Genome reference consortium

The goal of the Genome Reference Consortium (GRC) is to ensure that the human, mouse and zebrafish reference assemblies are biologically relevant by closing gaps, fixing errors and representing complex variation.

The GRC is a collaboration between the The Wellcome Trust Sanger Institute (WTSI), the Washington University Genome Sciences Center (WUGSC), the European Bioinformatics Institute (EBI) and the The National Center for Biotechnology Information (NCBI).

The NCBI hosts the GRC home pages

News about the GRC activities can be found in our blog. If you want to keep up with major and minor assembly releases and other events, subcribe to our announcement list.

Upcoming assembly releases and remapping

The new human genome assembly, GRCh38, is now publicly available. More information can be found in our blog.

A new zebrafish assembly, GRCz10, is planned for early 2014. This new assembly release will benefit from hundreds of gap closures, adjustment of clone overlaps and new clones being added. On top of this, clones and clone contigs are being re-ordered and reoriented according to data from optical mapping and additional SATmap markers.

When the GRC produces a new major assembly release, this alters the chromosome coordinates. It is possible to convert the chromosome coordinates of annotation based on an older release into the coordinates for the equivalent sequence in a new release using the NCBI's Remap tool. The sequence alignments between major releases that underlie the Remap tool are available from the GRC website; for instance, alignments between the mouse MGSCv37 and GRCm38 assemblies are available via the GRC mouse page following the ftp link.

Information

View genome issues in browsers

In order to view the regions currently under review please go e.g. to the tabular overview of issues under review as listed on the right or attach a DAS source to your browser. We currently provide DAS sources for genome browsers like Ensembl. For attaching the available DAS sources to Ensembl please follow the links below, which will take you to an arbitrary entry locus from which you can move on.

  • human assembly GRCh37 (live Ensembl)
  • human assembly GRCh38 will appear shortly
  • mouse assembly GRCm38 (live Ensembl)
  • zebrafish assembly Zv9 (live Ensembl)

More ways of investigating

The PGPviewer is a genome browser for easy evaluation of the most current tilepaths. It contains the GRC species plus a few others and might help you with your region of interest.

We also provide the ChromoView TPF/AGP viewer for reference genomes and their alternative assembly regions. It shows the current tiling path of sequences and the overlaps between them which are used to make the consensus for each assembly.

Publications

Your input

We provide mechanisms by which the scientific community can report loci in need of further review. Information about loci currently under review and genome assembly production cycles are available for human, mouse and zebrafish. More information about the zebrafish genome project can be found here

Please use the links on the right to find out more.

Updates

  • 24th December 2013: GRCh38 is now publicly available
    More in our blog.
  • 13th September 2013: GRCh38 submitted to Genbank
    The new human genome assembly, GRCh38 has been submitted to Genbank and we are awaiting its public release in the week commencing the 23rd of September.
  • 2nd August 2013: Freeze date for GRCh38 build
    Today the clone path for the next human genome assembly is frozen. GRCh38 will comprise a majorly updated clone path with hundreds of issues being fixed, the correction of SNPs and indels according to 1000genomes data and the addition of centromere sequences.
  • 17th April 2013: Zebrafish Genome Paper Published
    The paper describing the zebrafish genome sequence and its relationship to the human genome has been published. If you are interested in the sequence details, make sure to have a look at the supplementary material.
  • 6th Oct 2010: GRC expands to include Zebrafish Genome
    After the release of the integrated zebrafish genome assembly Zv9 by the Wellcome Trust Sanger Institute, the genome sequence has now been handed over to the Genome Reference Consortium (GRC) for continued maintenance and further improvements. The GRC is currently working on replacing whole genome shotgun sequence with high quality finished clone sequence, closing remaining gaps and placing yet unlocalized sequence. More details can be found here.
  • 16th Aug 2010: Second patch release GRCh37.p2
    In this release, 70 patches were added, 52 were of type Novel and 18 were of type Fix. There were 20 issues resolved in this release. Additionally, the MT sequence was added to this assembly
  • 5th Aug 2010: First update to GRCh37 released in Ensembl

    Ensembl release 59 includes the first human assembly patches released by the Genome Reference Consortium (GRC). The ongoing genome improvements are now made available to the community via minor releases called patches. The patches do not change the chromosome coordinate system but do provide either a new alternate haplotype (novel patch) or provide a preview of the chromosome tiling path for that region in the next major release (fix patch). The patched update GRCh37.p1 affects only 2 regions of the reference assembly.The patch update GRCh37.p1 includes:

    • Fix Patch: HG79_PATCH (GL339450.1) on chromosome 9, correction for the ABO gene.
    • Novel Patch: HSCHR5_1_CTG1 (GL339449.1) on chromosome 5. This patch provides an alternative region (haplotype).

    The two patched regions have undergone preliminary gene annotation. Human cDNAs with their annotated ORFs were aligned to the genome using the Exonerate cdna2genome model to generate coding transcripts. We expect future patch releases on a quarterly basis.

  • 10th Mar 2010: First patch release GRCh37.p1
    The GRC has released the first patch update to a genome assembly, GRCh37.p1. The patches contain loci corrections (fix patches) as well as new alternate version (novel patches) and can be applied without disrupting the GRCh37 coordinate system.
  • 17th Dec 2009: Nature editorial about the GRC
    Dedicated scientists are working hard to close the gaps, fix the errors and finally complete the human genome sequence. Elie Dolgin looks at how close they are.
  • 8th Oct 2009: GRC annual meeting at Hinxton
    The GRC met at Hinxton to discuss the plans for the coming year. Mouse will probably see a new assembly release, whereas for human there will be releases of patches to account for necessary changes to GRCh37. The GRC has agreed to take on the maintenance of the zebrafish genome from 2010 onwards.
  • 18th Jul 2009: Interview with Deanna Church on the GRC efforts
    In Sequence (GenomeWeb) published an interview with Deanna Church on defining alternate loci in the Human Reference Genome.
  • 14th Jul 2009: GRCh37 released in Ensembl
    Ensembl are pleased to announce the inclusion of the latest human assembly, GRCh37, into release 55. Ensembl Human thus includes a new Human core db with new gene set and all new data, plus assembly mappings between GRCh37 and NCBI36, NCBI35 and NCBI34. It will also introduce a new Havana merge set which adds coding genes, and for the first time a merge with non-coding genes. In addition there is a new other_features db containing the est-genes models.
  • 6th Apr 2009: Ensembl Project preview of GRCh37
    The Ensembl project released a preview of the new version of the human genome assembly GRCh37.
  • 3rd Mar 2009: Human genome assembly GRCh37 released
    The human genome assembly GRCh37 has been released today and is available both from ftp and Genbank/EMBL.
  • 14th Oct 2008: Chromoview TPF/AGP viewer
    The Sanger Institute now provides the ChromoView TPF/AGP viewer for reference genomes and their alternative assembly regions. It shows the current tiling path of sequences and the overlaps between them which are used to make the consensus for each assembly.
  • 22nd May 2008: DAS source for genome issues
    A DAS (Distributed Annotation System) source is available for genome browsers that highlights all regions reported as problematic. You can attach this source via simply clicking the link above, taking you to an example in the Ensembl browser.
  • 7th May 2008: Genome Reference Consortium start announced
    The Genome Reference Consortium was introduced to the public at the 'Biology of Genomes' meeting at Cold Spring Harbour today. The consortium has started its work to resolve the last remaining shortcomings of the human and mouse genomes.
* quick link - http://q.sanger.ac.uk/ndm0g928