ArticleNucleic acids research2018
A survey of localized sequence rearrangements in human DNA.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.BMC genomics · 2026Article
- The analyses of human MCPH1 DNA repair machinery and genetic variations.Open medicine (Warsaw, Poland) · 2024Article
- Sequencing through hyperexpanded Friedreich's ataxia-GAA repeats by nanopore technology: implications in genotype-phenotype correlation.Brain communications · 2023Article
- Finding Rearrangements in Nanopore DNA Reads with LAST and dnarrange.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Multiple genome alignment in the telomere-to-telomere assembly era.Genome biology · 2022Review
- Hornerin deposits in neuronal intranuclear inclusion disease: direct identification of proteins with compositionally biased regions in inclusions.Acta neuropathologica communications · 2022Article
- A pipeline for complete characterization of complex germline rearrangements from long DNA reads.Genome medicine · 2020Article
- Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements.GigaScience · 2020Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- How sequence alignment scores correspond to probability models.Bioinformatics (Oxford, England) · 2020Article
- Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease.Nature genetics · 2019Article
- Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads.Genome biology · 2019Article
- NanoPipe-a web server for nanopore MinION sequencing data analysis.GigaScience · 2019Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what types of complex mutation occur, and we cannot routinely characterize arbitrarily-complex mutations in a high-throughput, genome-wide manner. Long-read DNA sequencing methods (e.g. PacBio, nanopore) are promising for this task, because one read may encompass a whole complex mutation. We describe an analysis pipeline to characterize arbitrarily-complex 'local' mutations, i.e. intrachromosomal mutations encompassed by one DNA read. We apply it to nanopore and PacBio reads from one human cell line (NA12878), and survey sequence rearrangements, both real and artifactual. Almost all the real rearrangements belong to recurring patterns or motifs: the most common is tandem multiplication (e.g. heptuplication), but there are also complex patterns such as localized shattering, which resembles DNA damage by radiation. Gene conversions are identified, including one between hemoglobin gamma genes. This study demonstrates a way to find intricate rearrangements with any number of duplications, deletions, and repositionings. It demonstrates a probability-based method to resolve ambiguous rearrangements involving highly similar sequences, as occurs in gene conversion. We present a catalog of local rearrangements in one human cell line, and show which rearrangement patterns occur.
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