Genehunter linkage analysis study

GeneHunter - omicX

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Allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores and in a powerful method of non-parametric linkage analysis. Quick calculations involving dozens of markers, even in pedigrees with inbreeding and marriage loops, is possible with GENEHUNTER.

GeneHunter - omicX

Genetic linkage analysis in the age ... - PubMed Central (PMC)

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Linkage analysis was the predominant statistical genetic mapping approach used in the latter half of the twentieth century. More recently, the focus shifted to association studies of complex traits that analyse common variants, which have a modest effect.

Genetic linkage analysis in the age ... - PubMed Central (PMC)

Genetic Linkage Analysis - an overview | ScienceDirect Topics

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Genetic Linkage Analysis. Genetic linkage analysis is a mainstay of disease gene identification, and additional methods such as SNP-based genetic maps and whole-exome sequencing approaches have enhanced robustness of the zebrafish model (Bradley et al., 2007; Guryev et al., 2006).

Genetic Linkage Analysis - an overview | ScienceDirect Topics

Comparison of GENEHUNTER and MFLINK for analysis of COGA ...

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Comparison of GENEHUNTER and MFLINK for analysis of COGA linkage data ... model-free methods of linkage analysis, the GENEHUNTER [Kruglyak and Lander, …

Comparison of GENEHUNTER and MFLINK for analysis of COGA ...

Genetic linkage analysis bioinformatics tools | GWAS - omicX

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For many years, linkage analysis was the primary tool used for the genetic mapping of Mendelian and complex traits with familial aggregation. Linkage analysis was largely supplanted by the wide adoption of genome-wide association studies (GWASs). However, with the recent increased use of whole-genome sequencing (WGS), linkage analysis is again emerging as an important and powerful analysis ...

Genetic linkage analysis bioinformatics tools | GWAS - omicX

Genetic linkage studies - ScienceDirect

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9/23/2005 · Results of genetic linkage studies are often reported in the form of LOD scores. These scores are actually based on likelihood ratios. The use of maximum likelihood in genetic linkage analysis was originally proposed in 1947. 4 Its use became widespread once Morton 5 published his log-odd (LOD) tables, which enabled the sequential analysis of family-based linkage studies.

Genetic linkage studies - ScienceDirect

Genomewide Linkage Analysis of Body Mass Index across 28 ...

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We performed a genomewide linkage analysis of six separate measurements of body mass index (BMI) taken over a span of 28 years, from 1971 to 1998, in the Framingham Heart Study. Variance-components linkage analysis was performed on 330 families, using 401 polymorphic markers. The number of ...

Genomewide Linkage Analysis of Body Mass Index across 28 ...

Comparison of linkage analysis methods for ... - BMC Genetics

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12/31/2003 · High triglycerides (TG) and low high-density lipoprotein cholesterol (HDL-C) jointly increase coronary disease risk. We performed linkage analysis for TG/HDL-C ratio in the Framingham Heart Study data as a quantitative trait, using methods implemented in LINKAGE, GENEHUNTER (GH), MCLINK, and SOLAR. Results were compared to each other and to those from a previous evaluation using SOLAR …

Comparison of linkage analysis methods for ... - BMC Genetics

Linkage analysis of alcohol dependence using MOD scores ...

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12/30/2005 · In particular, we performed parametric single-marker linkage analysis using MLINK of the LINKAGE package (for the microsatellite data), as well as multipoint MOD-score analysis with GENEHUNTER-MODSCORE (for the microsatellite and SNP data). By use of two liability classes, different penetrances were assigned to males and females.

Linkage analysis of alcohol dependence using MOD scores ...

Genetic linkage studies - The Lancet

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9/17/2005 · Linkage analysis is used to map genetic loci by use of observations of related individuals. We provide an introduction to methods commonly used to map loci that predispose to disease. Linkage analysis methods can be applied to both major gene disorders (parametric linkage) and complex diseases (model-free or non-parametric linkage). Evidence for linkage is most commonly expressed …

Genetic linkage studies - The Lancet

Genome-Wide Linkage Analysis of Large Multiple ...

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This study aims to identify new CAD genetic loci through a large-scale linkage analysis of 24 large and multigenerational families with 433 family members (GeneQuest II).

Genome-Wide Linkage Analysis of Large Multiple ...

GENEHUNTER: Application to analysis of bipolar pedigrees ...

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TY - JOUR. T1 - GENEHUNTER. T2 - Genetic Epidemiology. AU - Li, Hongzhe. AU - Schaid, Daniel J. PY - 1997. Y1 - 1997. N2 - A newly developed nonparametric multipoint linkage analysis (NPL) by Kruglyak et al. [1996] was applied to the data set from the Johns Hopkins Bipolar Study available through the GAW10 workshop.

