Collapsed methylation quantitative trait loci analysis for low frequency and rare variants.

Abstract:

BACKGROUND:Single variant approaches have been successful in identifying DNA methylation quantitative trait loci (mQTL), although as with complex traits they lack the statistical power to identify the effects from rare genetic variants. We have undertaken extensive analyses to identify regions of low frequency and rare variants that are associated with DNA methylation levels. METHODS:We used repeated measurements of DNA methylation from five different life stages in human blood, taken from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Variants were collapsed across CpG islands and their flanking regions to identify variants collectively associated with methylation, where no single variant was individually responsible for the observed signal. All analyses were undertaken using the sequence kernel association test. RESULTS:For loci where no individual variant mQTL was observed based on a single variant analysis, we identified 95 unique regions where the combined effect of low frequency variants (MAF ≤ 5%) provided strong evidence of association with methylation. For loci where there was previous evidence of an individual variant mQTL, a further 3 regions provided evidence of association between multiple low frequency variants and methylation levels. Effects were observed consistently across 5 different time points in the lifecourse and evidence of replication in the TwinsUK and Exeter cohorts was also identified. CONCLUSION:We have demonstrated the potential of this novel approach to mQTL analysis by analysing the combined effect of multiple low frequency or rare variants. Future studies should benefit from applying this approach as a complementary follow up to single variant analyses.

journal_name

Hum Mol Genet

journal_title

Human molecular genetics

authors

Richardson TG,Shihab HA,Hemani G,Zheng J,Hannon E,Mill J,Carnero-Montoro E,Bell JT,Lyttleton O,McArdle WL,Ring SM,Rodriguez S,Campbell C,Smith GD,Relton CL,Timpson NJ,Gaunt TR

doi

10.1093/hmg/ddw283

subject

Has Abstract

pub_date

2016-10-01 00:00:00

pages

4339-4349

issue

19

eissn

0964-6906

issn

1460-2083

pii

ddw283

journal_volume

25

pub_type

杂志文章
  • The telomere lengthening mechanism in telomerase-negative immortal human cells does not involve the telomerase RNA subunit.

    abstract::According to the telomere hypothesis of senescence, the progressive shortening of telomeres that occurs upon division of normal somatic cells eventually leads to cellular senescence. The immortalisation of human cells is associated with the acquisition of a telomere maintenance mechanism which is usually dependent upo...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/6.6.921

    authors: Bryan TM,Marusic L,Bacchetti S,Namba M,Reddel RR

    更新日期:1997-06-01 00:00:00

  • Sarcoidosis HLA class II genotyping distinguishes differences of clinical phenotype across ethnic groups.

    abstract::The HLA class II (DRB1 and DQB1) associations with sarcoidosis have been studied by several groups but often without consistent results. In this paper, we consider the hypothesis that observed inconsistencies relate to distinct, genetically encoded disease phenotypes which differ in prevalence between centres. We ther...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq325

    authors: Sato H,Woodhead FA,Ahmad T,Grutters JC,Spagnolo P,van den Bosch JM,Maier LA,Newman LS,Nagai S,Izumi T,Wells AU,du Bois RM,Welsh KI

    更新日期:2010-10-15 00:00:00

  • Familial paroxysmal kinesigenic dyskinesia is associated with mutations in the KCNA1 gene.

    abstract::Paroxysmal kinesigenic dyskinesia (PKD) is a heterogeneous movement disorder characterized by recurrent dyskinesia attacks triggered by sudden movement. PRRT2 has been identified as the first causative gene of PKD. However, it is only responsible for approximately half of affected individuals, indicating that other lo...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx430

    authors: Yin XM,Lin JH,Cao L,Zhang TM,Zeng S,Zhang KL,Tian WT,Hu ZM,Li N,Wang JL,Guo JF,Wang RX,Xia K,Zhang ZH,Yin F,Peng J,Liao WP,Yi YH,Liu JY,Yang ZX,Chen Z,Mao X,Yan XX,Jiang H,Shen L,Chen SD,Zhang LM,Tan

    更新日期:2018-02-15 00:00:00

  • Overexpression of yeast hsp104 reduces polyglutamine aggregation and prolongs survival of a transgenic mouse model of Huntington's disease.

