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Multiple Testing for SNP-SNP Interactions [PDF]
Statistical Applications in Genetics and Molecular Biology, 2007 Most genetic diseases are complex, i.e. associated to combinations of SNPs rather than individual SNPs. In the last few years, this topic has often been addressed in terms of SNP-SNP interaction patterns given as expressions linked by logical operators.
S Weidinger +4 more
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SNP-VISTA: An interactive SNP visualization tool [PDF]
BMC Bioinformatics, 2005 Abstract Background Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative ...
Inna Dubchak +10 more
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SNP by SNP by environment interaction network of alcoholism [PDF]
BMC Systems Biology, 2017 Alcoholism has a strong genetic component. Twin studies have demonstrated the heritability of a large proportion of phenotypic variance of alcoholism ranging from 50-80%. The search for genetic variants associated with this complex behavior has epitomized sequence-based studies for nearly a decade. The limited success of genome-wide association studies
Gil Alterovitz +3 more
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SNP-Flankplus: SNP ID-centric retrieval for SNP flanking sequences [PDF]
Bioinformation, 2008 The flanking sequences provided by dbSNP of NCBI are usually short and fixed length without further extension, thus making the design of appropriate PCR primers difficult. Here, we introduce a tool named "SNP-Flankplus" to provide a web environment for retrieval of SNP flanking sequences from both the dbSNP and the nucleotide databases of NCBI. Two SNP
Li-Yeh Chuang +3 more
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SNP+ to predict dropout rates in SNP arrays
Conservation Genetics Resources, 2022 AbstractGenotyping individuals using forensic or non-invasive samples such as hair or fecal samples increases the risk of allelic amplification failure (dropout) due to the low quality and quantity of DNA. One way to decrease genotyping errors is to increase the number of replicates per sample.
Sastre Alaiz, Natalia +2 more
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SNPsyn: detection and exploration of SNP–SNP interactions [PDF]
Nucleic Acids Research, 2011 SNPsyn (http://snpsyn.biolab.si) is an interactive software tool for the discovery of synergistic pairs of single nucleotide polymorphisms (SNPs) from large genome-wide case-control association studies (GWAS) data on complex diseases. Synergy among SNPs is estimated using an information-theoretic approach called interaction analysis.
Curk, Tomaz, Rot, Gregor, Zupan, Blaz
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SNP-SNP interactions in breast cancer susceptibility [PDF]
BMC Cancer, 2006 AbstractBackgroundBreast cancer predisposition genes identified to date (e.g., BRCA1 and BRCA2) are responsible for less than 5% of all breast cancer cases. Many studies have shown that the cancer risks associated with individual commonly occurring single nucleotide polymorphisms (SNPs) are incremental.
Laurent Briollais +12 more
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SNP interaction pattern identifier (SIPI): an intensive search for SNP–SNP interaction patterns [PDF]
Bioinformatics, 2016 Abstract Motivation Testing SNP–SNP interactions is considered as a key for overcoming bottlenecks of genetic association studies. However, related statistical methods for testing SNP–SNP interactions are underdeveloped.
Adam S. Kibel +47 more
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SNP locator: a candidate SNP selection tool [PDF]
International Journal of Data Mining, Modelling and Management, 2013 [Abstract] In this work, a data integration approach using a federated model based on a service oriented architecture (SOA) is presented. The BioMOBY middleware was used to implement each service which is part of the integration process. As an example of usage of this architecture, a web tool for candidate SNP selection has been developed.
Seoane, José A. +5 more
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