|
Home
News
Citegeist
|
Browse Groups
Search Groups
Journals
|
FAQs
Howto
Discussion
|
 |
 CiteULike |
 |
 CiteULike |
|
 |
Mouse Genome-Wide Association Mapping Needs Linkage Analysis to Avoid False-Positive Loci |
Reviews
[Write a review of this article]
There are no reviews of this article
Find related articles from these CiteULike users Find related articles with these CiteULike tags
Posting HistoryNEW AbstractWe carried out genome-wide association (GWA) studies in inbred mouse strains characterized for their lung tumor susceptibility phenotypes (spontaneous or urethane-induced) with panels of 12,959 (13K) or 138,793 (140K) single-nucleotide polymorphisms (SNPs). Above the statistical thresholds, we detected only SNP rs3681853 on Chromosome 5, two SNPs in the pulmonary adenoma susceptibility 1 (Pas1) locus, and SNP rs4174648 on Chromosome 16 for spontaneous tumor incidence, urethane-induced tumor incidence, and urethane-induced tumor multiplicity, respectively, with the 13K SNP panel, but only the Pas1 locus with the 140K SNP panel. Haplotype analysis carried out in the latter panel detected four additional loci. Loci reported in previous GWA studies failed to replicate. Genome-wide genetic linkage analysis in urethane-treated (BALB/c×C3H/He)F2, (BALB/c×SWR/J)F2, and (A/J×C3H/He)F2 mice showed that Pas1, but none of the other loci detected previously or herein by GWA, had a significant effect. The Lasc1 gene, identified by GWA as a functional element (Nat. Genet., 38:888–95, 2006), showed no genetic effects in the two independent intercross mouse populations containing both alleles, nor was it expressed in mouse normal lung or lung tumors. Our results indicate that GWA studies in mouse inbred strains can suffer a high rate of false-positive results and that such an approach should be used in conjunction with classical linkage mapping in genetic crosses.
BibTeX record RIS record005 05 1 10-7 1343 1792 2 2004 21860 22 22578 227876 25 30 4316 4398 62c99 62g05 62g07 62g08 62g99 62h30 62h99 62n02 62p10 77 ability account accuracy acgh action active ad adaboost adaptive additional additive addressing adherence adjusted adjustment adjuvant admixture adults africa african against agents age-structured agglomeration aggregating aggregation agilent aic aid aids akaike algorithm algorithms alignment alkanes allele alleles allocation alpha-spending alternative alu-repeat alzheimer alzheimers americans an anaemia analyses analysis analytical anchor-based and androgens aneuploidy aneurysms anglicanism annealing annotation anthrax antiasthmatic antibacterial anticancer antigen antiretroviral apoe applications apportionment apprenticeship approach approximate approximation aptitude aquatic arcing area areas array array-based arrays arterial artery ascertainment assembly assessment assistants association association-analysis assortative assurance asthma asthma-related astrology asymptotic asymptotics at atherosclerosis atmospheric attitude attitudes attributable attributes audit augmentation autism autoimmunity autologous automatic average averaging b back-fitting background backward bacterial bagging bandwidth banking barrier based baseline base-line basics bayes bayesian bcg be belief below benchmarks berre best beta betadefensin bias biased biases bibliography bic binary binomial bioinformatics biological biology biomarker biomarkers biometric biometrical biometrics biostatistical biostatistics biplot birth bivariate block blue board body bonferroni boolean boosting bootstrap bootstrapping borrowing boundary bowel box box-cox brca1 brca2 breast brugs bruno building burden by ca125 calcification calculation calculations calling cancer candidate canonical carcinogenesis carcinoma cardiac cardiovascular care caries carlo carried cart case casecontrol case-control case-only cases categorical categorization causal causative cd4 cell cellcycle censored censoring census center centromere cerevisiae cervus cgh chain chance change changepoint change-point character characteristic characteristics chart check checking checks chemistry chemometrics chemotherapy chewing child chip chi-square chi-squared choice cholesky chromosomal cin circle circular class classes classic classication classiffication classiffier classification classifiers cleaning clinic clinical clinically closed cluster clustered clustering cnv coalescent cochran-armitage cocktail coding coefficient coefficients cohort cohort-studies coin col3a1 col5a1 col5a2 colitis collagen collectin colon color colorectal common community comparative compared comparison comparisons complete completely completly complex complexity component components composite composition