    abstract::Huntington's disease is a devastating neurodegenerative condition associated with the formation of intraneuronal aggregates by mutant huntingtin. Aggregate formation is a property shared by the nine related diseases caused by polyglutamine codon expansion mutations and also by other neurodegenerative conditions like P...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi372

    authors: Vacher C,Garcia-Oroz L,Rubinsztein DC

    更新日期:2005-11-15 00:00:00

  • Functional genomic screen and network analysis reveal novel modifiers of tauopathy dissociated from tau phosphorylation.

    abstract::A functional genetic screen using loss-of-function and gain-of-function alleles was performed to identify modifiers of tau-induced neurotoxicity using the 2N/4R (full-length) isoform of wild-type human tau expressed in the fly retina. We previously reported eye pigment mutations, which create dysfunctional lysosomes, ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr432

    authors: Ambegaokar SS,Jackson GR

    更新日期:2011-12-15 00:00:00

  • Serum calcium and risk of migraine: a Mendelian randomization study.

    abstract::Migraine affects ∼14% of the world's population, though not all predisposing causal risk factors are known. We used electronic health records, genetic co-heritability analysis, and a two-sample Mendelian Randomization (MR) design to determine if elevated serum calcium levels were associated with risk of migraine heada...

    journal_title:Human molecular genetics

    pub_type: 临床试验,杂志文章,多中心研究

    doi:10.1093/hmg/ddw416

    authors: Yin P,Anttila V,Siewert KM,Palotie A,Davey Smith G,Voight BF

    更新日期:2017-02-15 00:00:00

  • Homozygous mutation of PLCZ1 leads to defective human oocyte activation and infertility that is not rescued by the WW-binding protein PAWP.

    abstract::In mammals, sperm-oocyte fusion initiates Ca(2+) oscillations leading to a series of events called oocyte activation, which is the first stage of embryo development. Ca(2+) signaling is elicited by the delivery of an oocyte-activating factor by the sperm. A sperm-specific phospholipase C (PLCZ1) has emerged as the lik...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddv617

    authors: Escoffier J,Lee HC,Yassine S,Zouari R,Martinez G,Karaouzène T,Coutton C,Kherraf ZE,Halouani L,Triki C,Nef S,Thierry-Mieg N,Savinov SN,Fissore R,Ray PF,Arnoult C

    更新日期:2016-03-01 00:00:00

  • AAV9 delivered bispecific nanobody attenuates amyloid burden in the gelsolin amyloidosis mouse model.

    abstract::Gelsolin amyloidosis is a dominantly inherited, incurable type of amyloidosis. A single point mutation in the gelsolin gene (G654A is most common) results in the loss of a Ca2+  binding site in the second gelsolin domain. Consequently, this domain partly unfolds and exposes an otherwise buried furin cleavage site at t...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx056

    authors: Verhelle A,Nair N,Everaert I,Van Overbeke W,Supply L,Zwaenepoel O,Peleman C,Van Dorpe J,Lahoutte T,Devoogdt N,Derave W,Chuah MK,VandenDriessche T,Gettemans J

    更新日期:2017-04-01 00:00:00

  • Cytoglobin has bimodal: tumour suppressor and oncogene functions in lung cancer cell lines.

    abstract::Cytoglobin (CYGB) is frequently downregulated in many types of human malignancies, and its exogenous overexpression reduces proliferation of cancer cells. Despite its implied tumour suppressor (TSG) functions, its exact role in carcinogenesis remains unclear as CYGB upregulation is also associated with tumour hypoxia ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt174

    authors: Oleksiewicz U,Liloglou T,Tasopoulou KM,Daskoulidou N,Bryan J,Gosney JR,Field JK,Xinarianos G

    更新日期:2013-08-15 00:00:00

  • Characterization of the human jumonji gene.

    abstract::While constructing a cDNA library of human embryos, we have isolated a clone homologous to jumonji, a mouse gene required for neural tube formation. We have determined the complete coding sequence of the human homologue (JMJ) and deduced the amino acid sequence of the putative protein. We show here that human and mous...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.10.1637

    authors: Bergé-Lefranc JL,Jay P,Massacrier A,Cau P,Mattei MG,Bauer S,Marsollier C,Berta P,Fontes M

