szent Ferenc Állatotthon for providing us the samples. ...
doi:10.3389/fgene.2020.00315
pmid:32373156
pmcid:PMC7176982
fatcat:vdqhi5zhrnd7pbkcsc4oym3tya
Using large sequencing data sets to refine intragenic disease regions and prioritize clinical variant interpretation
2016
Genetics in Medicine
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ACKNOWLEDGMENTS We thank the many members of the Partners Healthcare Laboratory of Molecular Medicine (LMM) who carefully interpreted variant evidence to form the database used in this analysis. ...
Some of the data in this paper were presented at the American Society of Human Genetics (ASHG) annual meeting in Baltimore, Maryland, in 2015. ...
The ExAC database (N = 60,706 individuals) was used as a control data set. We statistically determined whether any domain(s) had a significant enrichment of variants in cases versus controls. ...
doi:10.1038/gim.2016.134
pmid:27657688
fatcat:h5mi4flhmffqdft2zs6f3lm6hm
Evolutionary and functional data power search for obsessive-compulsive disorder genes
[article]
2017
bioRxiv
pre-print
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Using a new method, PolyStrat, which prioritizes variants disrupting evolutionarily conserved, functional regions, we found four strongly associated genes when comparing 592 cases to 560 controls. ...
Our findings suggest synaptic adhesion as a key function in compulsive behaviors across three species, and demonstrate how combining targeted sequencing with functional annotations can identify potentially ...
A Broad Institute SPARC grant supported this work. ...
doi:10.1101/107193
fatcat:josvklbo4bed7ek22z2v6ge3qq
Whole-genome sequencing of patients with rare diseases in a national health system
2020
Nature
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Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. ...
Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare. ...
Acknowledgements This research was made possible through access to the data and findings generated by two pilot studies for the 100,000 Genomes Project. ...
doi:10.1038/s41586-020-2434-2
pmid:32581362
pmcid:PMC7610553
fatcat:vf54nxmq2vh6bmchrymyhwnsw4
Prioritizing genes for X-linked diseases using population exome data
2014
Human Molecular Genetics
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Yet, variant interpretation for the large amounts of genomic data remains a challenge given variation of uncertain significance and genes that lack disease annotation. ...
A low dN/dS ratio characterized genes associated with childhood disease and outcome. ...
The authors thank the NHLBI GO Exome Sequencing Project and its ongoing studies which produced and provided exome variant calls for data analyses: the Lung GO Sequencing Project (HL-102923), the WHI Sequencing ...
doi:10.1093/hmg/ddu473
pmid:25217573
pmcid:PMC4291241
fatcat:k7ivbfo56relfidopyfcmsdpny
Functional interpretation of non-coding sequence variation: Concepts and challenges
2013
Bioessays
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Trait-associated variants that are located distal to transcription start sites at gene-dense regions are particularly difficult to interpret. ...
In recent years, researchers have systematically assayed millions of common genetic variants across hundreds of thousands of individuals in genome-wide association studies (GWAS). ...
doi:10.1002/bies.201300126
pmid:24311363
pmcid:PMC3992842
fatcat:pvrbl3yk6jfbdovwpfmfi4s4ay
Opioid Use Disorder and Alternative mRNA Splicing in Reward Circuitry
2022
Genes
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Using a genome-wide association study (GWAS) of OUD, we found no evidence that DNA variants within or surrounding differentially spliced genes were implicated in the heritability of OUD. ...
Second, we tested whether alternative mRNA splicing regions were linked to genetic predisposition. ...
Thus, we tested DNA variants within 100 kb of the transcription start and end sites of a gene in our genetic enrichment tests. ...
doi:10.3390/genes13061045
fatcat:7rzsylv7ffdrnkjvzpzts3npe4
Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types
2020
Cell Reports
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We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits ...
Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. ...
Given that most risk variants in GWAS fall within non-coding regions, this finding suggests that disruption of TF binding may be a common mechanism by which genetic risk is conferred. ...
doi:10.1016/j.celrep.2020.108029
pmid:32814038
pmcid:PMC7462736
fatcat:lnjt2ouxv5ag3ehjzvygmbwsqe
Rare double sex and mab-3-related transcription factor 1 regulatory variants in severe spermatogenic failure
2015
Andrology
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The DMRT1 (doublesex and mab-3 related transcription factor 1) gene has long been linked to sex-determining pathways across vertebrates and is known to play an essential role in gonadal development and ...
One of these is a complex variant with a putative regulatory role (c.-223_-219CGAAA>T), located in the promoter region within a conserved sequence involved in Dmrt1 repression. ...
Acknowledgments The authors would like to thank Rui Pereira for the analysis of ancestry performed for one patient. ...
doi:10.1111/andr.12063
pmid:26139570
pmcid:PMC4802187
fatcat:nngps3h3znf3vjgotx55lzegcy
A practical guide for the functional annotation of genetic variations using SNPnexus
2013
Briefings in Bioinformatics
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, structural as well as conserved elements and retrieving links with previously reported genetic disease studies. ...
Broader functional annotation of known as well as putative genetic variations is a valuable mean for prioritizing targets in disease studies and large-scale genotyping projects. ...
INTRODUCTION Genome variations represent a valuable resource for investigating the genetic basis of diseases and are widely used for fine-scale genetic mapping and genome-wide association studies. ...
doi:10.1093/bib/bbt004
pmid:23395730
fatcat:atc3vyqaxndelotkti7tk7e7aq
Truncating variant burden in high-functioning autism and pleiotropic effects of LRP1 across psychiatric phenotypes
2019
Journal of Psychiatry & Neuroscience
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We aim to investigate whether the load of inherited truncating mutations contributes similarly to high-functioning autism, and to characterize genes that harbour de novo variants in high-functioning autism ...
to be involved in ASD have been identified. 5 Genetic studies conducted over the last 2 decades converge on a genetic model in which ASD genetic liability is shaped by both multiple common variants ...
sequencing studies have exponentially increased the identification of novel risk genes, starting to resolve most of the missing heritability in psychiatric disorders. ...
doi:10.1503/jpn.180184
pmid:31094488
pmcid:PMC6710089
fatcat:y4dhashcjjhwrcsl7cdgs2gwwq
Next-generation sequencing data analysis Xinkun Wan
2017
Briefings in Bioinformatics
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My sincere thanks also goes to my colleagues at the Institute of Human Genetics for a great working atmosphere and for helping me with all the big and small problems that are an unavoidable part of each ...
I would also like to thank Thomas Meitinger for giving me the opportunity to work on my project at his institute and for providing me with a lot of helpful adivce. ...
First of all I want to thank my supervisor Tim Strom for all his advice and guidance over the last couple of years and for giving me the freedom to work on many interesting topics. ...
doi:10.1093/bib/bbx038
fatcat:b7kevx76vjbuld6wdd6u2vnlay
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