Improving estimates of genetic maps: a meta-analysis-based approach.

Abstract:

:Inaccurate genetic (or linkage) maps can reduce the power to detect linkage, increase type I error, and distort haplotype and relationship inference. To improve the accuracy of existing maps, I propose a meta-analysis-based method that combines independent map estimates into a single estimate of the linkage map. The method uses the variance of each independent map estimate to combine them efficiently, whether the map estimates use the same set of markers or not. As compared with a joint analysis of the pooled genotype data, the proposed method is attractive for three reasons: (1) it has comparable efficiency to the maximum likelihood map estimate when the pooled data are homogeneous; (2) relative to existing map estimation methods, it can have increased efficiency when the pooled data are heterogeneous; and (3) it avoids the practical difficulties of pooling human subjects data. On the basis of simulated data modeled after two real data sets, the proposed method can reduce the sampling variation of linkage maps commonly used in whole-genome linkage scans. Furthermore, when the independent map estimates are also maximum likelihood estimates, the proposed method performs as well as or better than when they are estimated by the program CRIMAP. Since variance estimates of maps may not always be available, I demonstrate the feasibility of three different variance estimators. Overall, the method should prove useful to investigators who need map positions for markers not contained in publicly available maps, and to those who wish to minimize the negative effects of inaccurate maps.

journal_name

Genet Epidemiol

journal_title

Genetic epidemiology

authors

Stewart WC

doi

10.1002/gepi.20221

subject

Has Abstract

pub_date

2007-07-01 00:00:00

pages

408-16

issue

5

eissn

0741-0395

issn

1098-2272

journal_volume

31

pub_type

杂志文章
  • Parental genotype reconstruction: applications of haplotype relative risk to incomplete parental data.

    abstract::Intended to resolve the problem of constructing a matched population-based control sample, haplotype relative risk techniques frequently suffer from loss of power for late-onset diseases due to unavailability of parental genotypes that are required to form parent-offspring pairs. However, much of this missing informat...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/(SICI)1098-2272(1998)15:5<471::AID-GEPI3>3

    authors: Martin RB,Alda M,MacLean CJ

    更新日期:1998-01-01 00:00:00

  • Effect of physical activity on lipid levels in a population-based sample of men with and without the Arg192 variant of the human paraoxonase gene.

    abstract::The prevalence of cardiovascular risk factors in Gerona, Spain, is high for the low myocardial infarction incidence and mortality rates in the province. Physical activity is a protective factor against coronary heart disease. We investigated whether the genetic variants Q and R of the paraoxonase Gln-Arg 192 polymorph...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/(SICI)1098-2272(200003)18:3<276::AID-GEPI6

    authors: Sentí M,Aubó C,Elosua R,Sala J,Tomás M,Marrugat J

    更新日期:2000-03-01 00:00:00

  • Integration of multiomic annotation data to prioritize and characterize inflammation and immune-related risk variants in squamous cell lung cancer.

    abstract::Clinical trial results have recently demonstrated that inhibiting inflammation by targeting the interleukin-1β pathway can offer a significant reduction in lung cancer incidence and mortality, highlighting a pressing and unmet need to understand the benefits of inflammation-focused lung cancer therapies at the genetic...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.22358

    authors: Sun R,Xu M,Li X,Gaynor S,Zhou H,Li Z,Bossé Y,Lam S,Tsao MS,Tardon A,Chen C,Doherty J,Goodman G,Bojesen SE,Landi MT,Johansson M,Field JK,Bickeböller H,Wichmann HE,Risch A,Rennert G,Arnold S,Wu X,Melander O,

    更新日期:2021-02-01 00:00:00

  • Model selection and Bayesian methods in statistical genetics: summary of group 11 contributions to Genetic Analysis Workshop 15.

    abstract::The research presented in group 11 of the Genetic Analysis Workshop 15 (GAW15) falls into two major themes: Model selection approaches for gene mapping (both Bayesian and Frequentist); and other Bayesian methods. These methods either allow relaxation of some of the common assumptions, such as mode of inheritance, for ...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章,评审

    doi:10.1002/gepi.20285

    authors: Swartz MD,Thomas DC,Daw EW,Albers K,Charlesworth JC,Dyer TC,Fridley BL,Govil M,Kraft P,Kwon S,Logue MW,Oh C,Pique-Regi R,Saba L,Schumacher FR,Uh HW

