The ExAC browser: displaying reference data information from over 60 000 exomes
By Konrad J. Karczewski, B. Weisburd, B. Thomas, Matthew Solomonson, D. Ruderfer, D. Kavanagh, T. Hamamsy, M. Lek, Kaitlin E. Samocha, Beryl B. Cummings and 4 more. 2016
700 citations recorded by the source corpus.
Worldwide, hundreds of thousands of humans have had their genomes or exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, we present a lightweight, flexible browser framework to display large population datasets of genetic variation. We demonstrate its use for exome sequence data from 60,706 individuals in the Exome Aggregation Consortium (ExAC). The ExAC browser provides gene- and transcript-centric displays of variation, a critical view for clinical applications. Additionally, we provide a variant display, which includes population frequency and functional annotation data as well as short read support for the called variant. This browser is open-source, freely available, and has already been used extensively by clinical laboratories worldwide.
Subfields: Genetics, Molecular Biology
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Citations in the corpus
- Quantitative missense variant effect prediction using large-scale mutagenesis data (2017, neutral): “Moreover, a recent survey of genetic variation in humans revealed that each individual harbors 50 private missense variants, most of which are of unknown effect (Karczewski et al., 2017; Zou et al., 2016).”
- CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer (2017, methodology): “Additional variant information is imported through the MyVariant.info annotation API 12 , providing links to complementary resources and variant annotations such as ClinVar 6 , COSMIC 13 and ExAC 14 .”
- Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018, positive): “(F) Enrichment of 64 genes with switch isoforms for: ASD risk loci (81); CHD8 targets (103); FMRP targets (33); mutationally constraint genes (104); syndromic and highly ranked (1 and 2) genes from SFARI Gene database; vulnerable ASD genes (105); genes with probability of loss-of-function intoleranc”
- SynGO: an evidence-based, expert-curated knowledgebase for the synapse (2019, methodology): “224 Neuron 103, 217–234, July 17, 2019 incidence as other genes, we used the probability of being lossof-function-intolerant (pLI) obtained from the Exome Aggregation Consortium (ExAC; Karczewski et al., 2017).”