ArticleBMC bioinformatics2008
SNPLims: a data management system for genome wide association studies.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- Data management system for diabetes clinical trials: a pre-post evaluation study.BMC medical informatics and decision making · 2023Article
- A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data.Database : the journal of biological databases and curation · 2021Article
- Article
- A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units.BMC bioinformatics · 2014Article
- snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing.BMC bioinformatics · 2013Article
- SNPflow: a lightweight application for the processing, storing and automatic quality checking of genotyping assays.PloS one · 2013Article
- MolabIS--an integrated information system for storing and managing molecular genetics data.BMC bioinformatics · 2011Article
- Article
- GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis.Bioinformatics (Oxford, England) · 2010Article
- Article
- SNPit: a federated data integration system for the purpose of functional SNP annotation.Computer methods and programs in biomedicine · 2009Article
- eCOMPAGT -- efficient combination and management of phenotypes and genotypes for genetic epidemiology.BMC bioinformatics · 2009Article
- Genome-wide association studies: quality control and population-based measures.Genetic epidemiology · 2009Article
- New approaches to treatment of primary immunodeficiencies: fixing mutations with chemicals.Current opinion in allergy and clinical immunology · 2008Review
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 at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent progresses in genotyping technologies allow the generation high-density genetic maps using hundreds of thousands of genetic markers for each DNA sample. The availability of this large amount of genotypic data facilitates the whole genome search for genetic basis of diseases. We need a suitable information management system to efficiently manage the data flow produced by whole genome genotyping and to make it available for further analyses.
resultsWe have developed an information system mainly devoted to the storage and management of SNP genotype data produced by the Illumina platform from the raw outputs of genotyping into a relational database. The relational database can be accessed in order to import any existing data and export user-defined formats compatible with many different genetic analysis programs. After calculating family-based or case-control association study data, the results can be imported in SNPLims. One of the main features is to allow the user to rapidly identify and annotate statistically relevant polymorphisms from the large volume of data analyzed. Results can be easily visualized either graphically or creating ASCII comma separated format output files, which can be used as input to further analyses.
conclusionsThe proposed infrastructure allows to manage a relatively large amount of genotypes for each sample and an arbitrary number of samples and phenotypes. Moreover, it enables the users to control the quality of the data and to perform the most common screening analyses and identify genes that become "candidate" for the disease under consideration.
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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.