    更新日期:2007-01-01 00:00:00

  • Presidential address: Six open questions to genetic epidemiologists.

    abstract::Given the rapid pace with which genomics and other -omics disciplines are evolving, it is sometimes necessary to shift down a gear to consider more general scientific questions. In this line, in my presidential address I formulate six questions for genetic epidemiologists to ponder on. These cover the areas of reprodu...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.22191

    authors: König IR

    更新日期:2019-04-01 00:00:00

  • Trends in prenatal diagnosis of Down syndrome and other autosomal trisomies in Scotland 1990 to 1994, with associated cytogenetic and epidemiological findings.

    abstract::The present report summarizes findings on 670 cases of autosomal trisomy diagnosed in Scotland, with actual or expected dates of delivery in 1990 to 1994 inclusive. Cases were notified by cytogenetic service laboratories. There were 277 prenatal and 369 postnatal diagnoses and 24 spontaneous losses. Excluding the latt...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/(SICI)1098-2272(1999)16:2<179::AID-GEPI5>3

    authors: Carothers AD,Boyd E,Lowther G,Ellis PM,Couzin DA,Faed MJ,Robb A

    更新日期:1999-01-01 00:00:00

  • Joint analysis of multiple phenotypes using a clustering linear combination method based on hierarchical clustering.

    abstract::Emerging evidence suggests that a genetic variant can affect multiple phenotypes, especially in complex human diseases. Therefore, joint analysis of multiple phenotypes may offer new insights into disease etiology. Recently, many statistical methods have been developed for joint analysis of multiple phenotypes, includ...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.22263

    authors: Li X,Zhang S,Sha Q

    更新日期:2020-01-01 00:00:00

  • Score tests for familial correlation in genotyped-proband designs.

    abstract::In the genotyped-proband design, a proband is selected based on an observed phenotype, the genotype of the proband is observed, and then the phenotypes of all first-degree relatives are obtained. The genotypes of these first-degree relatives are not observed. Gail et al. [(1999) Genet Epidemiol] discuss likelihood ana...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/(SICI)1098-2272(200004)18:4<293::AID-GEPI3

    authors: Carroll RJ,Gail MH,Benichou J,Pee D

    更新日期:2000-04-01 00:00:00

  • Identification of gene-gene interactions in the presence of missing data using the multifactor dimensionality reduction method.

    abstract::Gene-gene interaction is believed to play an important role in understanding complex traits. Multifactor dimensionality reduction (MDR) was proposed by Ritchie et al. [2001. Am J Hum Genet 69:138-147] to identify multiple loci that simultaneously affect disease susceptibility. Although the MDR method has been widely u...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.20416

    authors: Namkung J,Elston RC,Yang JM,Park T

    更新日期:2009-11-01 00:00:00

  • Investigation of a candidate gene, environment, and G x E interaction using case-control and case-parent study designs.

    abstract::We investigated the independent contributions of a candidate gene and an environmental factor, and the presence of gene x environment (G x E) interaction, in the etiology of a disease in the Genetic Analysis Workshop (GAW) 12 problem 2 simulated data using a two-stage approach utilizing both case-control and case-pare...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.2001.21.s1.s843

    authors: Norris JM,Selinger-Leneman H,Génin E

    更新日期:2001-01-01 00:00:00

  • Novel likelihood ratio tests for screening gene-gene and gene-environment interactions with unbalanced repeated-measures data.

    abstract::There has been extensive literature on modeling gene-gene interaction (GGI) and gene-environment interaction (GEI) in case-control studies with limited literature on statistical methods for GGI and GEI in longitudinal cohort studies. We borrow ideas from the classical two-way analysis of variance literature to address...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.21744

    authors: Ko YA,Saha-Chaudhuri P,Park SK,Vokonas PS,Mukherjee B

    更新日期:2013-09-01 00:00:00

  • Linkage analysis in alcohol dependence.

    abstract::Alcohol dependence often is a familial disorder and has a genetic component. Research in causative factors of alcoholism is coordinated by a multi-center program, COGA [The Collaborative Study on the Genetics of Alcoholism, Begleiter et al., 1995]. We analyzed a subset of the COGA family sample, 84 pedigrees of Caucas...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.1370170768

    authors: Windemuth C,Hahn A,Strauch K,Baur MP,Wienker TF

    更新日期:1999-01-01 00:00:00

  • Bayesian linkage and segregation analysis: factoring the problem.

