Human Pangenome Reference Consortium

The Human Pangenome Reference Consortium aims to sequence 300 individuals, producing a pangenome of 600 haplotypes by around 2024. In their 2023 publication, a first draft human pangenome reference is presented. The study consists of 47 phased, diploid assemblies from a cohort of genetically diverse individuals.

Ensembl annotation of the human assemblies has been produced via a new mapping pipeline:

• A subset of the GENCODE 38 genes and transcripts have been annotated on each of the haploid assemblies. The subset excludes readthrough genes and genes on patches or haplotypes.
• For each gene, anchor sequences built from the surrounding region were used to locate the most likely corresponding region(s) in the target genome. A pairwise alignment of the reference and target regions was then carried out and used to map the exon coordinates and other features of the gene.
• In addition to the primary mapping, potential recent duplications and collapsed paralogues were identified by aligning canonical transcripts across the entire genome and searching for new mappings that did not overlap existing annotations.
• For more details on the annotation process, please refer to the 2023 publication (see Methods section: Ensembl Mapping Pipeline for Assembly Annotation)

Genomes and annotations are made available via our FTP site (see table below) and through the UCSC HPRC Assembly Hub