当前位置： SCI文献检索 > AMERICAN JOURNAL OF HUMAN GENETICS期刊下所有文献 > Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.

Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.

Abstract：

:We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our method employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers and thousands of samples. We compare genotype calls made with our method to genotype calls made with the BIRDSEED, CHIAMO, GenCall, and ILLUMINUS genotype-calling methods, using genotype data from the Illumina 550K and Affymetrix 500K arrays. We show that our method has higher genotype-call accuracy and yields fewer uncalled genotypes than competing methods. We perform single-marker analysis of data from the Wellcome Trust Case Control Consortium bipolar disorder and type 2 diabetes studies. For bipolar disorder, the genotype calls in the original study yield 25 markers with apparent false-positive association with bipolar disorder at a p < 10(-7) significance level, whereas genotype calls made with our method yield no associated markers at this significance threshold. Conversely, for markers with replicated association with type 2 diabetes, there is good concordance between genotype calls used in the original study and calls made by our method. Results from single-marker and haplotypic analysis of our method's genotype calls for the bipolar disorder study indicate that our method is highly effective at eliminating genotyping artifacts that cause false-positive associations in genome-wide association studies. Our new genotype-calling methods are implemented in the BEAGLE and BEAGLECALL software packages.

journal_name

Am J Hum Genet

journal_title

American journal of human genetics

authors

Browning BL,Yu Z

doi

10.1016/j.ajhg.2009.11.004

subject

Has Abstract

pub_date

2009-12-01 00:00:00

pages

847-61

issue

6

eissn

0002-9297

issn

1537-6605

pii

S0002-9297(09)00519-9

journal_volume

85

pub_type

杂志文章

相关文献

AMERICAN JOURNAL OF HUMAN GENETICS文献大全
  • Genomewide linkage scan identifies a novel susceptibility locus for restless legs syndrome on chromosome 9p.

    abstract：:Restless legs syndrome (RLS) is a common neurological disorder that affects 5%-12% of all whites. To genetically dissect this complex disease, we characterized 15 large and extended multiplex pedigrees, consisting of 453 subjects (134 affected with RLS). A familial aggregation analysis was performed, and SAGE FCOR was...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/420772

    authors： Chen S,Ondo WG,Rao S,Li L,Chen Q,Wang Q

    更新日期：2004-05-01 00:00:00

  • Exome sequencing identifies PDE4D mutations as another cause of acrodysostosis.

    abstract：:Acrodysostosis is a rare autosomal-dominant condition characterized by facial dysostosis, severe brachydactyly with cone-shaped epiphyses, and short stature. Moderate intellectual disability and resistance to multiple hormones might also be present. Recently, a recurrent mutation (c.1102C>T [p.Arg368*]) in PRKAR1A has...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1016/j.ajhg.2012.03.003

    authors： Michot C,Le Goff C,Goldenberg A,Abhyankar A,Klein C,Kinning E,Guerrot AM,Flahaut P,Duncombe A,Baujat G,Lyonnet S,Thalassinos C,Nitschke P,Casanova JL,Le Merrer M,Munnich A,Cormier-Daire V

    更新日期：2012-04-06 00:00:00

  • An alternate method for demonstration of bisphosphoglyceromutase (DPGM) on starch gels.

    abstract：:The phosphatase activity of bisphosphoglyceromutase (DPGM) was used to determine the phenotypes of the enzyme. DPGM was polymorphic in four Alaskan ethnic groups. ...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors： Scott EM,Wright RC

    更新日期：1982-11-01 00:00:00

  • A collection of ordered tetranucleotide-repeat markers from the human genome. The Utah Marker Development Group.

    abstract：:A collection of 1,069 human PCR-based genetic markers has been developed, and their distribution over the 22 autosomes and the X chromosome has been determined. Each marker was developed around a short-tandem-repeat DNA sequence. The majority (85%) of the markers described here were selected to contain tetranucleotide...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors：

    更新日期：1995-09-01 00:00:00

  • Mosaic Activating Mutations in FGFR1 Cause Encephalocraniocutaneous Lipomatosis.

