ArticleProceedings of the National Academy of Sciences of the United States of America2014
Facilitated sequence counting and assembly by template mutagenesis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Accurate measurement of microsatellite length by disrupting its tandem repeat structure.Nucleic acids research · 2022Article
- Targeted de novo phasing and long-range assembly by template mutagenesis.Nucleic acids research · 2022Article
- Practical Considerations for Single-Cell Genomics.Current protocols · 2022Review
- Partial bisulfite conversion for unique template sequencing.Nucleic acids research · 2018Article
- Bisulfite-converted duplexes for the strand-specific detection and quantification of rare mutations.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Presently, inferring the long-range structure of the DNA templates is limited by short read lengths. Accurate template counts suffer from distortions occurring during PCR amplification. We explore the utility of introducing random mutations in identical or nearly identical templates to create distinguishable patterns that are inherited during subsequent copying. We simulate the applications of this process under assumptions of error-free sequencing and perfect mapping, using cytosine deamination as a model for mutation. The simulations demonstrate that within readily achievable conditions of nucleotide conversion and sequence coverage, we can accurately count the number of otherwise identical molecules as well as connect variants separated by long spans of identical sequence. We discuss many potential applications, such as transcript profiling, isoform assembly, haplotype phasing, and de novo genome assembly.
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