Genomics browsers & data resources
Released date: Sunday, September 3, 2017
Genomics browsers & genomic data resources
(which may be useful in the evaluation of DNA variants)
DECIPHER
(based at the Wellcome Trust Sanger Institute, UK)
A powerful database with integrated genome browser containing publicly-available data from well over 20,000 patients. it is used by the clinical community to share and compare phenotypic and genotypic data. Recently updated to incorporate the gnomAD Genome Aggregation Database)
Ensembl
(based at the Wellcome Trust Sanger Institute, UK)
Powerful genome browser that contains the Variant Effect Predictor, below.
UCSC Genome Browser
(Univ. of California Santa Cruz, USA)
GeneCards
(based at the Weizmann Institute of Science, Israel)
A source of extensive information regarding specific genes and proteins, collated automatically from at least 125 other online databases around the world, including genomic, transcriptomic, proteomic, genetic, clinical and functional data.
gnomAD Genome Aggregation Database
(funded by the Broad Institute, Cambridge, MA, USA)
Dataset spanning over 120,000 exome sequences and over 15,000 whole-genome sequences from unrelated individuals sequenced as part of various disease-specific and population genetic studies.
Human Gene Mutation Database (HGMD)
(based at Cardiff)
Database of genetic alterations responsible for human inherited disease
PolyPhen-2 (Polymorphism Phenotyping 2)
(based at Brigham & Women’s Hospital, Harvard Medical School, Boston, MA, USA
Online bioinformatic prediction of effects upon protein function of human non-synonymous single nucleotide substitutions (i.e. those DNA coding sequence variants that cause amino acid substitutions)
SIFT
(based at the J Craig Venter Institute: in the USA, in La Jolla, CA and Rockville, MD)
Another commonly-used method for in silico prediction of effects of amino acid substitution upon protein function.
Variant Effect Predictor (VEP) for genome build GRCh37 (or GRCh38)
(contained within the Enembl website)
VEP computationally predicts the possible effects of DNA variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence.
