ArticleGenome research2013
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers, 1 of them a synthesis that pooled it.
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Who cites it
161 citing papers in PubMed, 1 synthesis or guideline pooled it, 274 citations in OpenAlex.
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- The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2015Trial
- Genome-wide annotation of human multi-nucleotide variants reveals widespread functional differences from single nucleotide variants.Nature communications · 2026Article
- Pharmacologic Inhibition of PMS2 Induces MMR Deficiency and Response to Immune Checkpoint Blockade.Cancer discovery · 2026Article
- Unsupervised Deep Representation Learning and Probabilistic Clustering for the Systems-Level Discovery of Germline Mutation Signatures in Pediatric Cancers.Biomedicines · 2026Article
- LVV SMRTcap reveals extensive proviral variation in lentiviral vector-transduced CAR T cells.bioRxiv : the preprint server for biology · 2026Article
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- MuRaL-indel: a deep learning framework for building insertion and deletion mutation rate maps.Briefings in bioinformatics · 2026Article
- Paternal age effect in autosomal dominant or X-linked de novo variants identified by genome-wide sequencing.HGG advances · 2026Article
- Proteome-Wide Analysis of Human Deletions.Proteins · 2026Article
- Genomic architecture of insertion-deletion (indel) variants in beetal goats of India.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Molecular mechanisms and therapeutic strategies for the recurrent F9 (c.520 + 13 A > G) variant in hemophilia B.Human genomics · 2026Article
- Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes.PLoS pathogens · 2026Article
- The structural effects of indel polymorphisms outside the binding site on RNA-protein interactions are shaped by selection.PLoS computational biology · 2025Article
- Deep indel mutagenesis reveals the regulatory and modulatory architecture of alternative exon splicing.Nature communications · 2025Article
- Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations.Cell genomics · 2025Article
- Identification and Validation of Genus/Species-Specific Short InDels in Dairy Ruminants.BMC veterinary research · 2025Article
- Clinical profiling and medical management of Israeli individuals with Phelan McDermid syndrome.Orphanet journal of rare diseases · 2025Article
- Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function.Nature communications · 2025Article
- Article
101 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors at 11 institutions in 5 countries.
Funding
Abstract
Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 individuals representing three diverse human populations. We show that rates of indel mutagenesis are highly heterogeneous, with 43%-48% of indels occurring in 4.03% of the genome, whereas in the remaining 96% their prevalence is 16 times lower than SNPs. Polymerase slippage can explain upwards of three-fourths of all indels, with the remainder being mostly simple deletions in complex sequence. However, insertions do occur and are significantly associated with pseudo-palindromic sequence features compatible with the fork stalling and template switching (FoSTeS) mechanism more commonly associated with large structural variations. We introduce a quantitative model of polymerase slippage, which enables us to identify indel-hypermutagenic protein-coding genes, some of which are associated with recurrent mutations leading to disease. Accounting for mutational rate heterogeneity due to sequence context, we find that indels across functional sequence are generally subject to stronger purifying selection than SNPs. We find that indel length modulates selection strength, and that indels affecting multiple functionally constrained nucleotides undergo stronger purifying selection. We further find that indels are enriched in associations with gene expression and find evidence for a contribution of nonsense-mediated decay. Finally, we show that indels can be integrated in existing genome-wide association studies (GWAS); although we do not find direct evidence that potentially causal protein-coding indels are enriched with associations to known disease-associated SNPs, our findings suggest that the causal variant underlying some of these associations may be indels.
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