Practical aspects of imputation-driven meta-analysis of genome-wide association studies.

Abstract:

:Motivated by the overwhelming success of genome-wide association studies, droves of researchers are working vigorously to exchange and to combine genetic data to expediently discover genetic risk factors for common human traits. The primary tools that fuel these new efforts are imputation, allowing researchers who have collected data on a diversity of genotype platforms to share data in a uniformly exchangeable format, and meta-analysis for pooling statistical support for a genotype-phenotype association. As many groups are forming collaborations to engage in these efforts, this review collects a series of guidelines, practical detail and learned experiences from a variety of individuals who have contributed to the subject.

journal_name

Hum Mol Genet

journal_title

Human molecular genetics

authors

de Bakker PI,Ferreira MA,Jia X,Neale BM,Raychaudhuri S,Voight BF

doi

10.1093/hmg/ddn288

subject

Has Abstract

pub_date

2008-10-15 00:00:00

pages

R122-8

issue

R2

eissn

0964-6906

issn

1460-2083

pii

ddn288

journal_volume

17

pub_type

杂志文章
  • Wild-type huntingtin participates in protein trafficking between the Golgi and the extracellular space.

    abstract::Huntington disease (HD) is an autosomal dominant neurodegenerative disease caused by an expanded CAG trinucleotide repeat in the first exon of the HD gene, which results in a toxic polyglutamine stretch within huntingtin, the protein it encodes. Understanding the normal function of this essential protein is vital to u...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddl467

    authors: Strehlow AN,Li JZ,Myers RM

    更新日期:2007-02-15 00:00:00

  • Origin of the de novo duplication in Charcot-Marie-Tooth disease type 1A: unequal nonsister chromatid exchange during spermatogenesis.

    abstract::A 1.5 Mb duplication within 17p11.2 is the major mutation causing both autosomal dominant and sporadic Charcot-Marie-Tooth disease type 1A (CMT1A). An independent origin for the mutation in each family has been postulated. The proposed genetic mechanism causing the CMT1A duplication is unequal nonsister chromatid exch...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/2.12.2031

    authors: Palau F,Löfgren A,De Jonghe P,Bort S,Nelis E,Sevilla T,Martin JJ,Vilchez J,Prieto F,Van Broeckhoven C

    更新日期:1993-12-01 00:00:00

  • Structural analysis of the minisatellite present at the 3' end of the human apolipoprotein B gene: new definition of the alleles and evolutionary implications.

    abstract::The internal structure of different alleles of the minisatellite present at the 3' end of the apolipoprotein B (ApoB) gene has been analysed by different approaches including sequencing. The repeat unit arrangements of the minisatellite on 570 chromosomes belonging to European and African populations were thus determi...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.1.61

    authors: Buresi C,Desmarais E,Vigneron S,Lamarti H,Smaoui N,Cambien F,Roizes G

    更新日期:1996-01-01 00:00:00

  • Dystrophin conferral using human endothelium expressing HLA-E in the non-immunosuppressive murine model of Duchenne muscular dystrophy.

    abstract::Human leukocyte antigen (HLA)-E is a non-classical major histocompatibility complex class I (Ib) molecule, which plays an important role in immunosuppression. In this study, we investigated the immunomodulating effect of HLA-E in a xenogeneic system, using human placental artery-derived endothelial (hPAE) cells expres...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq458

    authors: Cui CH,Miyoshi S,Tsuji H,Makino H,Kanzaki S,Kami D,Terai M,Suzuki H,Umezawa A

    更新日期:2011-01-15 00:00:00

  • A region of human chromosome 9p required for testis development contains two genes related to known sexual regulators.

    abstract::Deletion of the distal short arm of chromosome 9 (9p) has been reported in a number of cases to be associated with gonadal dysgenesis and XY sex reversal, suggesting that this region contains one or more genes required in two copies for normal testis development. Recent studies have greatly narrowed the interval conta...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/8.6.989

    authors: Raymond CS,Parker ED,Kettlewell JR,Brown LG,Page DC,Kusz K,Jaruzelska J,Reinberg Y,Flejter WL,Bardwell VJ,Hirsch B,Zarkower D

