A genetics-led approach defines the drug target landscape of 30 immune-related traits.

Abstract:

:Most candidate drugs currently fail later-stage clinical trials, largely due to poor prediction of efficacy on early target selection1. Drug targets with genetic support are more likely to be therapeutically valid2,3, but the translational use of genome-scale data such as from genome-wide association studies for drug target discovery in complex diseases remains challenging4-6. Here, we show that integration of functional genomic and immune-related annotations, together with knowledge of network connectivity, maximizes the informativeness of genetics for target validation, defining the target prioritization landscape for 30 immune traits at the gene and pathway level. We demonstrate how our genetics-led drug target prioritization approach (the priority index) successfully identifies current therapeutics, predicts activity in high-throughput cellular screens (including L1000, CRISPR, mutagenesis and patient-derived cell assays), enables prioritization of under-explored targets and allows for determination of target-level trait relationships. The priority index is an open-access, scalable system accelerating early-stage drug target selection for immune-mediated disease.

journal_name

Nat Genet

journal_title

Nature genetics

authors

Fang H,ULTRA-DD Consortium.,De Wolf H,Knezevic B,Burnham KL,Osgood J,Sanniti A,Lledó Lara A,Kasela S,De Cesco S,Wegner JK,Handunnetthi L,McCann FE,Chen L,Sekine T,Brennan PE,Marsden BD,Damerell D,O'Callaghan CA,Boun

doi

10.1038/s41588-019-0456-1

subject

Has Abstract

pub_date

2019-07-01 00:00:00

pages

1082-1091

issue

7

eissn

1061-4036

issn

1546-1718

pii

10.1038/s41588-019-0456-1

journal_volume

51

pub_type

杂志文章
  • Germline BAP1 mutations predispose to malignant mesothelioma.

    abstract::Because only a small fraction of asbestos-exposed individuals develop malignant mesothelioma, and because mesothelioma clustering is observed in some families, we searched for genetic predisposing factors. We discovered germline mutations in the gene encoding BRCA1 associated protein-1 (BAP1) in two families with a hi...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.912

    authors: Testa JR,Cheung M,Pei J,Below JE,Tan Y,Sementino E,Cox NJ,Dogan AU,Pass HI,Trusa S,Hesdorffer M,Nasu M,Powers A,Rivera Z,Comertpay S,Tanji M,Gaudino G,Yang H,Carbone M

    更新日期:2011-08-28 00:00:00

  • An X-to-autosome retrogene is required for spermatogenesis in mice.

    abstract::We identified the gene carrying the juvenile spermatogonial depletion mutation (jsd), a recessive spermatogenic defect mapped to mouse chromosome 1 (refs. 1,2). We localized jsd to a 272-kb region and resequenced this area to identify the underlying mutation: a frameshift that severely truncates the predicted protein ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1390

    authors: Bradley J,Baltus A,Skaletsky H,Royce-Tolland M,Dewar K,Page DC

    更新日期:2004-08-01 00:00:00

  • Widespread adenine N6-methylation of active genes in fungi.

    abstract::N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in ea...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3859

    authors: Mondo SJ,Dannebaum RO,Kuo RC,Louie KB,Bewick AJ,LaButti K,Haridas S,Kuo A,Salamov A,Ahrendt SR,Lau R,Bowen BP,Lipzen A,Sullivan W,Andreopoulos BB,Clum A,Lindquist E,Daum C,Northen TR,Kunde-Ramamoorthy G,Schmitz RJ

    更新日期:2017-06-01 00:00:00

  • Mapping, cloning and genetic characterization of the region containing the Wilson disease gene.

    abstract::Wilson disease (WD) is an autosomal recessive disorder of copper transport which map to chromosome 13q14.3. In pursuit of the WD gene, we developed yeast artificial chromosome and cosmid contigs, and microsatellite markers which span the WD gene region. Linkage disequilibrium and haplotype analysis of 115 WD families ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1293-338

    authors: Petrukhin K,Fischer SG,Pirastu M,Tanzi RE,Chernov I,Devoto M,Brzustowicz LM,Cayanis E,Vitale E,Russo JJ