    更新日期:1996-10-01 00:00:00

  • Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene.

    abstract::Psoriasis is an immune-mediated skin disorder that is inherited as a multifactorial trait. Linkage studies have clearly identified a primary disease susceptibility locus lying within the major histocompatibility complex (MHC), but have generated conflicting results for other genomic regions. To overcome this difficult...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddn091

    authors: Capon F,Bijlmakers MJ,Wolf N,Quaranta M,Huffmeier U,Allen M,Timms K,Abkevich V,Gutin A,Smith R,Warren RB,Young HS,Worthington J,Burden AD,Griffiths CE,Hayday A,Nestle FO,Reis A,Lanchbury J,Barker JN,Trembath RC

    更新日期:2008-07-01 00:00:00

  • RNA editing alterations in a multi-ethnic Alzheimer disease cohort converge on immune and endocytic molecular pathways.

    abstract::Little is known about the post-transcriptional mechanisms that modulate the genetic effects in the molecular pathways underlying Alzheimer disease (AD), and even less is known about how these changes might differ across diverse populations. RNA editing, the process that alters individual bases of RNA, may contribute t...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz110

    authors: Gardner OK,Wang L,Van Booven D,Whitehead PL,Hamilton-Nelson KL,Adams LD,Starks TD,Hofmann NK,Vance JM,Cuccaro ML,Martin ER,Byrd GS,Haines JL,Bush WS,Beecham GW,Pericak-Vance MA,Griswold AJ

    更新日期:2019-09-15 00:00:00

  • Widespread enzymatic correction of CNS tissues by a single intracerebral injection of therapeutic lentiviral vector in leukodystrophy mouse models.

    abstract::Leukodystrophies are rare diseases caused by defects in the genes coding for lysosomal enzymes that degrade several glycosphingolipids. Gene therapy for leukodystrophies requires efficient distribution of the missing enzymes in CNS tissues to prevent demyelination and neurodegeneration. In this work, we targeted the e...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq099

    authors: Lattanzi A,Neri M,Maderna C,di Girolamo I,Martino S,Orlacchio A,Amendola M,Naldini L,Gritti A

    更新日期:2010-06-01 00:00:00

  • A mutational hot spot in keratin 10 (KRT 10) in patients with epidermolytic hyperkeratosis.

    abstract::Epidermolytic hyperkeratosis (EHK), (bullous congenital ichthyosiform erythroderma), is an autosomal dominant human skin disorder. Recently, we and others have described mutations in keratins 1 and 10 (K1 and K10) in patients with this disease. Structure-function models predict that these mutations would impair normal...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/2.12.2147

    authors: Rothnagel JA,Fisher MP,Axtell SM,Pittelkow MR,Anton-Lamprecht I,Huber M,Hohl D,Roop DR

    更新日期:1993-12-01 00:00:00

  • Rab11 rescues synaptic dysfunction and behavioural deficits in a Drosophila model of Huntington's disease.

    abstract::Synapse abnormalities in Huntington's disease (HD) patients can precede clinical diagnosis and neuron loss by decades. The polyglutamine expansion in the huntingtin (htt) protein that underlies this disorder leads to perturbations in many cellular pathways, including the disruption of Rab11-dependent endosomal recycli...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/dds117

    authors: Steinert JR,Campesan S,Richards P,Kyriacou CP,Forsythe ID,Giorgini F

    更新日期:2012-07-01 00:00:00

  • A mutation in the nerve growth factor beta gene (NGFB) causes loss of pain perception.

    abstract::Identification of genes associated with pain insensitivity syndromes can increase the understanding of the pathways involved in pain and contribute to the understanding of how sensory pathways relate to other neurological functions. In this report we describe the mapping and identification of the gene responsible for ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddh096

    authors: Einarsdottir E,Carlsson A,Minde J,Toolanen G,Svensson O,Solders G,Holmgren G,Holmberg D,Holmberg M

    更新日期:2004-04-15 00:00:00

  • Regulation of murine survival motor neuron (Smn) protein levels by modifying Smn exon 7 splicing.

