title: Sequence-specific error profile of Illumina sequencers.
abstract: We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this sequence-specific error (SSE) are: (i) inverted repeats and (ii) GGC sequences. We speculate that these sequences favor dephasing by inhibiting single-base elongation, by: (i) folding single-stranded DNA and (ii) altering enzyme preference. This phenomenon is a major cause of sequence coverage variability and of the unfavorable bias observed for population-targeted methods such as RNA-seq and ChIP-seq. Moreover, SSE is a potential cause of false single-nucleotide polymorphism (SNP) calls and also significantly hinders de novo assembly. This article highlights the importance of recognizing SSE and its underlying mechanisms in the hope of enhancing the potential usefulness of the Illumina sequencers.
authors.affiliation: Graduate School of Information Science, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.
authors.forename: Kensuke
authors.initials: K
authors.lastname: Nakamura
authors.forename: Taku
authors.initials: T
authors.lastname: Oshima
authors.forename: Takuya
authors.initials: T
authors.lastname: Morimoto
authors.forename: Shun
authors.initials: S
authors.lastname: Ikeda
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Yoshikawa
authors.forename: Yuh
authors.initials: Y
authors.lastname: Shiwa
authors.forename: Shu
authors.initials: S
authors.lastname: Ishikawa
authors.forename: Margaret C
authors.initials: MC
authors.lastname: Linak
authors.forename: Aki
authors.initials: A
authors.lastname: Hirai
authors.forename: Hiroki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Md
authors.initials: M
authors.lastname: Altaf-Ul-Amin
authors.forename: Naotake
authors.initials: N
authors.lastname: Ogasawara
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics; D020137:Base Pair Mismatch; D002874:Chromosome Mapping; D016680:Genome, Bacterial; D055029:Inverted Repeat Sequences; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA