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Vive la difference: naming structural variants in the human reference genome.

ABSTRACT: The HUGO Gene Nomenclature Committee has approved gene symbols for the majority of protein-coding genes on the human reference genome. To adequately represent regions of complex structural variation, the Genome Reference Consortium now includes alternative representations of some of these regions as part of the reference genome. Here, we describe examples of how we name novel genes in these regions and how this nomenclature is displayed on our website, http://genenames.org.

SUBMITTER: Seal RL

PROVIDER: S-EPMC3648363 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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Vive la différence: naming structural variants in the human reference genome.

Seal Ruth L RL Wright Mathew W MW Gray Kristian A KA Bruford Elspeth A EA

Human genomics 20130501

The HUGO Gene Nomenclature Committee has approved gene symbols for the majority of protein-coding genes on the human reference genome. To adequately represent regions of complex structural variation, the Genome Reference Consortium now includes alternative representations of some of these regions as part of the reference genome. Here, we describe examples of how we name novel genes in these regions and how this nomenclature is displayed on our website, http://genenames.org. ...[more]

PMID: 23634723

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Project description:BackgroundStructural variants comprise diverse genomic arrangements including deletions, insertions, inversions, and translocations, which can generally be detected in humans through sequence comparison to the reference genome. Among structural variants, insertions are the least frequently identified variants, mainly due to ascertainment bias in the reference genome, lack of previous sequence knowledge, and low complexity of typical insertion sequences. Though recent developments in long-read sequencing deliver promise in annotating individual non-reference insertions, population-level catalogues on non-reference insertion variants have not been identified and the possible functional roles of these hidden variants remain elusive.ResultsTo detect non-reference insertion variants, we developed a pipeline, InserTag, which generates non-reference contigs by local de novo assembly and then infers the full-sequence of insertion variants by tracing contigs from non-human primates and other human genome assemblies. Application of the pipeline to data from 2535 individuals of the 1000 Genomes Project helped identify 1696 non-reference insertion variants and re-classify the variants as retention of ancestral sequences or novel sequence insertions based on the ancestral state. Genotyping of the variants showed that individuals had, on average, 0.92-Mbp sequences missing from the reference genome, 92% of the variants were common (allele frequency > 5%) among human populations, and more than half of the variants were major alleles. Among human populations, African populations were the most divergent and had the most non-reference sequences, which was attributed to the greater prevalence of high-frequency insertion variants. The subsets of insertion variants were in high linkage disequilibrium with phenotype-associated SNPs and showed signals of recent continent-specific selection.ConclusionsNon-reference insertion variants represent an important type of genetic variation in the human population, and our developed pipeline, InserTag, provides the frameworks for the detection and genotyping of non-reference sequences missing from human populations.

Dataset Information

Vive la difference: naming structural variants in the human reference genome.

Publications

Vive la différence: naming structural variants in the human reference genome.

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