What's going on in the HGNC?

A whislestop tour of what we are working on now and in the future

Kristian Gray

What do the HGNC do?

HGNC aims

To create and approve nomenclature for all human protein-coding genes, pseudogenes & RNAs.
Reassign nomenclature for loci basing names on new functional data.
Group genes into families/sets.
Coordinate gene naming across vertebrates.
Collaborate with other nomenclature committees e.g Mouse, Rat and Chicken.
For vertebrates without a nomenclature committee we have created a new project called VGNC.

Specialist advisors & collaborator

Specialist advisors

116 people across the world that are our specialist advisors for particular gene families.

Full list can be seen on our specialist advisors page

Collaborators on complex gene families

Naming and grouping olfactory receptors: Tsviya Olender & Doron Lancet
Naming and grouping P450 genes: David Nelson & Jed Goldstone

Naming and curating genes

Assignment of gene symbols

Function: e.g. enzyme, complex subunit, receptor, transporter
Sequence comparison: e.g. ortholog, gene family member
Domain structures & motifs: e.g. TMEM#, WDR#
Other information from researchers, literature & databases: e.g. cellular location, associated phenotype, chromosomal location

Reassignment & coordination

Tools & resources

Curated cross references

Let's say that we have created a gene symbol record using NCBI gene 5989 and named it RFX1.

We can use the NCBI gene ID that we have attached to the record to curate links to Ensembl, Vega^* and pseudogene.org^*

Mapping Tool

Maintaining x-refs

SSU72P2 supporting evidence

xref updater

Gene family curation

Actin family

New HGNC website development

The current HGNC site

www.genenames.org

Static content served by Drupal 6 while dynamic content is perl CGI. This means two live servers with two sets of code and templates.
Site is fixed width for smaller monitors.
Not mobile or tablet friendly.

Beta website

beta.genenames.org

Worked with the UX team to see what we could do to improve the site.
Cleaner design.
Familiar flow through the website.
Improved search and facet options.
All running off one web server using AngularJS (1.6) and Jekyll.
Development carried out on developers own machines within a docker container cluster.
... and managed by the Gulp task runner to build, uglify and compress before release.
Carried out UX testing.

Planning on releasing the beta site to everyone this year.

VGNC

Vertebrate gene nomenclature committee

What is the VGNC?

New initiative to coordinate gene naming across vertebrates
Gene nomenclature will reflect homologous relationships across species
Consensus naming based on human
Data will be distributed to genomic databases and model organism databases
The new VGNC website will become a portal for all official vertebrate nomenclature

HCOP orthology assertion

Curation tools

Data pipeline

4 resources

3 resources

Complex gene family

Manual submission

Prototype species: Chimp

We have ~14800 named Chimp genes within the VGNC site.
Most are 1:1 Human to Chimp orthologs with 4 resources agreeing
Manually checked the results of the automation to test the pipeline.

Website

vertebrate.genenames.org

Design is taken from the new HGNC site
Branch of the same project to maximise code reuse

Future plans

HGNC curation

Naming of novel loci that have been predicted to be protein coding by Gencode.
Name lncRNAs if the models from Gencode and RefSeq are similar e.g LINC#.
Continue to name small RNAs in collaboration the resources.
Work in collaboration with TGMI to stabilise as many clinically relevant protein coding genes.
Work towards renaming all uninformative human symbols like C#orf#.