    abstract::Complex segregation analysis and linkage methods are mathematical techniques for the genetic dissection of complex diseases. They are used to delineate complex modes of familial transmission and to localize putative disease susceptibility loci to specific chromosomal locations. The computational problem of Bayesian li...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/1098-2272(2000)19:1+<::AID-GEPI8>3.0.CO;2-

    authors: Matthysse S

    更新日期:2000-01-01 00:00:00

  • An efficient study design to test parent-of-origin effects in family trios.

    abstract::Increasing evidence has shown that genes may cause prenatal, neonatal, and pediatric diseases depending on their parental origins. Statistical models that incorporate parent-of-origin effects (POEs) can improve the power of detecting disease-associated genes and help explain the missing heritability of diseases. In ma...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.22060

    authors: Yu X,Chen G,Feng R

    更新日期:2017-11-01 00:00:00

  • Extended HLA profile of an inbred isolate: the Schmiedeleut Hutterites of South Dakota.

    abstract::HLA-A, -B, -C, -DR, and -DQ typings of the Schmiedeleut Hutterites of South Dakota were collected as part of an ongoing genetic-epidemiologic study of HLA and fertility. A total of 1,082 individuals, including 852 married adults representative of the reproductive population of this isolate, were characterized for five...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.1370120106

    authors: Dawson DV,Ober C,Kostyu DD

    更新日期:1995-01-01 00:00:00

  • Explorative two-locus linkage analysis suggests a multiplicative interaction between the 7q32 and 16p13 myoclonic seizures-related photosensitivity loci.

    abstract::In traits suspected to be governed by at least two loci, linkage analysis incorporating the joint action of both loci may improve the power to detect linkage, increase the precision of estimating locus positions and provide insight into the underlying etiological mechanism. Recently, we mapped two susceptibility loci ...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.20190

    authors: Pinto D,Kasteleijn-Nolst Trenité DG,Cordell HJ,Mattheisen M,Strauch K,Lindhout D,Koeleman BP

    更新日期:2007-01-01 00:00:00

  • A Bayesian integrative genomic model for pathway analysis of complex traits.

    abstract::With new technologies, multiple types of genomic data are commonly collected on a single set of samples. However, standard analysis methods concentrate on a single data type at a time and ignore the relationships between genes, proteins, and biochemical reactions that give rise to complex phenotypes. In this paper, we...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.21628

    authors: Fridley BL,Lund S,Jenkins GD,Wang L

    更新日期:2012-05-01 00:00:00

  • Method for calculating risk associated with family history of a disease.

    abstract::A method is described for estimating excess relative risks of a disease from familial factors. Beginning with population-based series of cases and controls, a cohort of each subject's relatives is formed and checked for disease against a population based registry. The disease experience of the cohort formed from each ...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.1370120306

    authors: Kerber RA

    更新日期:1995-01-01 00:00:00

  • Genetic epidemiology of Menkes disease.

    abstract::Copper incorporation studies were performed on individuals from 58 pedigrees, comprising 140 sibships. As previously reported, there is considerable overlap between heterozygotes and normal homozygotes. Segregation analysis supports recessive inheritance of disease, with residual heritability for 64Cu uptake in cultur...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.1370030403

    authors: Horn N,Morton NE

    更新日期:1986-01-01 00:00:00

  • Adjustment for competing risk in kin-cohort estimation.

    abstract::Kin-cohort design can be used to study the effect of a genetic mutation on the risk of multiple events, using the same study. In this design, the outcome data consist of the event history of the relatives of a sample of genotyped subjects. Existing methods for kin-cohort estimation allow estimation of the risk of one ...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.10269

    authors: Chatterjee N,Hartge P,Wacholder S

    更新日期:2003-12-01 00:00:00

  • Genetic epidemiology with a capital "E".

    abstract::Three characteristics of genetic epidemiology that distinguish it from its parent disciplines are a focus on population-based research, a focus on the joint effects of genes and the environment, and the incorporation of the underlying biology of the disease into its conceptual models. These principles are illustrated ...

    journal_title:Genetic epidemiology

    pub_type:

    doi:10.1002/1098-2272(200012)19:4<289::AID-GEPI2>3.0.C

    authors: Thomas DC

    更新日期:2000-12-01 00:00:00

  • New simple tests for age-at-onset anticipation: application to panic disorder.