    更新日期:1993-12-01 00:00:00

  • A high observed substitution rate in the human mitochondrial DNA control region.

    abstract::The rate and pattern of sequence substitutions in the mitochondrial DNA (mtDNA) control region (CR) is of central importance to studies of human evolution and to forensic identity testing. Here, we report a direct measurement of the intergenerational substitution rate in the human CR. We compared DNA sequences of two ...

    journal_title:Nature genetics

    pub_type: 杂志文章,多中心研究

    doi:10.1038/ng0497-363

    authors: Parsons TJ,Muniec DS,Sullivan K,Woodyatt N,Alliston-Greiner R,Wilson MR,Berry DL,Holland KA,Weedn VW,Gill P,Holland MM

    更新日期:1997-04-01 00:00:00

  • Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations.

    abstract::Studies in experimental systems have identified a multitude of mutational mechanisms including DNA replication infidelity and DNA damage followed by inefficient repair or replicative bypass. However, the relative contributions of these mechanisms to human germline mutation remain unknown. Here, we show that error-pron...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-018-0285-7

    authors: Seplyarskiy VB,Akkuratov EE,Akkuratova N,Andrianova MA,Nikolaev SI,Bazykin GA,Adameyko I,Sunyaev SR

    更新日期:2019-01-01 00:00:00

  • Human Genome Variation 2006: emerging views on structural variation and large-scale SNP analysis.

    abstract::The eighth annual Human Genome Variation Meeting was held in September 2006 in the Hong Kong Special Administrative Region, China. The meeting highlighted recent advances in characterization of genetic variation, including genome-wide association studies and structural variation. ...

    journal_title:Nature genetics

    pub_type:

    doi:10.1038/ng0207-153

    authors: Abecasis G,Tam PK,Bustamante CD,Ostrander EA,Scherer SW,Chanock SJ,Kwok PY,Brookes AJ

    更新日期:2007-02-01 00:00:00

  • Physical and neurobehavioral determinants of reproductive onset and success.

    abstract::The ages of puberty, first sexual intercourse and first birth signify the onset of reproductive ability, behavior and success, respectively. In a genome-wide association study of 125,667 UK Biobank participants, we identify 38 loci associated (P < 5 × 10(-8)) with age at first sexual intercourse. These findings were t...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3551

    authors: Day FR,Helgason H,Chasman DI,Rose LM,Loh PR,Scott RA,Helgason A,Kong A,Masson G,Magnusson OT,Gudbjartsson D,Thorsteinsdottir U,Buring JE,Ridker PM,Sulem P,Stefansson K,Ong KK,Perry JRB

    更新日期:2016-06-01 00:00:00

  • Soluble epoxide hydrolase is a susceptibility factor for heart failure in a rat model of human disease.

    abstract::We aimed to identify genetic variants associated with heart failure by using a rat model of the human disease. We performed invasive cardiac hemodynamic measurements in F2 crosses between spontaneously hypertensive heart failure (SHHF) rats and reference strains. We combined linkage analyses with genome-wide expressio...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.129

    authors: Monti J,Fischer J,Paskas S,Heinig M,Schulz H,Gösele C,Heuser A,Fischer R,Schmidt C,Schirdewan A,Gross V,Hummel O,Maatz H,Patone G,Saar K,Vingron M,Weldon SM,Lindpaintner K,Hammock BD,Rohde K,Dietz R,Cook SA,Sc

    更新日期:2008-05-01 00:00:00

  • Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis.