    更新日期:1999-06-01 00:00:00

  • Hypermorphic and hypomorphic AARS alleles in patients with CMT2N expand clinical and molecular heterogeneities.

    abstract::Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes implicated in several dominant and recessive disease phenotypes. The canonical function of ARSs is to couple an amino acid to a cognate transfer RNA (tRNA). We identified three novel disease-associated missense mutations in the alanyl-tRNA synthetase...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddy290

    authors: Weterman MAJ,Kuo M,Kenter SB,Gordillo S,Karjosukarso DW,Takase R,Bronk M,Oprescu S,van Ruissen F,Witteveen RJW,Bienfait HME,Breuning M,Verhamme C,Hou YM,de Visser M,Antonellis A,Baas F

    更新日期:2018-12-01 00:00:00

  • The Menkes disease ATPase (ATP7A) is internalized via a Rac1-regulated, clathrin- and caveolae-independent pathway.

    abstract::The Menkes disease gene encodes a P-type transmembrane ATPase (ATP7A) that translocates cytosolic copper ions across intracellular membranes of compartments along the secretory pathway. ATP7A moves from the trans-Golgi network (TGN) to the cell surface in response to exogenously added copper ions and recycles back to ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddg166

    authors: Cobbold C,Coventry J,Ponnambalam S,Monaco AP

    更新日期:2003-07-01 00:00:00

  • Society and personal genome data.

    abstract::Genomic data offer a goldmine of information for understanding the contribution of genetic variation makes to health and disease. The potential of genomic medicine, to predict, diagnose, manage and treat genetic disease, is underpinned by accurate variant interpretation. This in itself hinges on the ability to access ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,评审

    doi:10.1093/hmg/ddy084

    authors: Middleton A

    更新日期:2018-05-01 00:00:00

  • Functional annotation of a novel NFKB1 promoter polymorphism that increases risk for ulcerative colitis.

    abstract::Nuclear Factor-kappaB (NF-kappaB) is a major transcription regulator of immune response, apoptosis and cell-growth control genes, and is upregulated in inflammatory bowel disease (IBD), both ulcerative colitis (UC) and Crohn's disease. The NFKB1 gene encodes the NF-kappaB p105/p50 isoforms. Genome-wide screens in IBD ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddh008

    authors: Karban AS,Okazaki T,Panhuysen CI,Gallegos T,Potter JJ,Bailey-Wilson JE,Silverberg MS,Duerr RH,Cho JH,Gregersen PK,Wu Y,Achkar JP,Dassopoulos T,Mezey E,Bayless TM,Nouvet FJ,Brant SR

    更新日期:2004-01-01 00:00:00

  • Cloning and characterization of the human choroideremia gene.

    abstract::Positional cloning has previously resulted in the identification of a gene which is disrupted by deletions in patients with the classic choroideremia (CHM) phenotype. More subtle mutations had been identified in 4 exons of the 3' portion but not elsewhere in the CHM gene. We have now isolated and characterized the com...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/3.7.1041

    authors: van Bokhoven H,van den Hurk JA,Bogerd L,Philippe C,Gilgenkrantz S,de Jong P,Ropers HH,Cremers FP

    更新日期:1994-07-01 00:00:00

  • Predominance of pathogenic missense variants in the RAD51C gene occurring in breast and ovarian cancer families.

    abstract::RAD51C was defined by Meindl et al. in 2010 as a high-risk gene involved in hereditary breast and ovarian cancers. Although this role seems to be clear, nowadays there is controversy about the indication of including the gene in routine clinical genetic testing, due to the lower prevalence or the absence of mutations ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/dds115

    authors: Osorio A,Endt D,Fernández F,Eirich K,de la Hoya M,Schmutzler R,Caldés T,Meindl A,Schindler D,Benitez J

    更新日期:2012-07-01 00:00:00

  • PGC-1alpha/beta induced expression partially compensates for respiratory chain defects in cells from patients with mitochondrial disorders.

