ArticleHuman mutation2010
Novel tools for extraction and validation of disease-related mutations applied to Fabry disease.
Article in Human mutation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 22 citations in OpenAlex.
- CorNet: Assigning function to networks of co-evolving residues by automated literature mining.PloS one · 2017Article
- Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.PLoS computational biology · 2016Article
- Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature.Journal of the American Medical Informatics Association : JAMIA · 2016Article
- Towards precision medicine: advances in computational approaches for the analysis of human variants.Journal of molecular biology · 2013Review
- tmVar: a text mining approach for extracting sequence variants in biomedical literature.Bioinformatics (Oxford, England) · 2013Article
- Annotating the biomedical literature for the human variome.Database : the journal of biological databases and curation · 2013Article
- Article
- Functional analysis of variant lysosomal acid glycosidases of Anderson-Fabry and Pompe disease in a human embryonic kidney epithelial cell line (HEK 293 T).Journal of inherited metabolic disease · 2012Article
- Drug design for ever, from hype to hope.Journal of computer-aided molecular design · 2012Article
- Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations.Bioinformatics (Oxford, England) · 2011Article
- Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature.Bioinformatics (Oxford, England) · 2011Article
- Prospects for the automated extraction of mutation data from the scientific literature.Human genomics · 2010Article
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genetic disorders are often caused by nonsynonymous nucleotide changes in one or more genes associated with the disease. Specific amino acid changes, however, can lead to large variability of phenotypic expression. For many genetic disorders this results in an increasing amount of publications describing phenotype-associated mutations in disorder-related genes. Keeping up with this stream of publications is essential for molecular diagnostics and translational research purposes but often impossible due to time constraints: there are simply too many articles to read. To help solve this problem, we have created Mutator, an automated method to extract mutations from full-text articles. Extracted mutations are crossreferenced to sequence data and a scoring method is applied to distinguish false-positives. To analyze stored and new mutation data for their (potential) effect we have developed Validator, a Web-based tool specifically designed for DNA diagnostics. Fabry disease, a monogenetic gene disorder of the GLA gene, was used as a test case. A structure-based sequence alignment of the alpha-amylase superfamily was used to validate results. We have compared our data with existing Fabry mutation data sets obtained from the HGMD and Swiss-Prot databases. Compared to these data sets, Mutator extracted 30% additional mutations from the literature.
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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.