    abstract：:Encephalocraniocutaneous lipomatosis (ECCL) is a sporadic condition characterized by ocular, cutaneous, and central nervous system anomalies. Key clinical features include a well-demarcated hairless fatty nevus on the scalp, benign ocular tumors, and central nervous system lipomas. Seizures, spasticity, and intellectu...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1016/j.ajhg.2016.02.006

    authors： Bennett JT,Tan TY,Alcantara D,Tétrault M,Timms AE,Jensen D,Collins S,Nowaczyk MJM,Lindhurst MJ,Christensen KM,Braddock SR,Brandling-Bennett H,Hennekam RCM,Chung B,Lehman A,Su J,Ng S,Amor DJ,University of Washington Ce

    更新日期：2016-03-03 00:00:00

  • Missense mutations in the copper transporter gene ATP7A cause X-linked distal hereditary motor neuropathy.

    abstract：:Distal hereditary motor neuropathies comprise a clinically and genetically heterogeneous group of disorders. We recently mapped an X-linked form of this condition to chromosome Xq13.1-q21 in two large unrelated families. The region of genetic linkage included ATP7A, which encodes a copper-transporting P-type ATPase mu...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1016/j.ajhg.2010.01.027

    authors： Kennerson ML,Nicholson GA,Kaler SG,Kowalski B,Mercer JF,Tang J,Llanos RM,Chu S,Takata RI,Speck-Martins CE,Baets J,Almeida-Souza L,Fischer D,Timmerman V,Taylor PE,Scherer SS,Ferguson TA,Bird TD,De Jonghe P,Feely SM,

    更新日期：2010-03-12 00:00:00

  • Promoter and 3'-untranslated-region haplotypes in the vitamin d receptor gene predispose to osteoporotic fracture: the rotterdam study.

    abstract：:Polymorphisms of the vitamin D receptor gene (VDR) have been shown to be associated with several complex diseases, including osteoporosis, but the mechanisms are unknown and study results have been inconsistent. We therefore determined sequence variation across the major relevant parts of VDR, including construction o...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/497438

    authors： Fang Y,van Meurs JB,d'Alesio A,Jhamai M,Zhao H,Rivadeneira F,Hofman A,van Leeuwen JP,Jehan F,Pols HA,Uitterlinden AG

    更新日期：2005-11-01 00:00:00

  • Inherited interleukin-12 deficiency: IL12B genotype and clinical phenotype of 13 patients from six kindreds.

    abstract：:Interleukin-12 (IL12) is a cytokine that is secreted by activated phagocytes and dendritic cells and that induces interferon-gamma production by natural-killer and T lymphocytes. It consists of two subunits, p35 and p40, which are encoded by IL12A and IL12B, respectively. The first reported patient with a genetic cyto...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/338625

    authors： Picard C,Fieschi C,Altare F,Al-Jumaah S,Al-Hajjar S,Feinberg J,Dupuis S,Soudais C,Al-Mohsen IZ,Génin E,Lammas D,Kumararatne DS,Leclerc T,Rafii A,Frayha H,Murugasu B,Wah LB,Sinniah R,Loubser M,Okamoto E,Al-Ghonaium

    更新日期：2002-02-01 00:00:00

  • Average heterozygosity revisited.

    abstract：:The estimate of heterozygosity and proportion of polymorphic loci for 33 red blood cell loci has been updated by the elimination of some loci of questionable status and the addition of data on 33 loci. The new figures for heterozygosity and proportion of polymorphic loci, .105 and .283, respectively, are based on 60 r...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors： Hedrick PW,Murray E

    更新日期：1978-07-01 00:00:00

  • Genome-wide insights into the patterns and determinants of fine-scale population structure in humans.

    abstract：:Studying genomic patterns of human population structure provides important insights into human evolutionary history and the relationship among populations, and it has significant practical implications for disease-gene mapping. Here we describe a principal component (PC)-based approach to studying intracontinental pop...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1016/j.ajhg.2009.04.015

    authors： Biswas S,Scheinfeldt LB,Akey JM

    更新日期：2009-05-01 00:00:00

  • Indications of linkage and association of Gilles de la Tourette syndrome in two independent family samples: 17q25 is a putative susceptibility region.