    abstract::The genetic architectures of common, complex diseases are largely uncharacterized. We modeled the genetic architecture underlying genome-wide association study (GWAS) data for rheumatoid arthritis and developed a new method using polygenic risk-score analyses to infer the total liability-scale variance explained by as...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2232

    authors: Stahl EA,Wegmann D,Trynka G,Gutierrez-Achury J,Do R,Voight BF,Kraft P,Chen R,Kallberg HJ,Kurreeman FA,Diabetes Genetics Replication and Meta-analysis Consortium.,Myocardial Infarction Genetics Consortium.,Kathiresan S,Wijmenga

    更新日期:2012-03-25 00:00:00

  • Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes.

    abstract::The human genome can be segmented into topologically associating domains (TADs), which have been proposed to spatially sequester genes and regulatory elements through chromatin looping. Interactions between TADs have also been suggested, presumably because of variable boundary positions across individual cells. Howeve...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-020-0647-9

    authors: Luppino JM,Park DS,Nguyen SC,Lan Y,Xu Z,Yunker R,Joyce EF

    更新日期:2020-08-01 00:00:00

  • New HLA-DPB1 alleles generated by interallelic gene conversion detected by analysis of sperm.

    abstract::The rate at which allelic diversity at the HLA loci evolves has been the subject of considerable controversy. The patchwork pattern of sequence polymorphism within the second exon of the HLA class II loci, particularly in the DPB1 locus, may have been generated by segmental exchange (gene conversion). We have analysed...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0895-407

    authors: Zangenberg G,Huang MM,Arnheim N,Erlich H

    更新日期:1995-08-01 00:00:00

  • Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development.

    abstract::We identified homozygous truncating mutations in HOXA1 in three genetically isolated human populations. The resulting phenotype includes horizontal gaze abnormalities, deafness, facial weakness, hypoventilation, vascular malformations of the internal carotid arteries and cardiac outflow tract, mental retardation and a...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1636

    authors: Tischfield MA,Bosley TM,Salih MA,Alorainy IA,Sener EC,Nester MJ,Oystreck DT,Chan WM,Andrews C,Erickson RP,Engle EC

    更新日期:2005-10-01 00:00:00

  • A literature network of human genes for high-throughput analysis of gene expression.

    abstract::We have carried out automated extraction of explicit and implicit biomedical knowledge from publicly available gene and text databases to create a gene-to-gene co-citation network for 13,712 named human genes by automated analysis of titles and abstracts in over 10 million MEDLINE records. The associations between gen...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0501-21

    authors: Jenssen TK,Laegreid A,Komorowski J,Hovig E

    更新日期:2001-05-01 00:00:00

  • Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia.

    abstract::Differences in three-dimensional (3D) chromatin architecture can influence the integrity of topologically associating domains (TADs) and rewire specific enhancer-promoter interactions, impacting gene expression and leading to human disease. Here we investigate the 3D chromatin architecture in T cell acute lymphoblasti...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-020-0602-9

    authors: Kloetgen A,Thandapani P,Ntziachristos P,Ghebrechristos Y,Nomikou S,Lazaris C,Chen X,Hu H,Bakogianni S,Wang J,Fu Y,Boccalatte F,Zhong H,Paietta E,Trimarchi T,Zhu Y,Van Vlierberghe P,Inghirami GG,Lionnet T,Aifantis I

    更新日期:2020-04-01 00:00:00

  • Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome.

    abstract::The genetic basis of most conditions characterized by congenital contractures is largely unknown. Here we show that mutations in the embryonic myosin heavy chain (MYH3) gene cause Freeman-Sheldon syndrome (FSS), one of the most severe multiple congenital contracture (that is, arthrogryposis) syndromes, and nearly one-...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1775

    authors: Toydemir RM,Rutherford A,Whitby FG,Jorde LB,Carey JC,Bamshad MJ

    更新日期:2006-05-01 00:00:00

  • Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate.

    abstract::Pioneer transcription factors establish new cell-fate competence by triggering chromatin remodeling. However, many features of pioneer action, such as their kinetics and stability, remain poorly defined. Here, we show that Pax7, by opening a unique repertoire of enhancers, is necessary and sufficient for specification...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-017-0035-2

    authors: Mayran A,Khetchoumian K,Hariri F,Pastinen T,Gauthier Y,Balsalobre A,Drouin J