compromise compstat computation computational computer computerized computers computing concentration conceptual condition conditional conducted conference conferring confidence confidence-interval confidentiality confirmation confounding confusion congenital conjugacy conjugate consent consistency consistent constant constitutional constrained construction constructive consultancy consultant consulting contain contextual contingency continuity continuous control controlled controls convolution conwaymaxwellpoisson copula copy copy-number coral coronary correction correlate correlated correlation correlations correspondence corsten corticosteroids cost costs cost-sensitive count counterfactuals counting covariance covariate covariates cox c_p criteria criterion criterion-referenced critical crohn crohn-disease cross cross-level cross-validation ct cubic cumulative curvature curve curves cycle cystic cytogenetics cytostatic dactylin dag dale damped darunavir darwin darwinism data database data-dependent data--estimation data-ink datasets dbld dce-mri de death decapping decayed decision decode decomposition degrees deletion deletions delta demonstrations density dental dependence dependent derivative descent design designs detection detection_limit development developmental deviance diabetes diagnosis diagnostic diagnostics diagrams dichotomization difference differential differentials differentiation dimension dimensional dimensionality directional dirichlet disco discordant discovery discrepancies discrepancy discrete discriminant discrimination discriminatory disease disease-free disequilibrium disomy disorder disparities display displaying dissolution distance distributed distribution distribution-based distributions divergence dna doctors doe dog domain d-optimality dose dose-dependent dose-finding doubly drills dropout drop-out dropouts drug drugs due dukes duplication duration early ecological ecology econometrics ectrodactyly editing eds education effect effective effectiveness effects effectsmodels efficacy efficiency efficient ehlersdanlos ehlers-danlos eigenvalues eigenvectors elementary elliptical em embryo embryos emergency empirical empirical-bayes enar end endophenotype endpoint end-point endpoints engineering entropy entry enumeration environmental eortc eortc-gu epa-emap epidemiologic epidemiological epidemiology epigenetic epistasis epoetin eqtl equation equations equilibrium equivalence error errors erythropoiesis-stimulating erythropoietin estimate estimated estimates -estimates estimating estimation estimator estimators etang ethics eugenics euler europe europeans evaluation evaluations event evidence evidence-based evolution evolutionary exact excess exclusive exhibited exhibits expansion expected expenditure experiment experimental experiments explained exploratory exponential exposure expression extraction extra-poisson factor factor-analysis factorial factors failure fallacy false famhap familial families family family-based familywise family-wise fast favorable fbat fdr fertilization fgfr2 fibrosis fight file-import-08-10-29 filled financing fine-scale finite firm first fisher fisherirwin fishers fitting five fixed fixture flashes f-like fluctuations foetal foetuses folded-noncentral-t followed foot for forecasting forest forests form forward four fourier frailty frame freedom frequency frequent from full function functional functions further gain gamma gamma-poisson gastrointestinal gaussian gee geisser-greenhouse gene gene-disease geneenvironment gene-environment genegene gene-gene gene-mapping gene-network generalised generalized genes gene_therapy genetic genetics genome genomewide genome-wide genomic genomic-control genomics genotype genotypephenotype genotype-phenotype genotypes genotypic genotyping geographic gibbs gini ginisimpson gllamm glmm global go gold gompertz goodness-of-fit gradient graduate grammatical graph graphical graphics graphs great grid gross groundwater group groups growing growth gui guide guidelines gum guttman-raveh gwa gwas habitat haematocrit half-t handsplit haplotype haplotypes haplotyping hapmap hardyweinberg hardy-weinberg hare harp hazard hazards health health-related heart heckman herds heritability heterogeneity heteroscedasticity heterozygosity hidden hierarchical high high-dimension histogram historical history hiv hla hmm homogeneity hospitalization hot hotelling-lawley hroc htsnps human hurricanes hutterites huynh-feldt hybridization hyperbolic hypothesis i ibd identical identifiable identify identity-by-descent identity-by-state ige ignorability ignorable ii iii ill-use image images imaging immune immunodeficiency imperfect important imprinting