title: In Silico Prediction of Deleteriousness for Nonsynonymous and Splice-Altering Single Nucleotide Variants in the Human Genome.
abstract: In silico prediction methods have increasingly been valuable and popular in molecular biology, especially in human genetics, for deleteriousness prediction to filter and prioritize huge amounts of DNA variation identified by sequencing human genomes. There is a rich collection of available methods developed upon different levels/aspects of knowledge about how DNA variations affect gene expression. Given the fact that their predictions are not always consistent or even opposite of what was expected, using consensus prediction or majority vote among these methods is preferred to trusting any single one. Because querying different databases for different methods is both tedious and time-consuming for such big data sets, one database integrating predictions from multiple databases can facilitate the process. In this chapter, we describe the general steps of obtaining comprehensive predictions and annotations for large numbers of variants from dbNSFP, the first and probably the most widely used database of its kind.
authors.affiliation: Center for Human Genetics, Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
authors.forename: Xueqiu
authors.initials: X
authors.lastname: Jian
authors.affiliation: Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler St, E529, Houston, TX, 77030, USA. xiaoming.liu@uth.tmc.edu.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Liu
mesh_terms: D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030541:Databases, Genetic; D015870:Gene Expression / Q000235:genetics; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
keywords: Database; Functional prediction; In silico; Nonsynonymous; Protocol; Single nucleotide variant; Splice site; dbNSFP; dbscSNV