    更新日期:2018-02-01 00:00:00

  • Enabling direct fate conversion with network biology.

    abstract::Current efforts in cellular disease modeling and regenerative medicine are limited by the paucity of cell types that can be generated in the laboratory. A new study introduces a computational framework, Mogrify, that uses network biology to predict combinations of transcription factors necessary for direct conversion ...

    journal_title:Nature genetics

    pub_type: 评论,新闻

    doi:10.1038/ng.3516

    authors: Cahan P

    更新日期:2016-03-01 00:00:00

  • Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia.

    abstract::Genome-wide association studies have identified common variants that only partially explain the genetic risk for type 2 diabetes (T2D). Using genome-wide association data from 1,376 French individuals, we identified 16,360 SNPs nominally associated with T2D and studied these SNPs in an independent sample of 4,977 Fren...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.443

    authors: Rung J,Cauchi S,Albrechtsen A,Shen L,Rocheleau G,Cavalcanti-Proença C,Bacot F,Balkau B,Belisle A,Borch-Johnsen K,Charpentier G,Dina C,Durand E,Elliott P,Hadjadj S,Järvelin MR,Laitinen J,Lauritzen T,Marre M,Mazur A,

    更新日期:2009-10-01 00:00:00

  • Susceptibility to insulin dependent diabetes mellitus maps to a 4.1 kb segment of DNA spanning the insulin gene and associated VNTR.

    abstract::Recent studies have demonstrated that a locus at 11p15.5 confers susceptibility to insulin dependent diabetes mellitus (IDDM). This locus has been shown to lie within a 19 kb region. We present a detailed sequence comparison of the predominant haplotypes found in this region in a population of French Caucasian IDDM pa...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng0793-305

    authors: Lucassen AM,Julier C,Beressi JP,Boitard C,Froguel P,Lathrop M,Bell JI

    更新日期:1993-07-01 00:00:00

  • Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration.

    abstract::We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.2202

    authors: Chiang C,Jacobsen JC,Ernst C,Hanscom C,Heilbut A,Blumenthal I,Mills RE,Kirby A,Lindgren AM,Rudiger SR,McLaughlan CJ,Bawden CS,Reid SJ,Faull RL,Snell RG,Hall IM,Shen Y,Ohsumi TK,Borowsky ML,Daly MJ,Lee C,Morton C

    更新日期:2012-03-04 00:00:00

  • The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.

    abstract::We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3× dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged ...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.807

    authors: Hu TT,Pattyn P,Bakker EG,Cao J,Cheng JF,Clark RM,Fahlgren N,Fawcett JA,Grimwood J,Gundlach H,Haberer G,Hollister JD,Ossowski S,Ottilar RP,Salamov AA,Schneeberger K,Spannagl M,Wang X,Yang L,Nasrallah ME,Bergelson J

    更新日期:2011-05-01 00:00:00

  • Distinct in vivo requirements for establishment versus maintenance of transcriptional repression.

    abstract::Low-level ectopic expression of the Runt transcription factor blocks activation of the Drosophila melanogaster segmentation gene engrailed (en) in odd-numbered parasegments and is associated with a lethal phenotype. Here we show, by using a genetic screen for maternal factors that contribute in a dose-dependent fashio...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng942

    authors: Wheeler JC,VanderZwan C,Xu X,Swantek D,Tracey WD,Gergen JP

    更新日期:2002-09-01 00:00:00

  • A single-nucleotide polymorphism tagging set for human drug metabolism and transport.

    abstract::Interindividual variability in drug response, ranging from no therapeutic benefit to life-threatening adverse reactions, is influenced by variation in genes that control the absorption, distribution, metabolism and excretion of drugs. We genotyped 904 single-nucleotide polymorphisms (SNPs) from 55 such genes in two po...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1488

    authors: Ahmadi KR,Weale ME,Xue ZY,Soranzo N,Yarnall DP,Briley JD,Maruyama Y,Kobayashi M,Wood NW,Spurr NK,Burns DK,Roses AD,Saunders AM,Goldstein DB

