title: Non-random DNA fragmentation in next-generation sequencing.
abstract: Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed "reads" are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA breaks are random and sequence-independent. However, previously we showed that for the sonicated restriction DNA fragments the rates of double-stranded breaks depend on the nucleotide sequence. In this work we analyzed genomic reads from NGS data and discovered that fragmentation methods based on the action of the hydrodynamic forces on DNA, produce similar bias. Consideration of this non-random DNA fragmentation may allow one to unravel what factors and to what extent influence the non-uniform coverage of various genomic regions.
authors.affiliation: Department of Physics, Moscow State University, Moscow, Russia.
authors.forename: Maria S
authors.initials: MS
authors.lastname: Poptsova
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Irina A
authors.initials: IA
authors.lastname: Il'icheva
authors.affiliation: Department of Physics, Moscow State University, Moscow, Russia.
authors.forename: Dmitry Yu
authors.initials: DY
authors.lastname: Nechipurenko
authors.affiliation: Department of Biology, Moscow State University, Moscow, Russia.
authors.forename: Larisa A
authors.initials: LA
authors.lastname: Panchenko
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Mingian V
authors.initials: MV
authors.lastname: Khodikov
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Nina Y
authors.initials: NY
authors.lastname: Oparina
authors.affiliation: Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Puschino, Moscow Region, Russia.
authors.forename: Robert V
authors.initials: RV
authors.lastname: Polozov
authors.affiliation: 1] Department of Physics, Moscow State University, Moscow, Russia [2] Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Yury D
authors.initials: YD
authors.lastname: Nechipurenko
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Sergei L
authors.initials: SL
authors.lastname: Grokhovsky