The GENCODE reference gene set is a combination of manual gene annotation from the Human and Vertebrate Analysis and Annotation (HAVANA) group (http://www.sanger.ac.uk/research/projects/vertebrategenome/havana/) and automatic gene annotation from Ensembl (Flicek et al. 2011). It is updated with every Ensembl release (approximately every 3 mo). Since manual annotation of the whole human genome is estimated to take until the end of 2012, the GENCODE releases are a combination of manual annotation from HAVANA and automatic annotation from Ensembl to ensure whole-genome coverage.
