title: Facilitated sequence counting and assembly by template mutagenesis.
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.
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 wigler@cshl.edu levy@cshl.edu.
authors.forename: Dan
authors.initials: D
authors.lastname: Levy
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 wigler@cshl.edu levy@cshl.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Wigler
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D008969:Molecular Sequence Data; D016296:Mutagenesis / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013698:Templates, Genetic
keywords: copy number variation; expression profiling; mutational tagging