    abstract::Members of the peroxisome proliferator-activated receptor gamma coactivator (PGC) family are potent inducers of mitochondrial biogenesis. We have tested the potential effect of increased mitochondrial biogenesis in cells derived from patients harboring oxidative phosphorylation defects due to either nuclear or mitocho...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddp093

    authors: Srivastava S,Diaz F,Iommarini L,Aure K,Lombes A,Moraes CT

    更新日期:2009-05-15 00:00:00

  • Genetic and chemical rescue of the Saccharomyces cerevisiae phenotype induced by mitochondrial DNA polymerase mutations associated with progressive external ophthalmoplegia in humans.

    abstract::The human POLG gene encodes the catalytic subunit of mitochondrial DNA polymerase gamma (pol gamma). Mutations in pol gamma are associated with a spectrum of disease phenotypes including autosomal dominant and recessive forms of progressive external ophthalmoplegia, spino-cerebellar ataxia and epilepsy, and Alpers-Hut...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddl219

    authors: Baruffini E,Lodi T,Dallabona C,Puglisi A,Zeviani M,Ferrero I

    更新日期:2006-10-01 00:00:00

  • Homozygous EEF1A2 mutation causes dilated cardiomyopathy, failure to thrive, global developmental delay, epilepsy and early death.

    abstract::Eukaryotic elongation factor 1A (EEF1A), is encoded by two distinct isoforms, EEF1A1 and EEF1A2; whereas EEF1A1 is expressed almost ubiquitously, EEF1A2 expression is limited such that it is only detectable in skeletal muscle, heart, brain and spinal cord. Currently, the role of EEF1A2 in normal cardiac development an...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx239

    authors: Cao S,Smith LL,Padilla-Lopez SR,Guida BS,Blume E,Shi J,Morton SU,Brownstein CA,Beggs AH,Kruer MC,Agrawal PB

    更新日期:2017-09-15 00:00:00

  • Variegated yet non-random rod and cone photoreceptor disease patterns in RPGR-ORF15-associated retinal degeneration.

    abstract::Mutations in the ORF15 exon of the RPGR gene cause a common form of X-linked retinitis pigmentosa, which often results in severe loss of vision. In dogs and mice, gene augmentation therapy has been shown to arrest the progressive degeneration of rod and cone photoreceptors. However, the distribution of potentially tre...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw361

    authors: Charng J,Cideciyan AV,Jacobson SG,Sumaroka A,Schwartz SB,Swider M,Roman AJ,Sheplock R,Anand M,Peden MC,Khanna H,Heon E,Wright AF,Swaroop A

    更新日期:2016-12-15 00:00:00

  • Cholesterol 24-hydroxylase defect is implicated in memory impairments associated with Alzheimer-like Tau pathology.

    abstract::Alzheimer's disease (AD) is characterized by both amyloid and Tau pathologies. The amyloid component and altered cholesterol metabolism are closely linked, but the relationship between Tau pathology and cholesterol is currently unclear. Brain cholesterol is synthesized in situ and cannot cross the blood-brain barrier:...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddv268

    authors: Burlot MA,Braudeau J,Michaelsen-Preusse K,Potier B,Ayciriex S,Varin J,Gautier B,Djelti F,Audrain M,Dauphinot L,Fernandez-Gomez FJ,Caillierez R,Laprévote O,Bièche I,Auzeil N,Potier MC,Dutar P,Korte M,Buée L,Blum D,

    更新日期:2015-11-01 00:00:00

  • Distortion of allelic expression of apolipoprotein E in Alzheimer's disease.

    abstract::The APOE epsilon4 allele is a strong genetic susceptibility factor for Alzheimer's disease. Interaction with other biological factors may modulate the effect of the apoE isoforms. However, previous work suggested that other genetic variability within the APOE locus, influencing the effect of the epsilon4 allele, may e...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/6.12.2151

    authors: Lambert JC,Pérez-Tur J,Dupire MJ,Galasko D,Mann D,Amouyel P,Hardy J,Delacourte A,Chartier-Harlin MC

    更新日期:1997-11-01 00:00:00

  • The p38 subunit of the aminoacyl-tRNA synthetase complex is a Parkin substrate: linking protein biosynthesis and neurodegeneration.