    abstract：:Gilles de la Tourette syndrome (GTS) is characterized by multiple motor and phonic tics and high comorbidity rates with other neurobehavioral disorders. It is hypothesized that frontal-subcortical pathways and a complex genetic background are involved in the etiopathogenesis of the disorder. The genetic basis of GTS r...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/424389

    authors： Paschou P,Feng Y,Pakstis AJ,Speed WC,DeMille MM,Kidd JR,Jaghori B,Kurlan R,Pauls DL,Sandor P,Barr CL,Kidd KK

    更新日期：2004-10-01 00:00:00

  • Cowden syndrome-affected patients with PTEN promoter mutations demonstrate abnormal protein translation.

    abstract：:Germline mutations of PTEN (phosphatase and tensin homolog deleted on chromosome 10) are associated with the multihamartomatous disorder Cowden syndrome (CS). Moreover, patients with CS with germline PTEN promoter mutations have aberrant PTEN protein expression and an increased frequency of breast cancer. Here, we exa...

    journal_title：American journal of human genetics

    pub_type： 杂志文章,多中心研究

    doi：10.1086/521051

    authors： Teresi RE,Zbuk KM,Pezzolesi MG,Waite KA,Eng C

    更新日期：2007-10-01 00:00:00

  • Sandhoff disease heterozygote detection: a component of population screening for Tay-Sachs disease carriers. I. Statistical methods.

    abstract：:Serum and leukocyte hexosaminidase profiles (total activity and percent heat-labile activity levels) in obligate Sandhoff disease (SHD) heterozygotes differ from those of obligate Tay-Sachs disease (TSD) heterozygotes and noncarrier individuals. We have developed a procedure to identify, with 95% sensitivity, carriers...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors： Cantor RM,Lim JS,Roy C,Kaback MM

    更新日期：1985-09-01 00:00:00

  • Mutations in SNRPE, which encodes a core protein of the spliceosome, cause autosomal-dominant hypotrichosis simplex.

    abstract：:Hypotrichosis simplex (HS) comprises a group of hereditary isolated alopecias that are characterized by a diffuse and progressive loss of hair starting in childhood and shows a wide phenotypic variability. We mapped an autosomal-dominant form of HS to chromosome 1q31.3-1q41 in a Spanish family. By direct sequencing, w...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1016/j.ajhg.2012.10.022

    authors： Pasternack SM,Refke M,Paknia E,Hennies HC,Franz T,Schäfer N,Fryer A,van Steensel M,Sweeney E,Just M,Grimm C,Kruse R,Ferrándiz C,Nöthen MM,Fischer U,Betz RC

    更新日期：2013-01-10 00:00:00

  • Management of Secondary Genomic Findings.

    abstract：:Secondary genomic findings are increasingly being returned to individuals as opportunistic screening results. A secondary finding offers the chance to identify and mitigate disease that may otherwise be unrecognized in an individual. As a form of screening, secondary findings must be considered differently from sequen...

    journal_title：American journal of human genetics

    pub_type： 杂志文章,评审

    doi：10.1016/j.ajhg.2020.05.002

    authors： Katz AE,Nussbaum RL,Solomon BD,Rehm HL,Williams MS,Biesecker LG

    更新日期：2020-07-02 00:00:00

  • A genomewide screen for generalized vitiligo: confirmation of AIS1 on chromosome 1p31 and evidence for additional susceptibility loci.

    abstract：:Generalized vitiligo is a common autoimmune disorder characterized by the development of white patches of skin and overlying hair due to loss of pigment-forming melanocytes from the involved areas. Family clustering of cases is not uncommon, in a pattern suggestive of multifactorial, polygenic inheritance, and there i...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/375451

    authors： Fain PR,Gowan K,LaBerge GS,Alkhateeb A,Stetler GL,Talbert J,Bennett DC,Spritz RA

    更新日期：2003-06-01 00:00:00

  • Dystrophin analysis in duchenne muscular dystrophy: use in fetal diagnosis and in genetic counseling.

