Intergenic GWAS SNPs are key components of the spatial and regulatory network for human growth.

Abstract:

:Meta-analysis of genome-wide association studies has resulted in the identification of hundreds of genetic variants associated with growth and stature. Determining how these genetic variants influence growth is important, but most are non-coding, and there is little understanding of how these variants contribute to adult height. To determine the mechanisms by which human variation contributes to growth, we combined spatial genomic connectivity (high-throughput conformation capture) with functional (gene expression, expression Quantitative Trait Loci) data to determine how non-genic loci associated with infant length, pubertal and adult height and contribute to gene regulatory networks. This approach identified intergenic single-nucleotide polymorphisms (SNPs) ∼85 kb upstream of FBXW11 that spatially connect with distant loci. These regulatory connections are reinforced by evidence of SNP-enhancer effects and altered expression in genes influencing the action of human growth hormone. Functional assays provided evidence for enhancer activity of the intergenic region near FBXW11 that harbors SNP rs12153391, which is associated with an expression Quantitative Trait Loci. Our results suggest that variants in this locus have genome-wide effects as key modifiers of growth (both overgrowth and short stature) acting through a regulatory network. We believe that the genes and pathways connected with this regulatory network are potential targets that could be investigated for diagnostic, prenatal and carrier testing for growth disorders. Finally, the regulatory networks we generated illustrate the power of using existing datasets to interrogate the contribution of intergenic SNPs to common syndromes/diseases.

journal_name

Hum Mol Genet

journal_title

Human molecular genetics

authors

Schierding W,Antony J,Cutfield WS,Horsfield JA,O'Sullivan JM

doi

10.1093/hmg/ddw165

subject

Has Abstract

pub_date

2016-08-01 00:00:00

pages

3372-3382

issue

15

eissn

0964-6906

issn

1460-2083

pii

ddw165

journal_volume

25

pub_type

杂志文章,meta分析
  • Different mechanisms cause imprinting defects at the IGF2/H19 locus in Beckwith-Wiedemann syndrome and Wilms' tumour.

    abstract::The parent of origin-dependent expression of the IGF2 and H19 genes is controlled by the imprinting centre 1 (IC1) consisting in a methylation-sensitive chromatin insulator. Deletions removing part of IC1 have been found in patients affected by the overgrowth- and tumour-associated Beckwith-Wiedemann syndrome (BWS). T...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddn031

    authors: Cerrato F,Sparago A,Verde G,De Crescenzo A,Citro V,Cubellis MV,Rinaldi MM,Boccuto L,Neri G,Magnani C,D'Angelo P,Collini P,Perotti D,Sebastio G,Maher ER,Riccio A

    更新日期:2008-05-15 00:00:00

  • Pharmacological chaperones as a potential therapeutic option in methylmalonic aciduria cblB type.

    abstract::Methylmalonic aciduria (MMA) cblB type is caused by mutations in the MMAB gene. This encodes the enzyme ATP:cob(I)alamin adenosyltransferase (ATR), which converts reduced cob(I)alamin to an active adenosylcobalamin cofactor. We recently reported the presence of destabilizing pathogenic mutations that retain some resid...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt217

    authors: Jorge-Finnigan A,Brasil S,Underhaug J,Ruíz-Sala P,Merinero B,Banerjee R,Desviat LR,Ugarte M,Martinez A,Pérez B

    更新日期:2013-09-15 00:00:00

  • NSDHL, an enzyme involved in cholesterol biosynthesis, traffics through the Golgi and accumulates on ER membranes and on the surface of lipid droplets.

    abstract::NSDHL, for NAD(P)H steroid dehydrogenase-like, encodes a sterol dehydrogenase or decarboxylase involved in the sequential removal of two C-4 methyl groups in post-squalene cholesterol biosynthesis. Mutations in this gene are associated with human CHILD syndrome (congenital hemidysplasia with ichthyosiform nevus and li...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddg321

    authors: Caldas H,Herman GE

    更新日期:2003-11-15 00:00:00

  • The product of X-linked Kallmann's syndrome gene (KAL1) affects the migratory activity of gonadotropin-releasing hormone (GnRH)-producing neurons.