    abstract::Parkinson's disease (PD) is a severe neurological disorder, characterized by the progressive degeneration of the dopaminergic nigrostriatal pathway and the presence of Lewy bodies (LBs). The discovery of genes responsible for familial forms of the disease has provided insights into its pathogenesis. Mutations in the p...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddg159

    authors: Corti O,Hampe C,Koutnikova H,Darios F,Jacquier S,Prigent A,Robinson JC,Pradier L,Ruberg M,Mirande M,Hirsch E,Rooney T,Fournier A,Brice A

    更新日期:2003-06-15 00:00:00

  • Non-manifesting AHI1 truncations indicate localized loss-of-function tolerance in a severe Mendelian disease gene.

    abstract::Determination of variant pathogenicity represents a major challenge in the era of high-throughput sequencing. Erroneous categorization may result if variants affect genes that are in fact dispensable. We demonstrate that this also applies to rare, apparently unambiguous truncating mutations of an established disease g...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddv022

    authors: Elsayed SM,Phillips JB,Heller R,Thoenes M,Elsobky E,Nürnberg G,Nürnberg P,Seland S,Ebermann I,Altmüller J,Thiele H,Toliat M,Körber F,Hu XJ,Wu YD,Zaki MS,Abdel-Salam G,Gleeson J,Boltshauser E,Westerfield M,Bolz HJ

    更新日期:2015-05-01 00:00:00

  • Autosomal dominant Charcot-Marie-Tooth axonal neuropathy mapped on chromosome 7p (CMT2D).

    abstract::Clinical, electrophysiological and genetic linkage studies were performed on a large autosomal dominant family with Charcot-Marie-Tooth axonal neuropathy type 2 (CMT2) with 38 members of which 14 were affected. Onset of the disease was between 16 and 30 years of age with weakness and atrophy of the hands more severe t...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.9.1373

    authors: Ionasescu V,Searby C,Sheffield VC,Roklina T,Nishimura D,Ionasescu R

    更新日期:1996-09-01 00:00:00

  • Genome-wide association study identifies a novel susceptibility gene for serum TSH levels in Chinese populations.

    abstract::Thyroid-stimulating hormone (TSH) is a sensitive indicator of thyroid function. High and low TSH levels reflect hypothyroidism and hyperthyroidism, respectively. Even within the normal range, small differences in TSH levels, on the order of 0.5-1.0 mU/l, are associated with significant differences in blood pressure, B...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu250

    authors: Zhan M,Chen G,Pan CM,Gu ZH,Zhao SX,Liu W,Wang HN,Ye XP,Xie HJ,Yu SS,Liang J,Gao GQ,Yuan GY,Zhang XM,Zuo CL,Su B,Huang W,Ning G,Chen SJ,Chen JL,Song HD,China Consortium for Genetics of Autoimmune Thyroid Disease.

    更新日期:2014-10-15 00:00:00

  • Signatures of adaptive evolution within human non-coding sequence.

    abstract::The human genome is often portrayed as consisting of three sequence types, each distinguished by their mode of evolution. Purifying selection is estimated to act on 2.5-5.0% of the genome, whereas virtually all remaining sequence is considered to have evolved neutrally and to be devoid of functionality. The third mode...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,评审

    doi:10.1093/hmg/ddl182

    authors: Ponting CP,Lunter G

    更新日期:2006-10-15 00:00:00

  • Cerebral small-vessel disease protein HTRA1 controls the amount of TGF-β1 via cleavage of proTGF-β1.

    abstract::Cerebral small-vessel disease is a common disorder in elderly populations; however, its molecular basis is not well understood. We recently demonstrated that mutations in the high-temperature requirement A (HTRA) serine peptidase 1 (HTRA1) gene cause a hereditary cerebral small-vessel disease, cerebral autosomal reces...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddr063

    authors: Shiga A,Nozaki H,Yokoseki A,Nihonmatsu M,Kawata H,Kato T,Koyama A,Arima K,Ikeda M,Katada S,Toyoshima Y,Takahashi H,Tanaka A,Nakano I,Ikeuchi T,Nishizawa M,Onodera O

    更新日期:2011-05-01 00:00:00

  • Non-disjunction of chromosome 13.

