ArticleBMC bioinformatics2006
PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 2 of them syntheses that pooled it.
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Who cites it
32 citing papers in PubMed, 2 syntheses or guidelines pooled it, 53 citations in OpenAlex.
- 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
- On the validity of within-nuclear-family genetic association analysis in samples of extended families.Statistical applications in genetics and molecular biology · 2015Article
- Article
- Family-based association test using normal approximation to gene dropping null distribution.BMC proceedings · 2014Article
- Germline missense variants in the BTNL2 gene are associated with prostate cancer susceptibility.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2013Article
- DNA repair polymorphisms influence the risk of second neoplasm after treatment of childhood acute lymphoblastic leukemia.Journal of cancer research and clinical oncology · 2012Article
- Contribution of TMC6 and TMC8 (EVER1 and EVER2) variants to cervical cancer susceptibility.International journal of cancer · 2012Article
- Identification of six loci associated with pelvic organ prolapse using genome-wide association analysis.Obstetrics and gynecology · 2011Article
- Validity and power of association testing in family-based sampling designs: evidence for and against the common wisdom.Genetic epidemiology · 2011Article
- Effective sample size: Quick estimation of the effect of related samples in genetic case-control association analyses.Computational biology and chemistry · 2011Article
- Strategies for selection of subjects for sequencing after detection of a linkage peak.BMC proceedings · 2011Article
- Automated construction and testing of multi-locus gene-gene associations.Bioinformatics (Oxford, England) · 2011Article
- PSEUDOMARKER: a powerful program for joint linkage and/or linkage disequilibrium analysis on mixtures of singletons and related individuals.Human heredity · 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
- Associations of 9p21 variants with cutaneous malignant melanoma, nevi, and pigmentation phenotypes in melanoma-prone families with and without CDKN2A mutations.Familial cancer · 2010Article
- Family-based association analysis of 42 hereditary prostate cancer families identifies the Apolipoprotein L3 region on chromosome 22q12 as a risk locus.Human molecular genetics · 2010Article
- Pedigree association: assigning individual weights to pedigree members for genetic association analysis.BMC proceedings · 2009Article
- Genome-wide association studies and the genetic dissection of complex traits.American journal of hematology · 2009Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundWe present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows for a mixture of pedigree members and independent individuals to be analyzed together, to test genetic markers and qualitative or quantitative traits. Our software, PedGenie, uses Monte Carlo significance testing to provide a valid test for related individuals that can be applied to any test statistic, including transmission disequilibrium statistics. Single locus at a time, composite genotype tests, and haplotype analyses may all be performed. We illustrate the validity and functionality of PedGenie using simulated and real data sets. For the real data set, we evaluated the role of two tagging-single nucleotide polymorphisms (tSNPs) in the DNA repair gene, NBS1, and their association with female breast cancer in 462 cases and 572 controls selected to be BRCA1/2 mutation negative from 139 high-risk Utah breast cancer families.
resultsThe results from PedGenie were shown to be valid both for accurate p-value calculations and consideration of pedigree structure in the simulated data set. A nominally significant association with breast cancer was observed with the NBS1 tSNP rs709816 for carriage of the rare allele (OR = 1.61, 95% CI = 1.10-2.35, p = 0.019).
conclusionPedGenie is a flexible and valid statistical tool that is intuitively simple to understand, makes efficient use of all the data available from pedigrees without requiring trimming, and is flexible to the types of tests to which it can be applied. Further, our analyses of real data indicate NBS1 may play a role in the genetic etiology of heritable breast cancer.
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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.