    abstract::X-linked Kallmann's syndrome (KS) is a genetic disease characterized by anosmia and hypogonadism due to impairment in the development of olfactory axons and in the migration of gonadotropin-releasing hormone (GnRH)-producing neurons. Deletions or point mutations of a gene located at Xp22.3 (KAL1) are responsible for t...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddh309

    authors: Cariboni A,Pimpinelli F,Colamarino S,Zaninetti R,Piccolella M,Rumio C,Piva F,Rugarli EI,Maggi R

    更新日期:2004-11-15 00:00:00

  • A small molecule p75NTR ligand normalizes signalling and reduces Huntington's disease phenotypes in R6/2 and BACHD mice.

    abstract::Decreases in the ratio of neurotrophic versus neurodegenerative signalling play a critical role in Huntington’s disease (HD) pathogenesis and recent evidence suggests that the p75 neurotrophin receptor (NTR) contributes significantly to disease progression. p75NTR signalling intermediates substantially overlap with th...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw316

    authors: Simmons DA,Belichenko NP,Ford EC,Semaan S,Monbureau M,Aiyaswamy S,Holman CM,Condon C,Shamloo M,Massa SM,Longo FM

    更新日期:2016-11-15 00:00:00

  • Whole-exome imputation of sequence variants identified two novel alleles associated with adult body height in African Americans.

    abstract::Adult body height is a quantitative trait for which genome-wide association studies (GWAS) have identified numerous loci, primarily in European populations. These loci, comprising common variants, explain <10% of the phenotypic variance in height. We searched for novel associations between height and common (minor all...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu361

    authors: Du M,Auer PL,Jiao S,Haessler J,Altshuler D,Boerwinkle E,Carlson CS,Carty CL,Chen YD,Curtis K,Franceschini N,Hsu L,Jackson R,Lange LA,Lettre G,Monda KL,National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing

    更新日期:2014-12-15 00:00:00

  • Cloning, chromosomal mapping and expression pattern of the mouse Brca2 gene.

    abstract::A proportion of human breast cancers result from an inherited predisposition to the disease. Mutations in the BRCA2 gene confer a high risk of breast cancer and are responsible for almost half of these cases. The recent cloning of the human BRCA2 gene has revealed that it encodes a large protein having little signific...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/6.2.291

    authors: Connor F,Smith A,Wooster R,Stratton M,Dixon A,Campbell E,Tait TM,Freeman T,Ashworth A

    更新日期:1997-02-01 00:00:00

  • Prevention of polyglutamine oligomerization and neurodegeneration by the peptide inhibitor QBP1 in Drosophila.

    abstract::Polyglutamine (polyQ) diseases are a growing class of inherited neurodegenerative diseases including Huntington's disease, which are caused by abnormal expansions of the polyQ stretch in each unrelated disease protein. The expanded polyQ stretch is thought to confer toxic properties on the disease proteins through alt...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddg144

    authors: Nagai Y,Fujikake N,Ohno K,Higashiyama H,Popiel HA,Rahadian J,Yamaguchi M,Strittmatter WJ,Burke JR,Toda T

    更新日期:2003-06-01 00:00:00

  • Increased levels of phosphoinositides cause neurodegeneration in a Drosophila model of amyotrophic lateral sclerosis.

    abstract::The Vesicle-associated membrane protein (VAMP)-Associated Protein B (VAPB) is the causative gene of amyotrophic lateral sclerosis 8 (ALS8) in humans. Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease characterized by selective death of motor neurons leading to spasticity, muscle atrophy an...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt118

    authors: Forrest S,Chai A,Sanhueza M,Marescotti M,Parry K,Georgiev A,Sahota V,Mendez-Castro R,Pennetta G

    更新日期:2013-07-01 00:00:00

  • Myogenic program dysregulation is contributory to disease pathogenesis in spinal muscular atrophy.

    abstract::Mutations in the survival motor neuron (SMN1) gene lead to the neuromuscular disease spinal muscular atrophy (SMA). Although SMA is primarily considered as a motor neuron disease, the importance of muscle defects in its pathogenesis has not been fully examined. We use both primary cell culture and two different SMA mo...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu142

    authors: Boyer JG,Deguise MO,Murray LM,Yazdani A,De Repentigny Y,Boudreau-Larivière C,Kothary R