    abstract::Recently, testing for anticipation has received renewed interest. It is well known that standard statistical methods are inappropriate for this purpose due to problems of sampling bias. Few statistical tests have been proposed for comparing mean age of onset in affected parents with mean age of onset in affected child...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.20057

    authors: Tsai WY,Heiman GA,Hodge SE

    更新日期:2005-04-01 00:00:00

  • Commingling analysis of memory performance in elderly men.

    abstract::Smalley et al. [(1992) Genet Epidemiol 9:333-345] found evidence of a mixture of two distributions in memory performance among offspring of patients with dementia of the Alzheimer type (DAT), suggesting that these groups reflect genotypic subgroups of carriers and non-carriers of a putative DAT gene. One prediction of...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.1370110506

    authors: Palmer CG,Wolkenstein BH,La Rue A,Swan GE,Smalley SL

    更新日期:1994-01-01 00:00:00

  • Pleiotropy and principal components of heritability combine to increase power for association analysis.

    abstract::When many correlated traits are measured the potential exists to discover the coordinated control of these traits via genotyped polymorphisms. A common statistical approach to this problem involves assessing the relationship between each phenotype and each single nucleotide polymorphism (SNP) individually (PHN); and t...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.20257

    authors: Klei L,Luca D,Devlin B,Roeder K

    更新日期:2008-01-01 00:00:00

  • Parental transmission and D18S37 allele sharing in bipolar affective disorder.

    abstract::We combined the five chromosome 18 bipolar affective disorder data sets provided by GAW10, totaling 185 families with 3,394 individuals, and performed analysis of differential parental transmission and chromosome 18 marker allele sharing in families with transmission through fathers vs those through mothers. Results i...

    journal_title:Genetic epidemiology

    pub_type: 临床试验,杂志文章

    doi:10.1002/(SICI)1098-2272(1997)14:6<665::AID-GEPI19>

    authors: Lin JP,Bale SJ

    更新日期:1997-01-01 00:00:00

  • Design of artificial neural network and its applications to the analysis of alcoholism data.

    abstract::Artificial neural networks were applied to the alcoholism data to reveal nonlinear relationships between intermediate phenotypes, marker identity-by-descent sharing, and the affection status. A variable number of hidden units were considered to achieve a balance between the minimal mean-squared error and over-fitting ...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.1370170738

    authors: Li W,Haghighi F,Falk CT

    更新日期:1999-01-01 00:00:00

  • Testing for association in SLE families.

    abstract::Systemic lupus erythematosus (SLE) is a complex disease which is partly determined by genetic factors which influence susceptibility to the disease phenotype. In this association study we try to define the high risk haplotypes which are responsible for this disease, together with other environmental factors. In many o...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.1370080607

    authors: Seuchter SA,Knapp M,Hartung K,Coldewey R,Kalden JR,Lakomek HJ,Peter HH,Deicher H,Baur MP

    更新日期:1991-01-01 00:00:00

  • Extensions to sib-pair linkage tests applicable to disorders characterized by delayed onset.

    abstract::Extensions of the approach to sib-pair linkage tests developed by Haseman and Elston [Behav Genet 2:3-19, 1972] are proposed which incorporate information on age of onset and age at examination. Alternate sources for the age of onset corrections are described, including models for the estimation of parameters associat...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.1370070607

    authors: Dawson DV,Kaplan EB,Elston RC

    更新日期:1990-01-01 00:00:00

  • Genome-wide association studies for discrete traits.

    abstract::Genome-wide association studies of discrete traits generally use simple methods of analysis based on chi(2) tests for contingency tables or logistic regression, at least for an initial scan of the entire genome. Nevertheless, more power might be obtained by using various methods that analyze multiple markers in combin...

    journal_title:Genetic epidemiology

    pub_type:

    doi:10.1002/gepi.20465

    authors: Thomas DC

    更新日期:2009-01-01 00:00:00

  • Tests for gene-environment interaction from case-control data: a novel study of type I error, power and designs.

    abstract::To evaluate the risk of a disease associated with the joint effects of genetic susceptibility and environmental exposures, epidemiologic researchers often test for non-multiplicative gene-environment effects from case-control studies. In this article, we present a comparative study of four alternative tests for intera...

    journal_title:Genetic epidemiology

    pub_type: 杂志文章

    doi:10.1002/gepi.20337

    authors: Mukherjee B,Ahn J,Gruber SB,Rennert G,Moreno V,Chatterjee N

    更新日期:2008-11-01 00:00:00