INFERNO: inferring the molecular mechanisms of noncoding genetic variants

Nucleic Acids Research
Alexandre Amlie-WolfLi-San Wang


The majority of variants identified by genome-wide association studies (GWAS) reside in the noncoding genome, affecting regulatory elements including transcriptional enhancers. However, characterizing their effects requires the integration of GWAS results with context-specific regulatory activity and linkage disequilibrium annotations to identify causal variants underlying noncoding association signals and the regulatory elements, tissue contexts, and target genes they affect. We propose INFERNO, a novel method which integrates hundreds of functional genomics datasets spanning enhancer activity, transcription factor binding sites, and expression quantitative trait loci with GWAS summary statistics. INFERNO includes novel statistical methods to quantify empirical enrichments of tissue-specific enhancer overlap and to identify co-regulatory networks of dysregulated long noncoding RNAs (lncRNAs). We applied INFERNO to two large GWAS studies. For schizophrenia (36,989 cases, 113,075 controls), INFERNO identified putatively causal variants affecting brain enhancers for known schizophrenia-related genes. For inflammatory bowel disease (IBD) (12,882 cases, 21,770 controls), INFERNO found enrichments of immune and digestive enhancers a...Continue Reading


May 1, 1992·Prostaglandins, Leukotrienes, and Essential Fatty Acids·J K YaoD P van Kammen
Jan 1, 1997·Journal of Psychopharmacology·M B Knable, D R Weinberger
Feb 8, 2005·Genome Biology·Jonathan BardMichael Ashburner
Jun 28, 2005·Nucleic Acids Research·Bing ZhangJay Snoddy
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Apr 16, 2010·Nature·Tae-Kyung KimMichael E Greenberg
Mar 29, 2011·Nature·Jason ErnstBradley E Bernstein
Nov 4, 2011·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Adam J FunkJames H Meador-Woodruff
Feb 2, 2012·Genome Biology·Christopher J MungallMelissa A Haendel
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Apr 12, 2012·Schizophrenia Bulletin·Konasale M PrasadVishwajit L Nimgaonkar
May 1, 2012·Journal of Thyroid Research·Nadine Correia SantosJoana Almeida Palha
Sep 7, 2012·The Journal of Biological Chemistry·Gabriel E Zentner, Peter C Scacheri
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Science·Matthew T MauranoJohn A Stamatoyannopoulos
Sep 8, 2012·Genome Research·Alan P BoyleMichael Snyder
May 10, 2013·Nature Reviews. Genetics·Evangelos Evangelou, John P A Ioannidis
May 25, 2013·Nucleic Acids Research·Jing WangBing Zhang
Dec 10, 2013·Nucleic Acids Research·Danielle WelterHelen Parkinson
Feb 4, 2014·Nature Methods·Graham R S RitchiePaul Flicek
Mar 13, 2014·Nature Reviews. Genetics·Daria ShlyuevaAlexander Stark
Mar 29, 2014·Nature·Robin AnderssonAlbin Sandelin
Jul 25, 2014·Nature·UNKNOWN Schizophrenia Working Group of the Psychiatric Genomics Consortium
Dec 5, 2014·Genome Medicine·Olivia Corradin, Peter C Scacheri
Feb 3, 2015·Nature Genetics·Brendan K Bulik-SullivanBenjamin M Neale
Feb 5, 2015·Nature Reviews. Molecular Cell Biology·Sven HeinzChristopher K Glass
Feb 12, 2015·Clinical Pharmacology and Therapeutics·K O Arseneau, F Cominelli
Feb 20, 2015·Nature·UNKNOWN Roadmap Epigenomics ConsortiumManolis Kellis
Mar 17, 2015·Current Psychiatry Reports·Emily G SeveranceRobert H Yolken
Mar 31, 2015·Nature Neuroscience·Daisuke TsuboiKozo Kaibuchi

❮ Previous
Next ❯


Sep 29, 2019·Journal of Alzheimer's Disease : JAD·Alexandre Amlie-WolfGerard D Schellenberg
Jul 3, 2019·Alzheimer's & Dementia : the Journal of the Alzheimer's Association·Michael W LutzOrnit Chiba-Falek
Mar 2, 2019·Nature Genetics·Brian W KunkleUNKNOWN Genetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer’s Disease Consortium (
Aug 17, 2019·Frontiers in Cellular Neuroscience·Elena PerenthalerTahsin Stefan Barakat
Jun 27, 2020·Alzheimer's & Dementia : the Journal of the Alzheimer's Association·Michael W LutzOrnit Chiba-Falek
Aug 28, 2020·Brain : a Journal of Neurology·Logan DumitrescuTimothy J Hohman
Aug 21, 2020·Proceedings of the National Academy of Sciences of the United States of America·Wenran LiWing Hung Wong
May 23, 2019·Nucleic Acids Research·Vincentius MartinRaluca Gordân
Nov 3, 2020·PLoS Computational Biology·Wei LiuHongyu Zhao
Apr 3, 2021·Alzheimer's & Dementia : the Journal of the Alzheimer's Association·Dmitry ProkopenkoRudolph E Tanzi
May 18, 2021·Clinical Pharmacology and Therapeutics·Yitian Zhou, Volker M Lauschke

❮ Previous
Next ❯

Methods Mentioned


Software Mentioned

custom awk

Related Concepts

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.