    更新日期:2005-01-01 00:00:00

  • Nalp1b controls mouse macrophage susceptibility to anthrax lethal toxin.

    abstract::The pathogenesis of Bacillus anthracis, the bacterium that causes anthrax, depends on secretion of three factors that combine to form two bipartite toxins. Edema toxin, consisting of protective antigen (PA) and edema factor (EF), causes the edema associated with cutaneous anthrax infections, whereas lethal toxin (LeTx...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng1724

    authors: Boyden ED,Dietrich WF

    更新日期:2006-02-01 00:00:00

  • Ocular albinism: evidence for a defect in an intracellular signal transduction system.

    abstract::G protein-coupled receptors (GPCRs) participate in the most common signal transduction system at the plasma membrane. The wide distribution of heterotrimeric G proteins in the internal membranes suggests that a similar signalling mechanism might also be used at intracellular locations. We provide here structural evide...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/12715

    authors: Schiaffino MV,d'Addio M,Alloni A,Baschirotto C,Valetti C,Cortese K,Puri C,Bassi MT,Colla C,De Luca M,Tacchetti C,Ballabio A

    更新日期:1999-09-01 00:00:00

  • A reference genome for pea provides insight into legume genome evolution.

    abstract::We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes,...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/s41588-019-0480-1

    authors: Kreplak J,Madoui MA,Cápal P,Novák P,Labadie K,Aubert G,Bayer PE,Gali KK,Syme RA,Main D,Klein A,Bérard A,Vrbová I,Fournier C,d'Agata L,Belser C,Berrabah W,Toegelová H,Milec Z,Vrána J,Lee H,Kougbeadjo A,Térézol

    更新日期:2019-09-01 00:00:00

  • Accelerated genetic drift on chromosome X during the human dispersal out of Africa.

    abstract::Comparisons of chromosome X and the autosomes can illuminate differences in the histories of males and females as well as shed light on the forces of natural selection. We compared the patterns of variation in these parts of the genome using two datasets that we assembled for this study that are both genomic in scale....

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.303

    authors: Keinan A,Mullikin JC,Patterson N,Reich D

    更新日期:2009-01-01 00:00:00

  • Mutation of NLRC4 causes a syndrome of enterocolitis and autoinflammation.

    abstract::Upon detection of pathogen-associated molecular patterns, innate immune receptors initiate inflammatory responses. These receptors include cytoplasmic NOD-like receptors (NLRs) whose stimulation recruits and proteolytically activates caspase-1 within the inflammasome, a multiprotein complex. Caspase-1 mediates the pro...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.3066

    authors: Romberg N,Al Moussawi K,Nelson-Williams C,Stiegler AL,Loring E,Choi M,Overton J,Meffre E,Khokha MK,Huttner AJ,West B,Podoltsev NA,Boggon TJ,Kazmierczak BI,Lifton RP

    更新日期:2014-10-01 00:00:00

  • Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33.

    abstract::Genome-wide association studies (GWAS) have identified ten loci harboring common variants that influence risk of developing colorectal cancer (CRC). To enhance the power to identify additional CRC risk loci, we conducted a meta-analysis of three GWAS from the UK which included a total of 3,334 affected individuals (ca...

    journal_title:Nature genetics

    pub_type: 杂志文章

    doi:10.1038/ng.670

    authors: Houlston RS,Cheadle J,Dobbins SE,Tenesa A,Jones AM,Howarth K,Spain SL,Broderick P,Domingo E,Farrington S,Prendergast JG,Pittman AM,Theodoratou E,Smith CG,Olver B,Walther A,Barnetson RA,Churchman M,Jaeger EE,Penegar

    更新日期:2010-11-01 00:00:00