ArticleBiometrics2012
Rapid testing of SNPs and gene-environment interactions in case-parent trio data based on exact analytic parameter estimation.
Article in Biometrics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility.Frontiers in immunology · 2021Trial
- A study of sex-specific genetic effects underlying risk of orofacial clefts also highlights the potential impact of sequencing errors due to short read mis-mapping.medRxiv : the preprint server for health sciences · 2026Article
- Estimation of direct and indirect polygenic effects and gene-environment interactions using polygenic scores in case-parent trio studies.Nature genetics · 2026Article
- Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines.PLoS computational biology · 2025Article
- Estimation of Direct and Indirect Polygenic Effects and Gene-Environment Interactions using Polygenic Scores in Case-Parent Trio Studies.medRxiv : the preprint server for health sciences · 2025Article
- SURFBAT: a surrogate family based association test building on large imputation reference panels.G3 (Bethesda, Md.) · 2025Article
- Insomnia Polygenic Component on Attention Deficit-Hyperactivity Disorder: Exploring this Association Using Genomic Data from Brazilian Families.Sleep science (Sao Paulo, Brazil) · 2024Article
- Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies.Genetic epidemiology · 2022Review
- Preterm birth and genitourinary tract infections: assessing gene-environment interaction.Pediatric research · 2021Article
- Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios.PLoS genetics · 2021Article
- Detecting Gene-Environment Interaction for Maternal Exposures Using Case-Parent Trios Ascertained Through a Case With Non-Syndromic Orofacial Cleft.Frontiers in cell and developmental biology · 2021Article
- Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21.Human genetics · 2020Article
- Gene-gene interactions between BMP4 and ARHGAP29 among non-syndromic cleft lip only (NSCLO) trios from western Han Chinese population.International journal of clinical and experimental pathology · 2020Article
- Article
- Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent trios.Genetic epidemiology · 2017Article
- New insights from GWAS for the cleft palate among han Chinese population.Medicina oral, patologia oral y cirugia bucal · 2017Article
- Genome-Wide Analysis of Gene-Gene and Gene-Environment Interactions Using Closed-Form Wald Tests.Genetic epidemiology · 2015Article
- Replication of 13q31.1 association in nonsyndromic cleft lip with cleft palate in Europeans.American journal of medical genetics. Part A · 2015Article
- ACN9 and alcohol dependence: family-based association analysis in multiplex alcohol dependence families.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2015Article
- Analytic power and sample size calculation for the genotypic transmission/disequilibrium test in case-parent trio studies.Biometrical journal. Biometrische Zeitschrift · 2014Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Case-parent trio studies concerned with children affected by a disease and their parents aim to detect single nucleotide polymorphisms (SNPs) showing a preferential transmission of alleles from the parents to their affected offspring. A popular statistical test for detecting such SNPs associated with disease in this study design is the genotypic transmission/disequilibrium test (gTDT) based on a conditional logistic regression model, which usually needs to be fitted by an iterative procedure. In this article, we derive exact closed-form solutions for the parameter estimates of the conditional logistic regression models when testing for an additive, a dominant, or a recessive effect of a SNP, and show that such analytic parameter estimates also exist when considering gene-environment interactions with binary environmental variables. Because the genetic model underlying the association between a SNP and a disease is typically unknown, it might further be beneficial to use the maximum over the gTDT statistics for the possible effects of a SNP as test statistic. We therefore propose a procedure enabling a fast computation of the test statistic and the permutation-based p-value of this MAX gTDT. All these methods are applied to whole-genome scans of the case-parent trios from the International Cleft Consortium. These applications show our procedures dramatically reduce the required computing time compared to the conventional iterative methods allowing, for example, the analysis of hundreds of thousands of SNPs in a few minutes instead of several hours.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.