    abstract::We performed a molecular study with 21 microsatellites on a sample of 82 trisomy 13 conceptuses, the largest number of cases studied to date. The parental origin was determined in every case and in 89% the extra chromosome 13 was of maternal origin with an almost equal number of maternal MI and MII errors. The latter ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddm148

    authors: Bugge M,Collins A,Hertz JM,Eiberg H,Lundsteen C,Brandt CA,Bak M,Hansen C,Delozier CD,Lespinasse J,Tranebjaerg L,Hahnemann JM,Rasmussen K,Bruun-Petersen G,Duprez L,Tommerup N,Petersen MB

    更新日期:2007-08-15 00:00:00

  • NOTCH, a new signaling pathway implicated in holoprosencephaly.

    abstract::Genetics of Holoprosencephaly (HPE), a congenital malformation of the developing human forebrain, is due to multiple genetic defects. Most genes that have been implicated in HPE belong to the sonic hedgehog signaling pathway. Here we describe a new candidate gene isolated from array comparative genomic hybridization r...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq556

    authors: Dupé V,Rochard L,Mercier S,Le Pétillon Y,Gicquel I,Bendavid C,Bourrouillou G,Kini U,Thauvin-Robinet C,Bohan TP,Odent S,Dubourg C,David V

    更新日期:2011-03-15 00:00:00

  • Trinucleotide expansion mutations in the cartilage oligomeric matrix protein (COMP) gene.

    abstract::Pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED) are two human autosomal dominant skeletal dysplasias characterized by variable short stature, joint laxity and early-onset degenerative joint disease. Both disorders can result from mut-ations in the gene for cartilage oligomeric matrix protein (COMP...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/8.1.123

    authors: Délot E,King LM,Briggs MD,Wilcox WR,Cohn DH

    更新日期:1999-01-01 00:00:00

  • Multiple deletions of mtDNA in two brothers with sideroblastic anemia and mitochondrial myopathy and in their asymptomatic mother.

    abstract::Two brothers presented with a clinical picture characterized by sideroblastic anemia, mild pancreatic insufficiency and progressive muscle weakness. The presence of an associated permanent basal lactic acidemia raised the suspicion of a mitochondrial disease. A muscle biopsy performed in both siblings proved the prese...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/3.11.1945

    authors: Casademont J,Barrientos A,Cardellach F,Rötig A,Grau JM,Montoya J,Beltrán B,Cervantes F,Rozman C,Estivill X

    更新日期:1994-11-01 00:00:00

  • Localization and functional analyses of the MLC1 protein involved in megalencephalic leukoencephalopathy with subcortical cysts.

    abstract::Mutations in the MLC1 gene are responsible for one form of the neurological disorder megalencephalic leukoencephalopathy with subcortical cysts (MLC). The disease is a type of vacuolating myelinopathy. The biochemical properties and the function of the MLC1 protein are unknown. To characterize MLC1, we generated polyc...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddh291

    authors: Teijido O,Martínez A,Pusch M,Zorzano A,Soriano E,Del Río JA,Palacín M,Estévez R

    更新日期:2004-11-01 00:00:00

  • Cellular stressors may alter islet hormone cell proportions by moderation of alternative splicing patterns.

    abstract::Changes to islet cell identity in response to type 2 diabetes (T2D) have been reported in rodent models, but are less well characterized in humans. We assessed the effects of aspects of the diabetic microenvironment on hormone staining, total gene expression, splicing regulation and the alternative splicing patterns o...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz094

    authors: Jeffery N,Richardson S,Chambers D,Morgan NG,Harries LW

    更新日期:2019-08-15 00:00:00

  • Zebrafish: bridging the gap between development and disease.

    abstract::The zebrafish has been the model of choice amongst developmental biologists for many years. This small freshwater species offers many advantages to the study of organ and tissue development that are not provided by other model systems. Against this background, modern molecular genetic approaches are being applied to e...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,评审

    doi:10.1093/hmg/9.16.2443

    authors: Dodd A,Curtis PM,Williams LC,Love DR

    更新日期:2000-10-01 00:00:00