1. Future Plans for the HGNC (Questions, Answers, and More Questions) Elspeth Bruford

2. 1.continue naming of human protein-coding genes, pseudogenes & RNA genes 2.continue reassignment of uninformative symbols based on functional data 3.coordinate gene naming across vertebrates 4.assign gene names within complex families across vertebrate species (olfactory receptors, cytochrome P450s) Currently Funded Aims (2012-2017)

3. 1.continue naming of human protein-coding genes, pseudogenes & RNA genes – largely maintenance for protein coding genes 2.continue reassignment of uninformative symbols based on functional data – continual 3.coordinate gene naming across vertebrates – increase in effort and priority (key aim?) 4.assign gene names within complex families across vertebrate species (olfactory receptors, cytochrome P450s) – new families? 5. ? anything else? Future Funded Aims (2017-2022?)

4. Funding Sources Current U41 funding from NHGRI ends 30.6.2017 Apply for renewal in cycle III (09.2016) Current Biomedical Resources grant from Wellcome Trust ends 31.8.17 Apply for renewal in 2017 (preliminary application ~11.2016) Should we consider applying to anywhere else?

5. Protein coding genes Follow-up to Proteogenomics workshop - potential disambiguation of some problem cases addition of ~70 novel protein coding loci from Havana Protein nomenclature – working with UniProt updates to UniProt naming guidelines jamboree for updating protein names in 2016

6. Renaming Literature searches for C#orfs, KIAAs, FAMs etc Name clean-up and comparison with UniProt Q2: replacing Roman numerals, removing kDA Standardisation (G-protein coupled vs G protein- coupled) Removing/updating phenotype based names how far to go…

7. Q3: phenotype-based names BRCA1, “breast cancer 1” > “BRCA1, DNA repair associated” or…? BRCA2, “breast cancer 2” > “BRCA2, DNA repair associated” or …? ABO, “ABO blood group (transferase A, alpha 1-3- N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase)” > “ABO blood group” or “ABO, alpha 1-3-N- acetylgalactosaminyltransferase and alpha 1-3- galactosyltransferase” or…?

8. Complex loci Locus types: complex cases segregating pseudogenes: pseudogene/protein coding pseudogenes/lncRNAs smORFs: lncRNA/protein coding MT-RNR2: rRNA/protein coding Retain primary locus type per symbol, and include additional field (name?) containing SO terms encapsulating complexity

9. RNA naming issues Q7: Italicise RNA gene products? Q8A: Predicted small RNA genes: – new locus type? Q8B: naming snoRNA-like genes: – SNORAX# and SNORDX#?

10. Q9: Bidirectional promoters Grzechnik et al 2014, TiBS lncRNA “head to head” (TSSs < 1 kb) with coding gene on antisense strand implications for transcription of both loci currently denoted in gene name, e.g. FOXG1-AS1, “FOXG1 antisense RNA 1 (head to head)” Mattick & Rinn, 2015 suggested using “BI” prefix to coding gene symbol recent community consultation suggests referencing head-to-head orientation, e.g. SYMBOL-HTH or naming as lincRNAs

11. Gene Naming Across Vertebrates Semi-automated naming of consensus 1:1 orthologs as identified by 4 comprehensive orthology resources: Ensembl Compara NCBI Gene orthology groups (replacing Homologene) OMA Panther What species next? chimp > cow > dog > horse > ? chicken and other avians??

12. Gene Naming Across Vertebrates Strengthening links with other nomenclature committees and other species’ communities? New complex families? Q1: Name formats for C#orf transferral Q4: Species abbreviations Q5: Species-specific experts/panel (e.g. Jeff Rogers at Duke for primates?)

13. VGNC To release a beta version of the http://vgnc.genenames.org site early in 2016, containing data from chimpanzee http://vgnc.genenames.org To run new species through the automated gene naming process, beginning with cow and dog To continue adding new tools to our internal curation website https://herd.genenames.org as required to assist our curators to work effectivelyhttps://herd.genenames.org To work with our gene family expert collaborators to produce a set of tools to enable large scale gene family curation

14. Q6: VGNC website

16. Computing Expand REST API to include gene families Replace drupal static web pages – Using Jekyll + AngularJS + Bootstrap + Grunt Redesign symbol reports – include multiple accessions e.g. UniProt, CCDS Continue to publically release code on Github

17. Current HGNC internal postGreSQL DB works, but needs to be refactored as discussed in 2014 SAB meeting This year new tools for curators and new features for our users have taken precedence Unforeseen EBI IT hardware changes also must take precedence However the work done in designing a new schema for a new DB has been used as a starting point for the VGNC DBs Database Redesign

18. Creative Commons? Public copyright licence, now on version 4.0 Different types allow adaptations of your work to be shared? yes no yes, as long as others share alike CC0 – public domain mark

19. Q10: Social Media

20. Complex Gene Families Olfactory receptors – Tsviya Cytochrome P450s – Jed & David

21. Future plans 1.Classifying additional mammalian repertoires 2.Developing HORDE.

22. Candidates for classification: 1.Chimpanzee 2.Cat 3.Pig 4.Horse 5.Elephant

23. HORDE: Developing the database to contain many mammalian OR repertoire.

24. Future plans

25. 27 REMAINING PROTEOMES IN THE RP75 SET (2221 SEQUENCES)