ArticleBMC medical genomics2019
GTX.Digest.VCF: an online NGS data interpretation system based on intelligent gene ranking and large-scale text mining.
Article in BMC medical genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Phased T2T genome assemblies facilitate the mining of disease-resistance genes inHorticulture research · 2025Article
- RNA editing landscape of adipose tissue in polycystic ovary syndrome provides insight into the obesity-related immune responses.Frontiers in endocrinology · 2024Article
- Systematic optimization of host-directed therapeutic targets and preclinical validation of repositioned antiviral drugs.Briefings in bioinformatics · 2022Article
- Variomes: a high recall search engine to support the curation of genomic variants.Bioinformatics (Oxford, England) · 2022Article
- A novel variant of the IFITM5 gene within the 5'-UTR causes neonatal transverse clavicular fracture: Expanding the genetic spectrum.Molecular genetics & genomic medicine · 2020Article
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Authors and funding
10 authors.
Funding
Abstract
backgroundAn important task in the interpretation of sequencing data is to highlight pathogenic genes (or detrimental variants) in the field of Mendelian diseases. It is still challenging despite the recent rapid development of genomics and bioinformatics. A typical interpretation workflow includes annotation, filtration, manual inspection and literature review. Those steps are time-consuming and error-prone in the absence of systematic support. Therefore, we developed GTX.Digest.VCF, an online DNA sequencing interpretation system, which prioritizes genes and variants for novel disease-gene relation discovery and integrates text mining results to provide literature evidence for the discovery. Its phenotype-driven ranking and biological data mining approach significantly speed up the whole interpretation process.
resultsThe GTX.Digest.VCF system is freely available as a web portal at http://vcf.gtxlab.com for academic research. Evaluation on the DDD project dataset demonstrates an accuracy of 77% (235 out of 305 cases) for top-50 genes and an accuracy of 41.6% (127 out of 305 cases) for top-5 genes.
conclusionsGTX.Digest.VCF provides an intelligent web portal for genomics data interpretation via the integration of bioinformatics tools, distributed parallel computing, biomedical text mining. It can facilitate the application of genomic analytics in clinical research and practices.
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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.