ArticleGenome research2010
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
165 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Heritable L1 Retrotransposition Events During Development: Understanding Their Origins: Examination of heritable, endogenous L1 retrotransposition in mice opens up exciting new questions and research directions.BioEssays : news and reviews in molecular, cellular and developmental biology · 2018Pooled it
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- Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy.Molecular therapy. Methods & clinical development · 2023Article
- Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing.BMC genomics · 2023Article
- Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus.G3 (Bethesda, Md.) · 2023Article
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- Towards mouse genetic-specific RNA-sequencing read mapping.PLoS computational biology · 2022Article
- Comparative genomics ofMicrobial genomics · 2022Article
- Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors.Cell genomics · 2022Article
- SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains.Cell genomics · 2022Article
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
- The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally.The ISME journal · 2022Article
- Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers.Genome research · 2022Article
- Massive QTL analysis identifies pleiotropic genetic determinants for stress resistance, aroma formation, and ethanol, glycerol and isobutanol production in Saccharomyces cerevisiae.Biotechnology for biofuels · 2021Article
- Gv1, a Zinc Finger Gene Controlling Endogenous MLV Expression.Molecular biology and evolution · 2021Article
- De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families.American journal of human genetics · 2021Article
- Novel Genetic Rearrangements in Hepatitis B Virus: Complex Structural Variations and Structural Variation Polymorphisms.Viruses · 2021Review
105 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Structural variation (SV) is a rich source of genetic diversity in mammals, but due to the challenges associated with mapping SV in complex genomes, basic questions regarding their genomic distribution and mechanistic origins remain unanswered. We have developed an algorithm (HYDRA) to localize SV breakpoints by paired-end mapping, and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons and segmental duplications; however, our analysis of the C57BL/6J reference strain shows that incomplete reference genome assemblies are a major source of noise. We report 7196 SVs between the two strains, more than two-thirds of which are due to transposon insertions. Of the remainder, 59% are deletions (relative to the reference), 26% are insertions of unlinked DNA, 9% are tandem duplications, and 6% are inversions. To investigate the origins of SV, we characterized 3316 breakpoint sequences at single-nucleotide resolution. We find that approximately 16% of non-transposon SVs have complex breakpoint patterns consistent with template switching during DNA replication or repair, and that this process appears to preferentially generate certain classes of complex variants. Moreover, we find that SVs are significantly enriched in regions of segmental duplication, but that this effect is largely independent of DNA sequence homology and thus cannot be explained by non-allelic homologous recombination (NAHR) alone. This result suggests that the genetic instability of such regions is often the cause rather than the consequence of duplicated genomic architecture.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.