improvement imputation imputed in inadmissibility inbreeding include incomplete inconsistent increments independence independent indeterminism index indicating indicator indirect induction inequality infancy infant infections inference inference--estimation inferences inflammation inflammatory inflation influence influential informatics information informative inhaled inheritance initiation initiative instability instability-selection institutional instrumental instruments intensity interaction interactions interactive interclass interim intermittent international interpretation interruption interval interval-censored intervals intervention intima-media intraclass intra-class intra-cluster intra-unit inverse irb ironmortality irt is isolation item item-response itemsets iterative iv ivivc jackknife jackknifing jamesstein joint journals jsm jump kallekrein kaplanmeier kaplan-meier karyotyping kempton kernel kidney klk k-means knots knowledge known kolmogorov-smirnov kriging kullbackleibler kullback-leibler labor laboratory labs lag lago lam-mpi large large-sample lasso lassoelastic last latent layout ld learning least lectin leibniz leo leonard less leukocyte level liaison life likelihood likelihood_ratio_test likely limit lindley lindleys linear linearization linkage literacy literate litter litters llull local localization loci lod loess log logic logistic logit loglinear log-normal logrank log-rank longitudinal looks loss low lsd lshort lsp1 ltr lung m machine machine_learning mage-tab magnetic mahalanobis making malformation mallows management mannose-binding mannwhitney mann-whitney many map3k1 mapping maps marginal marginalized marital marker markers market markov mars martingale martingales masking matched maternity mathematical mating matrix maximally maximin maximized maximum max-statistic may mbl2 mcmc mcnemars mdr mdu meaningful measurable measure measurement measurements measures mechanism median medical medicine meiosis mendelian menopausal mentoring mesothelioma message metaanalysis meta-analysis metadata meteorology method methodology methods methylation microarray microarray_data_analysis microarrays microdeletion microsatellite migraine migration minimal minimally minimax minimum mining misclassification mising missclassification missing missing-data missingness misspecification misspecified mitosis mixed mixed-effects mixture mode model model-based model-donor modeling modelling models model-selection moderate modification modified modifier molecular monitoring monotone monte monte-carlo morbidity more mortality most motives mpi mri mrmc mrna msc1991 multiallelic multicase multicenter multidimensional multifactor multilevel multilocus multi-locus multinomial multinormal multiple multiple_testing multiply multipoint multireader multiregional multisite multistage multistation multi-syndrome multivariate mutagenesis mutation navigenics23andme nearest negative neighbour neoplasm nested net network networks neural next-gen-sequencing neyman nlmixed n-mode nominal nomograms non-centrality non-ignorability nonignorable noninformative nonlinear non-linear non-local non-monotone nonorthogonal nonparametric non-parametric nonparametrics nonproportional nonrandomly nonresponse non-response non-small-cell normal not novel nuclear nucleotide nuisance null number numerical nutritional objective object-oriented observation observational observations observed observer octocorallia odds of on oncovax one-sided one-stage operating operation optimal optimization or ordered ordering orderings ordinal ordination oscillation osteoporosis out outbreak outcome outcomes outliers ovarian over overall overdispersion oxidative ozone p package packages pain pair paired pairs pairwise panel paradigm paradox parallel parameter parametric parentage partial partially partition partitioning partitions passing paternity pathology pathway patient pattern patternmixture pattern-mixture pca pdf pedagogical pedagogy pedigree penalized penalty performance perl permutation permutations persistent personal personal_genomics pharmaceutical pharmacoeconomics pharmacogenetics pharmacogenomics pharmacotherapy phase phasing phenomena phenotype phenotypes phylogeny phytosociological pie piecewise pivotal placebo plan plant plaque plausible playfair pleiotropy pleural plot pmvd pocock point poisson pollution polygenic polymorphism polymorphisms polynomial polynomials polytomous pooling population population-based population_stratification positive post posterior posteriori postnatal poststratification power powerful ppv practice precision-referenced prediction predictive predictor predictors preference prenatal prentice preprocessing prevalence