ArticleBMC bioinformatics2007
PedGenie: meta genetic association testing in mixed family and case-control designs.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 3 of them syntheses that pooled it.
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
16 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Fine-mapping CASP8 risk variants in breast cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2012Pooled it
- A role for XRCC2 gene polymorphisms in breast cancer risk and survival.Journal of medical genetics · 2011Pooled it
- Genetic variants in XRCC2: new insights into colorectal cancer tumorigenesis.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2009Pooled it
- Article
- Contribution of TMC6 and TMC8 (EVER1 and EVER2) variants to cervical cancer susceptibility.International journal of cancer · 2012Article
- The nuclear transcription factor PKNOX2 is a candidate gene for substance dependence in European-origin women.PloS one · 2011Article
- Haplotype association analyses in resources of mixed structure using Monte Carlo testing.BMC bioinformatics · 2010Article
- Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor.BMC medical genetics · 2010Article
- Genome-wide association studies and the genetic dissection of complex traits.American journal of hematology · 2009Review
- Five polymorphisms and breast cancer risk: results from the Breast Cancer Association Consortium.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2009Article
- Replication of the 10q11 and Xp11 prostate cancer risk variants: results from a Utah pedigree-based study.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2009Article
- A breast cancer risk haplotype in the caspase-8 gene.Cancer research · 2009Article
- Meta association of colorectal cancer confirms risk alleles at 8q24 and 18q21.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2009Article
- On combining triads and unrelated subjects data in candidate gene studies: an application to data on testicular cancer.Human heredity · 2009Article
- MHC loci affecting cervical cancer risk: distinguishing the effects of HLA-DQB1 and non-HLA genes TNF, LTA, TAP1 and TAP2.Genes and immunity · 2008Article
- Catmap: case-control and TDT meta-analysis package.BMC bioinformatics · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundPedGenie software, introduced in 2006, includes genetic association testing of cases and controls that may be independent or related (nuclear families or extended pedigrees) or mixtures thereof using Monte Carlo significance testing. Our aim is to demonstrate that PedGenie, a unique and flexible analysis tool freely available in Genie 2.4 software, is significantly enhanced by incorporating meta statistics for detecting genetic association with disease using data across multiple study groups.
methodsMeta statistics (chi-squared tests, odds ratios, and confidence intervals) were calculated using formal Cochran-Mantel-Haenszel techniques. Simulated data from unrelated individuals and individuals in families were used to illustrate meta tests and their empirically-derived p-values and confidence intervals are accurate, precise, and for independent designs match those provided by standard statistical software.
resultsPedGenie yields accurate Monte Carlo p-values for meta analysis of data across multiple studies, based on validation testing using pedigree, nuclear family, and case-control data simulated under both the null and alternative hypotheses of a genotype-phenotype association.
conclusionPedGenie allows valid combined analysis of data from mixtures of pedigree-based and case-control resources. Added meta capabilities provide new avenues for association analysis, including pedigree resources from large consortia and multi-center studies.
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What OpenQuestion holds
Registered trials
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.