Abstract
The reference human genome sequence is inarguably the most important and widely used resource in the fields of human genetics and genomics. It has transformed the conduct of biomedical sciences and brought invaluable benefits to the understanding and improvement of human health. However, the commonly used reference sequence has profound limitations, because across much of its span, it represents the sequence of just one human haplotype. This single, monoploid reference structure presents a critical barrier to representing the broad genomic diversity in the human population. In this review, we discuss the modernization of the reference human genome sequence to a more complete reference of human genomic diversity, known as a human pangenome.
Highlights
Over the past two decades, we have seen unprecedented advancements in DNA sequencing technologies, bioinformatics, and clinical genetics
The increase in the amount of genomic variation data in numerous databases [e.g., dbSNP [128]] and other high-quality reference genome sequences with diverse haplotypes made it difficult to host and build tooling to fully integrate these data relative to the reference coordinate system. These challenges motivated the development of a new human pangenome reference structure, one that was fully capable of representing diversity across a large number of genomes and was supported with the necessary bioinformatics pipelines to ensure the mapping of short sequencing reads, detection of genomic variants, and discovery of functional elements [52, 82, 110]
As we reflect on the impact that it has had on the field of genomics, it is apparent that the lessons we have learned are invaluable
Summary
Over the past two decades, we have seen unprecedented advancements in DNA sequencing technologies, bioinformatics, and clinical genetics. These challenges motivated the development of a new human pangenome reference structure, one that was fully capable of representing diversity across a large number of genomes and was supported with the necessary bioinformatics pipelines to ensure the mapping of short sequencing reads, detection of genomic variants, and discovery of functional elements [52, 82, 110].
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