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3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk [article]

Ning Liu, Timothy Sadlon, Ying Ying Wong, Stephen M Pederson, James Breen, Simon C Barry
2020 bioRxiv   pre-print
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

Mufassra Naz, Martin Hofmann-Apitius
2016 Journal of Systems and Integrative Neuroscience  
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

Dennis R Grayson, Alessandro Guidotti
2016 Epigenomics  
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

Dávid Jónás, Sára Sándor, Kitti Tátrai, Balázs Egyed, Enikö Kubinyi
2020 Frontiers in Genetics  
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

Sami S. Amr, Saeed H. Al Turki, Matthew Lebo, Mahdi Sarmady, Heidi L. Rehm, Ahmad N. Abou Tayoun
2016 Genetics in Medicine  
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]

Hyun Ji Noh, Ruqi Tang, Jason Flannick, Colm O Dushlaine, Ross Swofford, Daniel Howrigan, Diane P Genereux, Jeremy Johnson, Gerard van Grootheest, Edna Grunblatt, Erik Andersson, Diana R Djurfeldt (+20 others)
2017 bioRxiv   pre-print
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

Ernest Turro, NIHR BioResource for the 100,000 Genomes Project, William J. Astle, Karyn Megy, Stefan Gräf, Daniel Greene, Olga Shamardina, Hana Lango Allen, Alba Sanchis-Juan, Mattia Frontini, Chantal Thys, Jonathan Stephens (+51 others)
2020 Nature  
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

Xiaoyan Ge, Pui-Yan Kwok, Joseph T.C. Shieh
2014 Human Molecular Genetics  
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

Dirk S. Paul, Nicole Soranzo, Stephan Beck
2013 Bioessays  
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

Spencer B. Huggett, Ami S. Ikeda, John E. McGeary, Karla R. Kaun, Rohan H. C. Palmer
2022 Genes  
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

Cory C. Funk, Alex M. Casella, Segun Jung, Matthew A. Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, Ben Heavner, Kyle Chard, Yukai Xiao, Gustavo Glusman, Nilufer Ertekin-Taner (+9 others)
2020 Cell Reports  
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

A. C. Lima, F. Carvalho, J. Gonçalves, S. Fernandes, P. I. Marques, M. Sousa, A. Barros, S. Seixas, A. Amorim, D. F. Conrad, A. M. Lopes
2015 Andrology  
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

A. Z. Dayem Ullah, N. R. Lemoine, C. Chelala
2013 Briefings in Bioinformatics  
, 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

Bàrbara Torrico, Alex D. Shaw, Roberto Mosca, Norma Vivó-Luque, Amaia Hervás, Noèlia Fernàndez-Castillo, Patrick Aloy, Mònica Bayés, Janice M. Fullerton, Bru Cormand, Claudio Toma
2019 Journal of Psychiatry & Neuroscience  
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

Christian T. K.-H. Stadtländer
2017 Briefings in Bioinformatics  
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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