    更新日期:2014-08-15 00:00:00

  • A small-molecule Nrf1 and Nrf2 activator mitigates polyglutamine toxicity in spinal and bulbar muscular atrophy.

    abstract::Spinal and bulbar muscular atrophy (SBMA, also known as Kennedy's disease) is one of nine neurodegenerative disorders that are caused by expansion of polyglutamine-encoding CAG repeats. Intracellular accumulation of abnormal proteins in these diseases, a pathological hallmark, is associated with defects in protein hom...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw073

    authors: Bott LC,Badders NM,Chen KL,Harmison GG,Bautista E,Shih CC,Katsuno M,Sobue G,Taylor JP,Dantuma NP,Fischbeck KH,Rinaldi C

    更新日期:2016-05-15 00:00:00

  • Inhibition of death-associated protein kinase 1 attenuates the phosphorylation and amyloidogenic processing of amyloid precursor protein.

    abstract::Extracellular deposition of amyloid-beta (Aβ) peptide, a metabolite of sequential cleavage of amyloid precursor protein (APP), is a critical step in the pathogenesis of Alzheimer's disease (AD). While death-associated protein kinase 1 (DAPK1) is highly expressed in AD brains and its genetic variants are linked to AD r...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw114

    authors: Kim BM,You MH,Chen CH,Suh J,Tanzi RE,Ho Lee T

    更新日期:2016-06-15 00:00:00

  • Pre-natal manifestation of systemic developmental abnormalities in spinal muscular atrophy.

    abstract::Spinal muscular atrophy (SMA) is a neuromuscular disease caused by mutations in survival motor neuron 1 (SMN1). SMN-restoring therapies have recently emerged; however, preclinical and clinical studies revealed a limited therapeutic time window and systemic aspects of the disease. This raises a fundamental question of ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddaa146

    authors: Motyl AAL,Faller KME,Groen EJN,Kline RA,Eaton SL,Ledahawsky LM,Chaytow H,Lamont DJ,Wishart TM,Huang YT,Gillingwater TH

    更新日期:2020-09-29 00:00:00

  • Initiation of the breakage-fusion-bridge mechanism through common fragile site activation in human breast cancer cells: the model of PIP gene duplication from a break at FRA7I.

    abstract::Gene amplification plays a critical role in tumor progression. Hence, understanding the factors triggering this process in human cancers is an important concern. Unfortunately, the structures formed at early stages are usually unavailable for study, hampering the identification of the initiating events in tumors. Here...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/11.23.2887

    authors: Ciullo M,Debily MA,Rozier L,Autiero M,Billault A,Mayau V,El Marhomy S,Guardiola J,Bernheim A,Coullin P,Piatier-Tonneau D,Debatisse M

    更新日期:2002-11-01 00:00:00

  • Panning for gold: genome-wide scanning for linkage in type 1 diabetes.

    abstract::Genome-wide scans for linkage of chromosome regions to type 1 diabetes in affected sib pair families have revealed that the major susceptibility locus resides within the major histocompatibility complex (MHC) on chromosome 6p21 (lambda S = 2.4). It is recognized that the MHC contains multiple susceptibility loci (refe...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,评审

    doi:10.1093/hmg/5.supplement_1.1443

    authors: Todd JA,Farrall M

    更新日期:1996-01-01 00:00:00

  • A functional polymorphism of the Galphaq (GNAQ) gene is associated with accelerated mortality in African-American heart failure.

    abstract::Galphaq, encoded by the human GNAQ gene, is an effector subunit of the Gq heterotrimeric G-protein and the convergence point for signaling of multiple Gq-coupled neurohormonal receptors. To identify naturally occurring mutations that could modify GNAQ transcription, we examined genomic DNA isolated from 355 normal sub...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddm229

    authors: Liggett SB,Kelly RJ,Parekh RR,Matkovich SJ,Benner BJ,Hahn HS,Syed FM,Galvez AS,Case KL,McGuire N,Odley AM,Sparks L,Kardia SL,Dorn GW 2nd