    abstract：:In this report we describe the use of dystrophin analysis both in the diagnosis of Duchenne muscular dystrophy (DMD) in an aborted fetus and in genetic counseling. Our consultand's initial carrier risk, as based on family history and creatine kinase determinations, was calculated as 0.6%. DNA analysis of her family (a...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors： Bieber FR,Hoffman EP,Amos JA

    更新日期：1989-09-01 00:00:00

  • Prenatal screening for cystic fibrosis carriers: an economic evaluation.

    abstract：:The cloning of the CFTR gene has made it technically possible to avert the unwanted birth of a child with cystic fibrosis (CF). Several large trials offering prenatal CF carrier screening suggest that such screening is practical and that identified carriers generally use the information obtained. Therefore, a critical...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/302042

    authors： Rowley PT,Loader S,Kaplan RM

    更新日期：1998-10-01 00:00:00

  • Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes.

    abstract：:Animal microRNAs (miRNAs) regulate gene expression through base pairing to their targets within the 3' untranslated region (UTR) of protein-coding genes. Single-nucleotide polymorphisms (SNPs) located within such target sites can affect miRNA regulation. We mapped annotated SNPs onto a collection of experimentally sup...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/519979

    authors： Sethupathy P,Borel C,Gagnebin M,Grant GR,Deutsch S,Elton TS,Hatzigeorgiou AG,Antonarakis SE

    更新日期：2007-08-01 00:00:00

  • Serum protein polymorphisms in four populations of Afghanistan.

    abstract：:Gene frequencies of the serum proteins third component of complement (C3) transferrin (Tf), haptoglobin (Hp), group specific component (Gc), serum cholinesterase (E1), alpha1-antitrypsin (Pi), beta2-glycoprotein I (Bg), and ceruloplasmin (Cp) in the Tajiks, Pushtoons, Hazaras, and Usbeks in Afghanistan were reported. ...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors： Rahimi AG,Goedde HW,Flatz G,Kaifie S,Benkmann HG,Delbrück H

    更新日期：1977-07-01 00:00:00

  • Genotype/Phenotype analysis of a photoreceptor-specific ATP-binding cassette transporter gene, ABCR, in Stargardt disease.

    abstract：:Mutation scanning and direct DNA sequencing of all 50 exons of ABCR were completed for 150 families segregating recessive Stargardt disease (STGD1). ABCR variations were identified in 173 (57%) disease chromosomes, the majority of which represent missense amino acid substitutions. These ABCR variants were not found in...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/302251

    authors： Lewis RA,Shroyer NF,Singh N,Allikmets R,Hutchinson A,Li Y,Lupski JR,Leppert M,Dean M

    更新日期：1999-02-01 00:00:00

  • A point mutation in an intronic branch site results in aberrant splicing of COL5A1 and in Ehlers-Danlos syndrome type II in two British families.

    abstract：:Ehlers-Danlos syndrome (EDS) is a heterogeneous group of connective-tissue disorders characterized by skin fragility, joint laxity, and skeletal deformities. Type V collagen appears to have a causal role in EDS types I and II, which show phenotypic overlap and may sometimes be allelic. Type V collagen can exist as a h...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/301948

    authors： Burrows NP,Nicholls AC,Richards AJ,Luccarini C,Harrison JB,Yates JR,Pope FM

    更新日期：1998-08-01 00:00:00

  • Human serum deoxyribonuclease I (DNase I) polymorphism: pattern similarities among isozymes from serum, urine, kidney, liver, and pancreas.

    abstract：:We have devised a zymogram method with high sensitivity and resolution for investigating molecular heterogeneity and genetic polymorphism of deoxyribonuclease I. A combination technique of polyacrylamide-gel isoelectric-focusing electrophoresis and the newly developed zymogram method have led to the discovery of genet...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors： Kishi K,Yasuda T,Ikehara Y,Sawazaki K,Sato W,Iida R

    更新日期：1990-07-01 00:00:00

  • A quantitative-trait analysis of human plasma-dopamine beta-hydroxylase activity: evidence for a major functional polymorphism at the DBH locus.