    abstract::Proximal spinal muscular atrophy (SMA) is caused by mutations in the survival motor neuron gene (SMN1). In humans, two nearly identical copies of SMN exist and differ only by a single non-polymorphic C-->T nucleotide transition in exon 7. SMN1 contains a 'C' nucleotide at the +6 position of exon 7 and produces primari...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/10.23.2727

    authors: DiDonato CJ,Lorson CL,De Repentigny Y,Simard L,Chartrand C,Androphy EJ,Kothary R

    更新日期:2001-11-01 00:00:00

  • Inhibition of GSK3β improves hippocampus-dependent learning and rescues neurogenesis in a mouse model of fragile X syndrome.

    abstract::Fragile X syndrome (FXS), a common inherited form of intellectual disability with learning deficits, results from a loss of fragile X mental retardation protein (FMRP). Despite extensive research, treatment options for FXS remain limited. Since FMRP is known to play an important role in adult hippocampal neurogenesis ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr501

    authors: Guo W,Murthy AC,Zhang L,Johnson EB,Schaller EG,Allan AM,Zhao X

    更新日期:2012-02-01 00:00:00

  • Characterization of FMR1 proteins isolated from different tissues.

    abstract::FMR1 protein expression was studied in different tissues. In human, monkey and murine tissues, high molecular mass FMR1 proteins (67-80 kDa) are found, as shown in lymphoblastoid cells lines. The identity of these proteins was confirmed by their absence in tissues from patients with the fragile X syndrome and a FMR1 k...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/4.5.895

    authors: Verheij C,de Graaff E,Bakker CE,Willemsen R,Willems PJ,Meijer N,Galjaard H,Reuser AJ,Oostra BA,Hoogeveen AT

    更新日期:1995-05-01 00:00:00

  • Inferring Recombination Patterns In African Populations.

    abstract::While several high-resolution recombination maps exist for European-descent populations, the recombination landscape of African populations remains relatively understudied. Given that there is high genetic divergence among groups in Africa, it is possible that recombination hotspots also diverge significantly. Both li...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddab020

    authors: Eeden G,Uren C,Möller M,Henn BM

    更新日期:2021-01-14 00:00:00

  • Novel glycogen synthase kinase 3 and ubiquitination pathways in progressive myoclonus epilepsy.

    abstract::Lafora progressive myoclonus epilepsy, caused by defective laforin or malin, insidiously present in normal teenagers with cognitive decline, followed by rapidly intractable epilepsy, dementia and death. Pathology reveals neurodegeneration with neurofibrillary tangle formation and Lafora bodies (LBs). LBs are deposits ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi306

    authors: Lohi H,Ianzano L,Zhao XC,Chan EM,Turnbull J,Scherer SW,Ackerley CA,Minassian BA

    更新日期:2005-09-15 00:00:00

  • Pael receptor induces death of dopaminergic neurons in the substantia nigra via endoplasmic reticulum stress and dopamine toxicity, which is enhanced under condition of parkin inactivation.

    abstract::Selective loss of dopaminergic neurons is the final common pathway in Parkinson's disease. Expression of Parkin associated endothelin-receptor like receptor (Pael-R) in mouse brain was achieved by injecting adenoviral vectors carrying a modified neuron-specific promoter and Cre recombinase into the striatum. Upregulat...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddl439

    authors: Kitao Y,Imai Y,Ozawa K,Kataoka A,Ikeda T,Soda M,Nakimawa K,Kiyama H,Stern DM,Hori O,Wakamatsu K,Ito S,Itohara S,Takahashi R,Ogawa S

    更新日期:2007-01-01 00:00:00

  • Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles.

    abstract::Neonatal dried blood spots (NDBS) are a widely banked sample source that enables retrospective investigation into early life molecular events. Here, we performed low-pass whole genome bisulfite sequencing (WGBS) of 86 NDBS DNA to examine early life Down syndrome (DS) DNA methylation profiles. DS represents an example ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddaa218

    authors: Laufer BI,Hwang H,Jianu JM,Mordaunt CE,Korf IF,Hertz-Picciotto I,LaSalle JM

    更新日期:2021-01-06 00:00:00

  • Characterisation of the exon structure of the Fanconi anaemia group C gene by vectorette PCR.