    更新日期:2007-11-15 00:00:00

  • Genome-wide association analysis of 350 000 Caucasians from the UK Biobank identifies novel loci for asthma, hay fever and eczema.

    abstract::Even though heritability estimates suggest that the risk of asthma, hay fever and eczema is largely due to genetic factors, previous studies have not explained a large part of the genetics behind these diseases. In this genome-wide association study, we include 346 545 Caucasians from the UK Biobank to identify novel ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz175

    authors: Johansson Å,Rask-Andersen M,Karlsson T,Ek WE

    更新日期:2019-12-01 00:00:00

  • Involvement of multiple developmental genes on chromosome 1p in lung tumorigenesis.

    abstract::Lung cancer is the leading cause of cancer death in North America. Despite advances in lung cancer treatment, the overall 5 year survival rate for those diagnosed with the disease is bleak presumably due to the late stage of diagnosis. Owing to the difficulty of early detection, preneoplastic specimens are rare. Howev...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi043

    authors: Garnis C,Campbell J,Davies JJ,Macaulay C,Lam S,Lam WL

    更新日期:2005-02-15 00:00:00

  • Multidimensional genome scans identify the combinations of genetic loci linked to diabetes-related phenotypes in mice.

    abstract::Most quantitative trait loci (QTL) studies have focused on detecting the genetic effects of individual QTLs. This study thoroughly dissected the genetic components of type 2 diabetic mice, including a search for epistatic interactions and multi-locus additive effects that result in variation in diabetes-related phenot...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi433

    authors: Togawa K,Moritani M,Yaguchi H,Itakura M

    更新日期:2006-01-01 00:00:00

  • Parkin functionally interacts with PGC-1α to preserve mitochondria and protect dopaminergic neurons.

    abstract::To understand the cause of Parkinson's disease (PD), it is important to determine the functional interactions between factors linked to the disease. Parkin is associated with autosomal recessive early-onset PD, and controls the transcription of PGC-1α, a master regulator of mitochondrial biogenesis. These two factors ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw418

    authors: Zheng L,Bernard-Marissal N,Moullan N,D'Amico D,Auwerx J,Moore DJ,Knott G,Aebischer P,Schneider BL

    更新日期:2017-02-01 00:00:00

  • Lipid-enriched diet rescues lethality and slows down progression in a murine model of VCP-associated disease.

    abstract::Valosin-containing protein (VCP)-associated disease caused by mutations in the VCP gene includes combinations of a phenotypically heterogeneous group of disorders such as hereditary inclusion body myopathy, Paget's disease of bone, frontotemporal dementia and amyotrophic lateral sclerosis. Currently, there are no effe...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt523

    authors: Llewellyn KJ,Nalbandian A,Jung KM,Nguyen C,Avanesian A,Mozaffar T,Piomelli D,Kimonis VE

    更新日期:2014-03-01 00:00:00

  • Interactome: gateway into systems biology.

    abstract::Protein-protein interactions are fundamental to all biological processes, and a comprehensive determination of all protein-protein interactions that can take place in an organism provides a framework for understanding biology as an integrated system. The availability of genome-scale sets of cloned open reading frames ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,评审

    doi:10.1093/hmg/ddi335

    authors: Cusick ME,Klitgord N,Vidal M,Hill DE

    更新日期:2005-10-15 00:00:00

  • Neuronal pentraxin 1 depletion delays neurodegeneration and extends life in Sandhoff disease mice.

    abstract::GM2 gangliosidoses are a group of lysosomal storage disorders which include Sandhoff disease and Tay-Sachs disease. Dysregulation of glutamate receptors has been recently postulated in the pathology of Sandhoff disease. Glutamate receptor association with neuronal pentraxins 1 and 2, and the neuronal pentraxin recepto...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw422

    authors: Hooper AWM,Alamilla JF,Venier RE,Gillespie DC,Igdoura SA

    更新日期:2017-02-15 00:00:00

  • Functional and genomic approaches reveal an ancient CHEK2 allele associated with breast cancer in the Ashkenazi Jewish population.