prevention principal principle prior prioritization priors probabilistic probabilities probability proc procedure procedures process processes processing procollagen product profession profile prognosis prognostic program programming progressive project propensity property prophylaxis proportion proportional prospective prostate protection protein proteomics protocol pruned pruning pseudolikelihood pseudo-likelihood psoriasis psychiatric psychology psychometric psychosocial public publishing pure p-value p-values pvm qol qtl quadratic quadrature quality quantile quantitative quantity quasi-coherence quasilikelihood quasi-likelihood quasi-likelihoodweighted questionnaires r r2 radiology radiotherapy random random-coefficient random_forest random-intercept randomisation randomization randomized randomness rank rank-based ranking rankings rasch rate rates ratio ratios rbnn rc-tdt reading real-donor realized receiver receiver-operating recist recommendations reconstruction recpam recursive reduced reduction redundancy reef reference regimens region regression regressions regularization relatedness relative release releve reliability relocation renal repeated repeatedmeasures replication report reporting representative reproducibility resampling re-sampling research resection residual residuals resonance respiratory response response-adaptive response-biased responses restricted retrospective reversible review ric ridge risk risks river rivers rjmcmc rna rob robust robustness roc role roma roots roughness routine rowcolumn r-squared rule rules rupture s saccharomyces safe safety sam sample sampler samples sample-size sampling sandwich sas sasweave scalability scale scan schizophrenia sciences score scoring screen screening screens seal second section section-to seeded segmentation segmented segregation selected selection self-assessed self-organising semilatent semiparametric sensitivity separation sequence sequencing sequential series services sets setting severity sex sex-linked seychelles shared shared-parameter shortcomings shrinkage sib siblings sigma signal significance significant simian similarity simplification simulated simulation simultaneous sine single single_cell singular sites size skill small smoking smooth smoothing snooping snp snps social sociobiology socioeconomic soft software sorbitol source spanning spatial species specification specificity spectra spline splines split splits splitting sports spotted sprint squares stacked stage standard standardization standardized starr statgen statistic -statistic statistical statisticians statistics statistucs status stein stem_cells stepwise stillbirths stochastic stopping stoppingcorrelated str strategic stratification strd strength stress strong structural structure students studies study studymixture subgroup subjects subject-specific subtree sugar sum sums supervised support surface surgery surrogate survey survival susceptibility svm swamping sweave sweden symbolism symptoms syndrome synthetic system systematic systems t table tables tagsnps target tdt teacher teaching teachingregressionanalysis techniques technology teeth tempering terrorism test tested testing testosterone tests testswilcoxon testu01 text-books than that the theorem theory therapeutics therapy these thickness third this three-level threshold thresholding time time-dependent times tipranavir tnrc9 to tools total toxicity toxicological trace trail training trait traits transform transformation transformations transition translational transmissiondisequilibrium transmitted transplantation treatment tree tree-based tree-constructed trees tree-structured treeval trend trend-adjusted trends treshold trial trials trinomial trio trivers-willard truncated truncation t-test tumor tumor-suppressor tumours turboveg tutorial tvu twin twins two two-by-two twoing two-phase two-sample two-stage type types ulcerative ulcerative_colitis ulcerative-colitis umbrella unbiased uncertainty unconditional under undercount underdispersion unformed uniform uniparental uni-syndrome univariate upd us usability usage used u-statistics v vaccination vaccine validation value values vapnik-chervonenkis variability variable variables variance variancestatistical variants variation vascular vector veds vegetation velocity verification versus virtually virus visual visualization visualizing vitro vocalizations volume vr22 wage wald warbler water waters wave waveforms we weakly weather wedge weibull weight weighted weights were which whole whole-genome wide wilcoxon winbugs with withdrawal within-area wnar womens would xylitol yeast zero zero-inflated zero-inflation zero-modified zeros z-score z-transformation