    abstract::A cDNA for Fanconi anaemia complementation group C (FACC) has recently been cloned. We have now isolated a yeast artificial chromosome clone containing the FACC gene, and used vectorette PCR to determine its exon structure. The 1674-nucleotide coding sequence of the gene is highly interrupted, and contains 14 exons ra...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/2.1.35

    authors: Gibson RA,Buchwald M,Roberts RG,Mathew CG

    更新日期:1993-01-01 00:00:00

  • Genome-wide association study identifies novel loci association with fasting insulin and insulin resistance in African Americans.

    abstract::Insulin resistance (IR) is a key determinant of type 2 diabetes (T2D) and other metabolic disorders. This genome-wide association study (GWAS) was designed to shed light on the genetic basis of fasting insulin (FI) and IR in 927 non-diabetic African Americans. 5 396 838 single-nucleotide polymorphisms (SNPs) were test...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/dds282

    authors: Chen G,Bentley A,Adeyemo A,Shriner D,Zhou J,Doumatey A,Huang H,Ramos E,Erdos M,Gerry N,Herbert A,Christman M,Rotimi C

    更新日期:2012-10-15 00:00:00

  • Post-weaning diet affects genomic imprinting at the insulin-like growth factor 2 (Igf2) locus.

    abstract::IGF2 loss of imprinting (LOI) is fairly prevalent and implicated in the pathogenesis of human cancer and developmental disease; however, the causes of this phenomenon are largely unknown. We determined whether the post-weaning diet of mice affects allelic expression and CpG methylation of Igf2. C57BL/6JxCast/EiJ F1 hy...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi484

    authors: Waterland RA,Lin JR,Smith CA,Jirtle RL

    更新日期:2006-03-01 00:00:00

  • Primary angle closure glaucoma (PACG) susceptibility gene PLEKHA7 encodes a novel Rac1/Cdc42 GAP that modulates cell migration and blood-aqueous barrier function.

    abstract::PLEKHA7, a gene recently associated with primary angle closure glaucoma (PACG), encodes an apical junctional protein expressed in components of the blood aqueous barrier (BAB). We found that PLEKHA7 is down-regulated in lens epithelial cells and in iris tissue of PACG patients. PLEKHA7 expression also correlated with ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx292

    authors: Lee MC,Shei W,Chan AS,Chua BT,Goh SR,Chong YF,Hilmy MH,Nongpiur ME,Baskaran M,Khor CC,Aung T,Hunziker W,Vithana EN

    更新日期:2017-10-15 00:00:00

  • A mutation in the mouse Amelx tri-tyrosyl domain results in impaired secretion of amelogenin and phenocopies human X-linked amelogenesis imperfecta.

    abstract::Amelogenesis imperfecta (AI) describes a broad group of clinically and genetically heterogeneous inherited defects of dental enamel bio-mineralization. Despite identification of a number of genetic mutations underlying AI, the precise causal mechanisms have yet to be determined. Using a multi-disciplinary approach, we...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq001

    authors: Barron MJ,Brookes SJ,Kirkham J,Shore RC,Hunt C,Mironov A,Kingswell NJ,Maycock J,Shuttleworth CA,Dixon MJ

    更新日期:2010-04-01 00:00:00

  • FGFR3 is a target of the homeobox transcription factor SHOX in limb development.

    abstract::The short stature homeobox gene SHOX encodes a transcription factor which is important for normal limb development. In humans, SHOX deficiency has been associated with various short stature syndromes including Leri-Weill dyschondrosteosis (LWD), Langer mesomelic dysplasia and Turner syndrome as well as non-syndromic i...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr030

    authors: Decker E,Durand C,Bender S,Rödelsperger C,Glaser A,Hecht J,Schneider KU,Rappold G

    更新日期:2011-04-15 00:00:00

  • Mitochondrial DNA polymerase-gamma and human disease.

    abstract::The maintenance of mitochondrial DNA (mtDNA) is critically dependent upon polymerase-gamma (pol-gamma), encoded by the nuclear gene POLG. Over the last 5 years, it has become clear that mutations of POLG are a major cause of human disease. Secondary mtDNA defects characterize these disorders, with mtDNA depletion, mul...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,评审

    doi:10.1093/hmg/ddl233

    authors: Hudson G,Chinnery PF

    更新日期:2006-10-15 00:00:00