GENEHUNTER: Application to analysis of bipolar pedigrees ...

Genetic linkage analysis in the age of whole-genome ...

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3/31/2015 · For many years, linkage analysis was the primary tool used for the genetic mapping of Mendelian and complex traits with familial aggregation. Linkage analysis was largely supplanted by …

Genetic linkage analysis in the age of whole-genome ...

73 questions in Linkage Analysis | Science topic

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Mind you, linkage disequilibrium is only a problem for multipoint linkage analysis, and when founders are missing. A few answers above mention 'highly informative SNPs'. 'Informative' in linkage ...

73 questions in Linkage Analysis | Science topic

Genomewide Linkage Analysis of Weight Change in the ...

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Genomewide Linkage Analysis of Weight Change in the ...

Genomewide Linkage Analysis of Weight Change in the ...

Linkage and association with pulmonary function measures ...

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11/1/2003 · For this study, additional markers were genotyped in the region to refine the location of linkage and test for association. Variance component linkage analysis was performed using GENEHUNTER, and family-based association tests were performed using FBAT.

Linkage and association with pulmonary function measures ...

Genome-wide linkage analysis to age at natural menopause ...

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The first genome-wide linkage study of variation in age at natural menopause identified a significant locus on the X chromosome and a suggestive locus on chromosome 9 (7 x 7 van Asselt, K.M., Kok, H.S., Putter, H., Wijmenga, C., Peeters, P.H., van der Schouw, Y.T. et al. Linkage analysis of extremely discordant and concordant sibling pairs ...

Genome-wide linkage analysis to age at natural menopause ...

Linkage analysis of ordinal traits for pedigree data - PNAS

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Linkage analysis of ordinal traits for pedigree data Rui Feng†, James F. Leckman‡, and Heping Zhang†‡§ †Department of Epidemiology and Public Health and ‡Yale Child Study Center, Yale University of School of Medicine, New Haven, CT 06250-8034 Edited by David O. Siegmund, Stanford University, Stanford, CA, and approved September 29, 2004 (received for review June 29, 2004)

Linkage analysis of ordinal traits for pedigree data - PNAS

Linkage analysis of ordinal traits for pedigree data | PNAS

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11/30/2004 · Linkage analysis is used routinely to map genes for human diseases and conditions. However, the existing linkage-analysis methods require that the diseases or conditions either be dichotomized or measured by a quantitative trait, such as blood pressure for hypertension. In the latter case, normality is generally assumed for the trait. However, many diseases and conditions, such as …

Linkage analysis of ordinal traits for pedigree data | PNAS

Comparison of GENEHUNTER and MFLINK for analysis of COGA ...

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We compared the NPL ALL statistic from GENEHUNTER with two-point and three-point MALODs and MFLODs from MFLINK for all autosomal markers in the Collaborative Study on the Genetics of Alcoholism (COGA) data set. In general MFLINK produced more significant results than GENEHUNTER and implicated two regions containing candidate genes (ADH3 and DRD2).

Comparison of GENEHUNTER and MFLINK for analysis of COGA ...

LOT - Linkage Analysis of Ordinal Traits > Collaborative ...

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LOT is a software program that performs linkage analysis of ordinal traits for pedigree data. It implements a latent-variable proportional-odds logistic model that relates inheritance patterns to …

LOT - Linkage Analysis of Ordinal Traits > Collaborative ...

Genome-wide linkage of 77 families from the African ...

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genetic linkage analysis on 77 AAHPC families as Linkage analyses of families with multiple affected further evidence for the segregation of potentially males, mostly from the Caucasian population, have important HPC susceptibility loci among our cohort. indicated that a subset may harbor rare dominant or This is the first report of genome-wide ...

Genome-wide linkage of 77 families from the African ...

Genetic linkage and association analysis in type 1 von ...

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Previous article in issue: Linkage analysis in families diagnosed with type 1 von Willebrand disease in the European study, molecular and clinical markers for the diagnosis and management of type 1 VWD ... All linkage analysis was performed using genehunter v2.1_r5 . …

Genetic linkage and association analysis in type 1 von ...

Genome-wide Linkage Analysis of Mandibular Prognathism in ...

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The existence of familial aggregation of mandibular prognathism (MP) suggests that genetic components play an important role in its etiology. In this study, a genome-wide linkage analysis to identify loci susceptible to MP was conducted with 90 affected sibling-pairs in 42 families, comprised of 40 Korean sibling-pairs and 50 Japanese sibling-pairs.

Genome-wide Linkage Analysis of Mandibular Prognathism in ...

