05 August, 2010

Human GRCh37 assembly patches

Ensembl release 59 includes the first human assembly patches released by the Genome Reference Consortium (GRC).

The goal of the GRC is to ensure that the human reference assembly is biologically relevant by closing gaps, fixing errors and representing complex variation. Their ongoing efforts are 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. Click here for an example region.

Novel Patch: HSCHR5_1_CTG1 (GL339449.1) on chromosome 5. This patch provides an alternative region (haplotype). Click here for an example region.

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.

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