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ClinVar: improving access to variant interpretations and supporting evidence.

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TLDR
ClinVar continues to make improvements to its search and retrieval functions.
Abstract
ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report. ClinVar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. Submissions may come from clinical providers providing their own interpretation of the variant ('provider interpretation') or from groups such as patient registries that primarily provide phenotypic information from patients ('phenotyping only'). ClinVar continues to make improvements to its search and retrieval functions. Several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.

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The DisGeNET knowledge platform for disease genomics: 2019 update.

TL;DR: The DisGeNET platform, a knowledge management platform integrating and standardizing data about disease associated genes and variants from multiple sources, is an interoperable resource supporting a variety of applications in genomic medicine and drug R&D.
Journal ArticleDOI

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program.

Daniel Taliun, +205 more
- 10 Feb 2021 - 
TL;DR: The Trans-Omics for Precision Medicine (TOPMed) project as discussed by the authors aims to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases.
Posted ContentDOI

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Daniel Taliun, +194 more
- 06 Mar 2019 - 
TL;DR: The nearly complete catalog of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and non-coding sequence variants to phenotypic variation as well as resources and early insights from the sequence data.
Journal ArticleDOI

A reference map of the human binary protein interactome

Katja Luck, +94 more
- 08 Apr 2020 - 
TL;DR: The utility of HuRI is demonstrated in identifying the specific subcellular roles of protein–protein interactions and in identifying potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases.
Journal ArticleDOI

ClinVar: improvements to accessing data.

TL;DR: The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file, and ClinVar's search engine has been fine-tuned for improved retrieval of search results.
References
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Journal ArticleDOI

A global reference for human genetic variation.

Adam Auton, +517 more
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TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
Journal ArticleDOI

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TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI

Analysis of protein-coding genetic variation in 60,706 humans

Monkol Lek, +106 more
- 18 Aug 2016 - 
TL;DR: The aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC) provides direct evidence for the presence of widespread mutational recurrence.
Journal ArticleDOI

ClinVar: public archive of relationships among sequence variation and human phenotype

TL;DR: To facilitate evaluation of the medical importance of each variant, ClinVar aggregates submissions with the same variation/phenotype combination, adds value from other NCBI databases, assigns a distinct accession of the format RCV000000000.0 and reports if there are conflicting clinical interpretations.
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