Genome-Wide Linkage to Chromosome 6 for Waist ...

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5/1/2004 · While several loci for BMI have been identified, it is not known whether genes underlie the process of regional fat deposition. We sought to test whether waist circumference, a measure of central adiposity, contains a genetic component. Variance components linkage analysis was performed on 330 families from the Framingham Heart Study original and offspring cohorts, using a 10-cM genome-wide ...

Genome-Wide Linkage to Chromosome 6 for Waist ...

Genome-wide linkage analysis to urinary microalbuminuria ...

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this analysis, we sought to test for heritability and linkage for microalbuminuria in the Framingham Heart Study, a community-based cohort study. METHODS TheFramingham Heart Study began in 1948 with the enrollment of 5209 men and women, 28 to 62 years of age at study entry, with subjects undergoing repeat ex-aminations every 2 years [15].

Genome-wide linkage analysis to urinary microalbuminuria ...

Linkage analysis of the simulated data – evaluations and ...

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The goal of this study is to evaluate, compare, and contrast several standard and new linkage analysis methods. First, we compare a recently proposed confidence set approach with MAPMAKER/SIBS. Then, we evaluate a new Bayesian approach that accounts

Linkage analysis of the simulated data – evaluations and ...

Genetic linkage and transmission disequilibrium of marker ...

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7/17/2001 · Linkage in the 1q41 region. GENEHUNTER PLUS (see reference of supplementary material) was used to perform multipoint nonparametric linkage analysis using the 11 markers shown in the total collection of 210 families with systemic lupus erythematosus and in a subset of 163 white families. Marker positions (cM) were estimated based on the ...

Genetic linkage and transmission disequilibrium of marker ...

Model-Free Tests for Genetic Linkage UNIT 1

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Y Model-Free Tests for Genetic Linkage UNIT 1.8 Christopher I. Amos, 1Audrey Schnell,2 Wei V. Chen, and Robert C. Elston3 1University of Texas, M.D. Anderson Cancer Center, Houston, Texas 2University of Washington, Seattle, Washington 3Case Western University, Cleveland, Ohio ABSTRACT This unit covers statistical methods of linkage analysis that do not require the assumption

Model-Free Tests for Genetic Linkage UNIT 1

Genome-wide linkage analysis to age at natural menopause ...

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Linkage Analysis Variance components linkage analysis implemented in Genehunter (14, 15) was used to perform the genome-wide linkage analyses. In variance component linkage analysis (16, 17), genotypic information at a chromosomal locus is used to decompose the phenotypic variance into components

Genome-wide linkage analysis to age at natural menopause ...

Linkage Analysis of a Composite Factor for the Multiple ...

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Multipoint variance components linkage analysis (GENEHUNTER version 2.1) of the MMS factor was conducted in the combined marker set sample. The greatest evidence for linkage was found on chromosome 2, with a peak LOD of 3.34 at 240 cM.

Linkage Analysis of a Composite Factor for the Multiple ...

Human Genetics: Linkage analysis and disease genetics

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Human Genetics: Linkage analysis and disease genetics Short Course, 10-15 August 2015. Organized by Profs. Liping Wei, Peking University, and Jurg Ott, Institute of Psychology CAS, a short course on Genetic Linkage and Association Analysis will be held at Peking University in Beijing, China, 10-15 August 2015.Course participants are expected to bring their own laptops to carry out hands-on ...

Human Genetics: Linkage analysis and disease genetics

A genome-wide ordered-subset linkage analysis for ...

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12/18/2007 · Rheumatoid arthritis (RA) is a chronic, complex autoimmune inflammatory disorder with poorly known etiology. Approximately 1% of the adult population is afflicted with RA. Linkage analysis of RA can be complicated by the presence of phenotypic and genetic heterogeneity. It is shown that the ordered-subset analysis (OSA) technique reduces heterogeneity, increases statistical power for …

A genome-wide ordered-subset linkage analysis for ...

Mega2: validated data-reformatting for linkage and ...

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12/5/2014 · In a typical study of the genetics of a complex human disease, many different analysis programs are used, to test for linkage and association. This requires extensive and careful data reformatting, as many of these analysis programs use differing input formats. Writing scripts to facilitate this can be tedious, time-consuming, and error-prone.

Mega2: validated data-reformatting for linkage and ...

Genome-wide scan linkage analysis for Parkinson’s disease ...

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12/1/2004 · Objective: To undertake a full genome-wide screen for Parkinson’s disease susceptibility loci. Methods: A genome-wide linkage study was undertaken in 227 affected sibling pairs from 199 pedigrees with Parkinson’s disease. The pedigree sample consisted of 188 pedigrees from five European countries, and 11 from the USA. Individuals were genotyped for 391 microsatellite markers at ∼10 cM ...