    abstract：:Dopamine-beta-hydroxylase (D beta H) catalyzes the conversion of dopamine to norepinephrine and is released from sympathetic neurons into the circulation. Plasma-D beta H activity varies widely between individuals, and a subgroup of the population has very low activity levels. Mounting evidence suggests that the DBH s...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/318198

    authors： Zabetian CP,Anderson GM,Buxbaum SG,Elston RC,Ichinose H,Nagatsu T,Kim KS,Kim CH,Malison RT,Gelernter J,Cubells JF

    更新日期：2001-02-01 00:00:00

  • NIPA1 gene mutations cause autosomal dominant hereditary spastic paraplegia (SPG6).

    abstract：:The hereditary spastic paraplegias (HSPs) are genetically heterogeneous disorders characterized by progressive lower-extremity weakness and spasticity. The molecular pathogenesis is poorly understood. We report discovery of a dominant negative mutation in the NIPA1 gene in a kindred with autosomal dominant HSP (ADHSP)...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/378817

    authors： Rainier S,Chai JH,Tokarz D,Nicholls RD,Fink JK

    更新日期：2003-10-01 00:00:00

  • Genetic determination of high-density lipoprotein-cholesterol and apolipoprotein A-1 plasma levels in a family study of cardiac catheterization patients.

    abstract：:Plasma levels of two lipoprotein risk factors, high-density lipoprotein-cholesterol (HDL-C) and apolipoprotein A-1 (apo A-1), have been shown to be negatively associated with the risk of developing coronary artery disease, and several reports have examined familial factors in HDL-C and apo A-1 levels. A number of stud...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors： Prenger VL,Beaty TH,Kwiterovich PO

    更新日期：1992-11-01 00:00:00

  • Teaching human genetics in biochemistry by computer literature searching.

    abstract：:We describe a new user-intense-learning experience that incorporates the teaching of clinical and research applications of human genetics in biochemistry while training first-year medical students to develop skills in computer access to the literature. Human genetics was incorporated into the biochemistry curriculum b...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：

    authors： Proud VK,Schmidt FJ,Johnson ED,Mitchell JA

    更新日期：1989-04-01 00:00:00

  • Defects in the Cell Signaling Mediator β-Catenin Cause the Retinal Vascular Condition FEVR.

    abstract：:Familial exudative vitreoretinopathy (FEVR) is an inherited blinding disorder characterized by the abnormal development of the retinal vasculature. The majority of mutations identified in FEVR are found within four genes that encode the receptor complex (FZD4, LRP5, and TSPAN12) and ligand (NDP) of a molecular pathway...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1016/j.ajhg.2017.05.001

    authors： Panagiotou ES,Sanjurjo Soriano C,Poulter JA,Lord EC,Dzulova D,Kondo H,Hiyoshi A,Chung BH,Chu YW,Lai CHY,Tafoya ME,Karjosukarso D,Collin RWJ,Topping J,Downey LM,Ali M,Inglehearn CF,Toomes C

    更新日期：2017-06-01 00:00:00

  • The Rare-Variant Generalized Disequilibrium Test for Association Analysis of Nuclear and Extended Pedigrees with Application to Alzheimer Disease WGS Data.

    abstract：:Whole-genome and exome sequence data can be cost-effectively generated for the detection of rare-variant (RV) associations in families. Causal variants that aggregate in families usually have larger effect sizes than those found in sporadic cases, so family-based designs can be a more powerful approach than population...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1016/j.ajhg.2016.12.001

    authors： He Z,Zhang D,Renton AE,Li B,Zhao L,Wang GT,Goate AM,Mayeux R,Leal SM

    更新日期：2017-02-02 00:00:00

  • BRCA2 T2722R is a deleterious allele that causes exon skipping.

    abstract：:Patients with a strong family history of breast cancer are often counseled to receive genetic screening for BRCA1 and BRCA2 mutations, the strongest known predictors of breast cancer. A major limitation of genetic testing is the number of inconclusive results due to unclassified BRCA1 and BRCA2 sequence variants. Many...

    journal_title：American journal of human genetics

    pub_type： 杂志文章

    doi：10.1086/342192

    authors： Fackenthal JD,Cartegni L,Krainer AR,Olopade OI

    更新日期：2002-09-01 00:00:00