NECTAR: a database of codon-centric missense variant annotations

Abstract

NECTAR (Non-synonymous Enriched Coding muTation ARchive; http://nectarmutation.org) is a database and web application to annotate disease-related and functionally important amino acids in human proteins. A number of tools are available to facilitate the interpretation of DNA variants identified in diagnostic or research sequencing. These typically identify previous reports of DNA variation at a given genomic location, predict its effects on transcript and protein sequence and may predict downstream functional consequences. Previous reports and functional annotations are typically linked by the genomic location of the variant observed. NECTAR collates disease-causing variants and functionally important amino acid residues from a number of sources. Importantly, rather than simply linking annotations by a shared genomic location, NECTAR annotates variants of interest with details of previously reported variation affecting the same codon. This provides a much richer data set for the interpretation of a novel DNA variant. NECTAR also identifies functionally equivalent amino acid residues in evolutionarily related proteins (paralogues) and, where appropriate, transfers annotations between them. As well as accessing these data through a web interface, users can upload batches of variants in variant call format (VCF) for annotation on-the-fly. The database is freely available to download from the ftp site: ftp://ftp.nectarmutation.org.

Figure 1.

The proportion of HGMD records by their variant types. The data are drawn from the HGMD professional (version 2013.1) where disease-causing mutations are tagged as either ‘DM’ or ‘DM?’, which is defined as ‘pathological mutations reported to be disease causing in the original literature report’. The question mark denotes that a degree of doubt has been found to exist with regard to pathogenicity.

Figure 2.

A schematic diagram of NECTAR framework. The Ensembl databases (Core, Variation and Compara) were downloaded and locally mirrored to speed up database queries using their API. UniProt XML files were also mirrored and parsed to construct an equivalent in-house SQL version. MySQL was used for the main back-end database management system and Perl for data processing. See the main text for the description of the workflow.

Figure 3.

Screen captures of the NECTAR website. (A) A GBrowse image shows the locations of disease-related amino acid substitutions and a Pfam domain (coloured in blue bar) along the sequence of MYL2 protein. A fine control of GBrowse image is possible if the image is being clicked. (B) One possible nonsense and seven missense variants are displayed at the Glu22 of MYL2 protein where Glu22Lys is originally reported by UniProt (VAR_004603). Their functional effects, predicted by SIFT and PolyPhen, are also shown. (C) Paralogue annotations of TPM4 are displayed. FTP links are coloured in red on the upper right corner. (D) NECTAR annotations are made on-the-fly from a user-provided VCF input. A variant is coloured in yellow because it makes the same amino acid substitutions as reported from the source (VAR_019844 from UniProt). The results can be downloaded as a spread sheet. The input was from http://nectarmutation.org/main/static/nectar_dummy.vcf.