ArticleAmerican journal of human genetics2004
Ignoring linkage disequilibrium among tightly linked markers induces false-positive evidence of linkage for affected sib pair analysis.
Article in American journal of human genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-Wide Linkage Study Meta-Analysis of Male Sexual Orientation.Archives of sexual behavior · 2021Pooled it
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- A new GTSeq resource to facilitate multijurisdictional research and management of walleyeEcology and evolution · 2022Article
- Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus).Molecular biology reports · 2021Article
- A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data.American journal of human genetics · 2019Article
- Mixtures with relatives and linked markers.International journal of legal medicine · 2016Article
- Can whole-exome sequencing data be used for linkage analysis?European journal of human genetics : EJHG · 2016Article
- Collapsed haplotype pattern method for linkage analysis of next-generation sequence data.European journal of human genetics : EJHG · 2015Article
- PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.Bioinformatics (Oxford, England) · 2015Article
- Whole exome sequencing in extended families with autism spectrum disorder implicates four candidate genes.Human genetics · 2015Article
- A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.International journal of legal medicine · 2015Article
- Germline mutations in MAP3K6 are associated with familial gastric cancer.PLoS genetics · 2014Article
- Value of Mendelian laws of segregation in families: data quality control, imputation, and beyond.Genetic epidemiology · 2014Article
- Detection of Mendelian consistent genotyping errors in pedigrees.Genetic epidemiology · 2014Article
- GIGI: an approach to effective imputation of dense genotypes on large pedigrees.American journal of human genetics · 2013Article
- Article
- Obtaining accurate p values from a dense SNP linkage scan.Human heredity · 2012Article
- Genome-wide high-density SNP linkage search for glioma susceptibility loci: results from the Gliogene Consortium.Cancer research · 2011Article
- Finding disease genes: a fast and flexible approach for analyzing high-throughput data.European journal of human genetics : EJHG · 2011Article
- The genetics of colored sequence synesthesia: suggestive evidence of linkage to 16q and genetic heterogeneity for the condition.Behavioural brain research · 2011Article
30 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
Most multipoint linkage programs assume linkage equilibrium among the markers being studied. The assumption is appropriate for the study of sparsely spaced markers with intermarker distances exceeding a few centimorgans, because linkage equilibrium is expected over these intervals for almost all populations. However, with recent advancements in high-throughput genotyping technology, much denser markers are available, and linkage disequilibrium (LD) may exist among the markers. Applying linkage analyses that assume linkage equilibrium to dense markers may lead to bias. Here, we demonstrated that, when some or all of the parental genotypes are missing, assuming linkage equilibrium among tightly linked markers where strong LD exists can cause apparent oversharing of multipoint identity by descent (IBD) between sib pairs and false-positive evidence for multipoint model-free linkage analysis of affected sib pair data. LD can also mimic linkage between a disease locus and multiple tightly linked markers, thus causing false-positive evidence of linkage using parametric models, particularly when heterogeneity LOD score approaches are applied. Bias can be eliminated by inclusion of parental genotype data and can be reduced when additional unaffected siblings are included in the analysis.
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