    abstract::Functional and genomic approaches can be integrated to screen efficiently for pathogenic alleles in founder populations. We applied such approaches to analysis of the cancer-associated cell cycle regulator CHEK2 in the Ashkenazi Jewish population. We first identified two extended haplotypes at CHEK2 that co-segregated...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi052

    authors: Shaag A,Walsh T,Renbaum P,Kirchhoff T,Nafa K,Shiovitz S,Mandell JB,Welcsh P,Lee MK,Ellis N,Offit K,Levy-Lahad E,King MC

    更新日期:2005-02-15 00:00:00

  • Mutations in Emery-Dreifuss muscular dystrophy and their effects on emerin protein expression.

    abstract::Seventeen families with Emery-Dreifuss muscular dystrophy (EDMD) have been studied both by DNA sequencing and by emerin protein expression. Fourteen had mutations in the X-linked emerin gene, while three showed evidence of autosomal inheritance. Twelve of the 14 emerin mutations caused early termination of translation...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/7.5.855

    authors: Manilal S,Recan D,Sewry CA,Hoeltzenbein M,Llense S,Leturcq F,Deburgrave N,Barbot J,Man N,Muntoni F,Wehnert M,Kaplan J,Morris GE

    更新日期:1998-05-01 00:00:00

  • Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios.

    abstract::Parental genetic relatedness may lead to adverse health and fitness outcomes in the offspring. However, the degree to which it affects human delivery timing is unknown. We use genotype data from ≃25 000 parent-offspring trios from the Norwegian Mother, Father and Child Cohort Study to optimize runs of homozygosity (RO...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddaa255

    authors: Sole-Navais P,Bacelis J,Helgeland Ø,Modzelewska D,Vaudel M,Flatley C,Andreassen O,Njølstad PR,Muglia LJ,Johansson S,Zhang G,Jacobsson B

    更新日期:2020-12-08 00:00:00

  • Alternative splicing in the fragile X gene FMR1.

    abstract::The FMR1 gene, associated with fragile X syndrome, has recently been cloned and the sequence of partial cDNA clones is known. We have determined additional cDNA sequences both at the 5' and 3' end. We have characterized the expressed gene by means of RT-PCR in various tissues and have found that alternative splicing t...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/2.4.399

    authors: Verkerk AJ,de Graaff E,De Boulle K,Eichler EE,Konecki DS,Reyniers E,Manca A,Poustka A,Willems PJ,Nelson DL

    更新日期:1993-04-01 00:00:00

  • CRIM1 haploinsufficiency causes defects in eye development in human and mouse.

    abstract::Colobomatous macrophthalmia with microcornea syndrome (MACOM, Online Mendelian Inheritance in Man (OMIM) 602499) is an autosomal dominantly inherited malformation of the eye, which is characterized by microcornea with increased axial length, coloboma of the iris and of the optic disc, and severe myopia. We performed w...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu744

    authors: Beleggia F,Li Y,Fan J,Elcioğlu NH,Toker E,Wieland T,Maumenee IH,Akarsu NA,Meitinger T,Strom TM,Lang R,Wollnik B

    更新日期:2015-04-15 00:00:00

  • Interactome analysis reveals that FAM161A, deficient in recessive retinitis pigmentosa, is a component of the Golgi-centrosomal network.

    abstract::Defects in FAM161A, a protein of unknown function localized at the cilium of retinal photoreceptor cells, cause retinitis pigmentosa, a form of hereditary blindness. By using different fragments of this protein as baits to screen cDNA libraries of human and bovine retinas, we defined a yeast two-hybrid-based FAM161A i...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddv085

    authors: Di Gioia SA,Farinelli P,Letteboer SJ,Arsenijevic Y,Sharon D,Roepman R,Rivolta C

    更新日期:2015-06-15 00:00:00

  • Expression of C9orf72-related dipeptides impairs motor function in a vertebrate model.

    abstract::Large expansions of hexanucleotide GGGGCC (G4C2) repeats (hundreds to thousands) in the first intron of the chromosome 9 open reading frame 72 (C9orf72) locus are the strongest known genetic factor associated with amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Different hypotheses exist about the...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddy083

    authors: Swaminathan A,Bouffard M,Liao M,Ryan S,Callister JB,Pickering-Brown SM,Armstrong GAB,Drapeau P

    更新日期:2018-05-15 00:00:00