ArticleBMC bioinformatics2011
SNPPicker: high quality tag SNP selection across multiple populations.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
10 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic polymorphisms associated with rubella virus-specific cellular immunity following MMR vaccination.Human genetics · 2014Pooled it
- Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies.BioData mining · 2019Article
- Evaluating information content of SNPs for sample-tagging in re-sequencing projects.Scientific reports · 2015Article
- Genetic markers associated with abstinence length in alcohol-dependent subjects treated with acamprosate.Translational psychiatry · 2014Article
- Variation in NF-κB signaling pathways and survival in invasive epithelial ovarian cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2014Article
- Risk of ovarian cancer and the NF-κB pathway: genetic association with IL1A and TNFSF10.Cancer research · 2014Article
- Polymorphisms in metabolism/antioxidant genes may mediate the effect of dietary intake on pancreatic cancer risk.Pancreas · 2013Article
- Article
- Article
- Germline predictors of androgen deprivation therapy response in advanced prostate cancer.Mayo Clinic proceedings · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundLinkage Disequilibrium (LD) bin-tagging algorithms identify a reduced set of tag SNPs that can capture the genetic variation in a population without genotyping every single SNP. However, existing tag SNP selection algorithms for designing custom genotyping panels do not take into account all platform dependent factors affecting the likelihood of a tag SNP to be successfully genotyped and many of the constraints that can be imposed by the user.
resultsSNPPicker optimizes the selection of tag SNPs from common bin-tagging programs to design custom genotyping panels. The application uses a multi-step search strategy in combination with a statistical model to maximize the genotyping success of the selected tag SNPs. User preference toward functional SNPs can also be taken into account as secondary criteria. SNPPicker can also optimize tag SNP selection for a panel tagging multiple populations. SNPPicker can optimize custom genotyping panels including all the assay-specific constraints of Illumina's GoldenGate and Infinium assays.
conclusionsA new application has been developed to maximize the success of custom multi-population genotyping panels. SNPPicker also takes into account user constraints including options for controlling runtime. Perl Scripts, Java source code and executables are available under an open source license for download at http://mayoresearch.mayo.edu/mayo/research/biostat/software.cfm.
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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.