ArticleBioinformatics (Oxford, England)2008
hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
14 citing papers in PubMed, 2 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
- 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
- Selecting Closely-Linked SNPs Based on Local Epistatic Effects for Haplotype Construction Improves Power of Association Mapping.G3 (Bethesda, Md.) · 2019Article
- Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus.Cancer research · 2016Article
- Evaluation of 41 candidate gene variants for obesity in the EPIC-Potsdam cohort by multi-locus stepwise regression.PloS one · 2013Article
- Rule-based induction method for haplotype comparison and identification of candidate disease loci.Genome medicine · 2012Article
- Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis.BMC medical genetics · 2012Article
- Automated construction and testing of multi-locus gene-gene associations.Bioinformatics (Oxford, England) · 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
- Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study.BMC proceedings · 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
- Haplotype-based analysis: a summary of GAW16 Group 4 analysis.Genetic epidemiology · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
summaryHaplotypes carry important information that can direct investigators towards underlying susceptibility variants, and hence multiple tagging single nucleotide polymorphisms (tSNPs) are usually studied in candidate gene association studies. However, it is often unknown which SNPs should be included in haplotype analyses, or which tests should be performed for maximum power. We have developed a program, hapConstructor, which automatically builds multi-locus SNP sets to test for association in a case-control framework. The multi-SNP sets considered need not be contiguous; they are built based on significance. An important feature is that the missing data imputation is carried out based on the full data, for maximal information and consistency. HapConstructor is implemented in a Monte Carlo framework and naturally extends to allow for significance testing and false discovery rates that account for the construction process and to related individuals. HapConstructor is a useful tool for exploring multi-locus associations in candidate genes and regions. AVAILABILITY: http://www-genepi.med.utah.edu/Genie.
Indexed as
Identifiers
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.