ArticleAmerican journal of human genetics2005
Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal.
Article in American journal of human genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
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Who cites it
71 citing papers in PubMed, 1 synthesis or guideline pooled it, 124 citations in OpenAlex.
- Common variation in the LMNA gene (encoding lamin A/C) and type 2 diabetes: association analyses in 9,518 subjects.Diabetes · 2007Pooled it
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- Population genetics of marmosets in Asian primate research centers and loci associated with epileptic risk revealed by whole-genome sequencing.Zoological research · 2023Article
- Race-Dependent Association of Single-Nucleotide Polymorphisms in TrkB Receptor in People Living with HIV and Depression.Neurotoxicity research · 2021Article
- The conserved ASTN2/BRINP1 locus at 9q33.1-33.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain.Scientific reports · 2021Article
- A linkage and exome study of multiplex families with bipolar disorder implicates rare coding variants of ANK3 and additional rare alleles at 10q11-q21.Journal of psychiatry & neuroscience : JPN · 2021Article
- PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species.Frontiers in plant science · 2021Article
- Genetics of Smoking Behaviors in American Indians.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2020Article
- Combining CDKN1A gene expression and genome-wide SNPs in a twin cohort to gain insight into the heritability of individual radiosensitivity.Functional & integrative genomics · 2019Article
- Variants in TTC25 affect autistic trait in patients with autism spectrum disorder and general population.European journal of human genetics : EJHG · 2017Article
- Comprehensive candidate gene analysis for symptomatic or asymptomatic outcomes of Leishmania infantum infection in Brazil.Annals of human genetics · 2017Article
- Fine mapping under linkage peaks for symptomatic or asymptomatic outcomes of Leishmania infantum infection in Brazil.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2016Article
- Relationship between cytokine expression patterns and clinical outcomes: two population-based birth cohorts.Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology · 2015Article
- Complex pedigrees in the sequencing era: to track transmissions or decorrelate?Genetic epidemiology · 2014Article
- Cntnap4 differentially contributes to GABAergic and dopaminergic synaptic transmission.Nature · 2014Article
- Fine mapping on chromosome 13q32-34 and brain expression analysis implicates MYO16 in schizophrenia.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2014Article
- A novel method, the Variant Impact On Linkage Effect Test (VIOLET), leads to improved identification of causal variants in linkage regions.European journal of human genetics : EJHG · 2014Article
- Combined linkage and family-based association analysis improves candidate gene detection in Genetic Analysis Workshop 18 simulation data.BMC proceedings · 2014Article
- Low-frequency intermediate penetrance variants in the ROCK1 gene predispose to Tetralogy of Fallot.BMC genetics · 2013Article
- Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
Abstract
Once genetic linkage has been identified for a complex disease, the next step is often association analysis, in which single-nucleotide polymorphisms (SNPs) within the linkage region are genotyped and tested for association with the disease. If a SNP shows evidence of association, it is useful to know whether the linkage result can be explained, in part or in full, by the candidate SNP. We propose a novel approach that quantifies the degree of linkage disequilibrium (LD) between the candidate SNP and the putative disease locus through joint modeling of linkage and association. We describe a simple likelihood of the marker data conditional on the trait data for a sample of affected sib pairs, with disease penetrances and disease-SNP haplotype frequencies as parameters. We estimate model parameters by maximum likelihood and propose two likelihood-ratio tests to characterize the relationship of the candidate SNP and the disease locus. The first test assesses whether the candidate SNP and the disease locus are in linkage equilibrium so that the SNP plays no causal role in the linkage signal. The second test assesses whether the candidate SNP and the disease locus are in complete LD so that the SNP or a marker in complete LD with it may account fully for the linkage signal. Our method also yields a genetic model that includes parameter estimates for disease-SNP haplotype frequencies and the degree of disease-SNP LD. Our method provides a new tool for detecting linkage and association and can be extended to study designs that include unaffected family members.
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