Genome-wide scan linkage analysis for Parkinson’s disease ...

Genome-wide linkage of 77 families from the African ...

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Genome-wide linkage of 77 families from the African American Hereditary Prostate Cancer Study (AAHPC) Agnes B. Baffoe-Bonnie, Rick A Kittles, Elizabeth Gillanders, Liang Ou, Asha George, Christiane Robbins, Chiledum Ahaghotu, James Bennett, William Boykin, Gerald Hoke, ...

Genome-wide linkage of 77 families from the African ...

Genomewide Linkage Analysis of Body Mass Index across 28 ...

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We performed a genomewide linkage analysis of six separate measurements of body mass index (BMI) taken over a span of 28 years, from 1971 to 1998, in the Framingham Heart Study. Variance-components linkage analysis was performed on 330 families, using 401 polymorphic markers.

Genomewide Linkage Analysis of Body Mass Index across 28 ...

Faster Multipoint Linkage Analysis Using Fourier ...

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The algorithm employs a fast Fourier transform on the group of pedigree inheritance patterns. It substantially improves the overall performance of the software package GENEHUNTER for performing linkage analysis. The Fourier representation opens up new research directions for pedigree analysis.

Faster Multipoint Linkage Analysis Using Fourier ...

On a Randomization Procedure in Linkage Analysis

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Am. J. Hum. Genet. 65:1449–1456, 1999 1449 On a Randomization Procedure in Linkage Analysis Hongyu Zhao,1,2 Kathleen R. Merikangas,1 and Kenneth K. Kidd2 1Department of Epidemiology and Public Health and 2Department of Genetics, Yale University School of Medicine, New Haven, CT Summary Although much theoretical work has been undertaken

On a Randomization Procedure in Linkage Analysis

Combination of Linkage and Association Studies for Brain ...

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We used a combination of a linkage study and an association study to explore the genetic background. Methods—A genome-wide linkage analysis was performed in 12 patients from 6 unrelated families using the GENEHUNTER program. A genome-wide association analysis of 26 cases and 30 controls was performed using a GeneChip 10K mapping array.

Combination of Linkage and Association Studies for Brain ...

Modest Evidence for Linkage and Possible Confirmation of ...

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reviews of these earlier linkage findings. Nurnberger et al. [1999] also discusses some of the candidate genes within these regions that have been targets of associa-tion studies. Turecki et al. [1997] performed a meta-analysis of nine previous studies that reported linkage

Modest Evidence for Linkage and Possible Confirmation of ...

Linkage analysis of high myopia susceptibility locus in 26 ...

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linkage peak and to look for other loci involved in high myopia, a novel study was conducted in an extended population. We were able to collect nine additional families. In this study, our goal is to perform a genome-wide scan (GWS) on these nine new families as well as the combined linkage analysis on the full sample of families. METHODS

Linkage analysis of high myopia susceptibility locus in 26 ...

Genome-Wide Scan for Linkage to Obesity-Associated ...

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of these families showed a high prevalence ( 70%) of obesity. Genome-wide scan using qualitative multipoint linkage analysis (GeneHunter 2.1; marker density 10 cM) was performed in the entire set of hypertensive families and the subset with high prevalence of obesity. In the scan involving all 55 families, the most significant loci (logarithm ...

Genome-Wide Scan for Linkage to Obesity-Associated ...

Abstract A64: Genome wide linkage and finemapping studies ...

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Parametric and nonparametric linkage analysis using GENEHUNTER and GENEHUNTER-PLUS programs in addition to Ordered Subset Analysis (OSA) and linear nonparametric allele sharing methods using ASM showed peaks at 11q22, 17p11 and Xq21. ... The African American Hereditary Prostate Cancer Study (AAHPC) was initiated to recruit African American ...

Abstract A64: Genome wide linkage and finemapping studies ...

Mega2, the Manipulation Environment for Genetic Analysis ...

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Mega2 (short for manipulation environment for genetic analysis) allows the applied statistical geneticist to convert one's data from several input formats to a large number output formats suitable for analysis by commonly used software packages.

Mega2, the Manipulation Environment for Genetic Analysis ...

Linkage analysis of HLA and candidate genes for celiac ...

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11/30/2001 · Linkage analysis of HLA and candidate genes for celiac disease in a North American family-based study. Susan L Neuhausen 1 Email author, Michael ... For linkage analysis, we used the ... for two-point analysis, and the GENEHUNTER program for both parametric and non-parametric (NPL) multi-point analyses. Two-point linkage in the ...

Linkage analysis of HLA and candidate genes for celiac ...
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