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Grc ashg2015 workshop_mudge
GENCODE provides manual gene annotation of the human genome based on cDNA, EST, genomic and protein sequences, as well as publication and comparative analysis data. It is a merge of annotation from HAVANA and Ensembl. GENCODE v23 contains over 60,000 genes made up of protein coding, long non-coding RNA and pseudogenes. It is the reference gene set for the ENCODE project and can be viewed on the UCSC genome browser and Ensembl. HAVANA annotation of new patches and alternative loci is ongoing to improve GENCODE.
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Grc ashg2015 workshop_mudge
- 1. HAVANA / Ensembl/ GENCODE annotation on GRCh38 Jonathan M. Mudge Wellcome Trust Sanger Institute HAVANA group
- 2. HAVANA provide manualgene annotation cDNAs ESTs Genomic sequence (human, mouse, zebrafish…) Protein Transcript model Publication data Comparative analyses Next generation datasets
- 3. Ensembl: computational genomeannotation
- 4. Ensembl genebuild basedon genomic alignments Not all Ensembl releases represent new genebuilds
- 5. GENCODE is aHAVANA / Ensembl merge … with 8 institutes contributing Run every 3-6 months GENCODEv23 released July 2015
- 6. 19,797 protein codinggenes 15,931 long non-coding RNA genes 14,477 pseudogenes Hum GENCODE v23: 60,498 genes containing 198, 619 transcripts CDS exon Non-coding / UTR 79,795 CDS transcripts due to alternative splicing 27,817 lncRNA transcripts 1,112 transcribed GENCODE is the geneset for ENCODE
- 7. GENCODE has adesignated web portal www.gencodegenes.org
- 8. GENCODE has adesignated web portal www.gencodegenes.org
- 9. Viewing GENCODE ingenome browsers www.ensembl.org Ensembl 81/82 = GENCODEv23
- 10. Viewing GENCODE ingenome browsers https://genome.ucsc.edu
- 11. HAVANA annotation canbe viewed in Vega vega.sanger.ac.uk V61 Jun1 2015 ‘update’ annotation
- 12. v20 was thefirst GENCODE on GRCh38 v19 on GRCh37 GRCh38 (1) HAVANA liftover (2) HAVANA reannotation (3) Merge into full new Ensembl genebuild (Ensembl release 76)
- 13. Most gene IDsare preserved on GRCh38 GRCh37 GRCh38 Gene IDs were transferred based on contig-contig mapping strategy … also used to map variation etc ESPN
- 14. GRCh37 GRCh37 patch GRCh38 Ensembl re-annotation ofSRGAP2 ENSG00000266028 ENSG00000266028 ENSG00000163486 Assembly Gene ID
- 15. • Fixed geneissues caused by 37 > 38 changes • Major QC performed • New complex regions on chr 1, 9, X • Alt loci / Haplotype annotation v20 was the first GENCODE on GRCh38 V19 on GRCh37 GRCh38 (1) HAVANA liftover (2) HAVANA reannotation (3) Merge into full new Ensembl genebuild (Ensembl release 76)
- 16. The new pericentromicregion of chr9 New p-arm Gaps closed / clones flipped round / clones moved to correct arm Optical mapping data Hundreds of new / rebuilt models Old p-arm
- 17. Ongoing strategy forpatch annotation Ensembl: annotate patches when released without full gene build HAVANA: prioritise certain fix / novel patches and alt loci for annotation • some patches don’t contain genes that need re-annotating • others are exceptionally complex NOVEL patch HG-2048 GRCh38.p3 HAVANA pseudogene
- 18. HAVANA LRC annotationon GRCh38 Annotation of 34 Leukoctye Receptor Complexes (LRCs) completed for v20 COX2 COX1 PGF1 PGF2 DM1A DM1B MC1B MC1A LILRs KIRs
- 19. GENCODE remains awork in progress … arguably, far from complete • We are missing genes, transcripts and exons • 1000s of our models are incomplete • Functional annotation is largely putative Which transcripts are functional? How do they function?
- 20. GRCh38 GENCODE incorporatesNextGen data Transcript capture and completion Functional annotation Next generation experimental data Short read data: querying transcript-level support of existing introns / exons examining expression patterns, e.g. tissue specificity Long read data: querying transcript-level support of existing introns / exons CAGE / RAMPAGE / PolyAseq: establishing start and end points of genes / transcripts Ribosome profiling: reappraising initiation codon usage Mass spectrometry: identifying novel protein-coding regions
- 21. GENCODE v23 comparedwith v19 v23 has 2,678 more genes… 548 less protein coding genes
- 22. In conclusion GENCODE isnow a GRCh38 genebuild Compared to GRCh37 builds it is: • More accurate • More comprehensive • More sophisticated We recommend you use GENCODEv23 on GRC38
- 23. Acknowledgements Major funding: GENCODE partners:Wellcome Trust Sanger Institute; European Bioinformatics Institute; The University of Lausanne; The Centre de Regulació Genòmica; The University of California, Santa Cruz; The Massachusetts Institute of Technology; Yale University; The Spanish National Cancer Research Centre.