title: Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.
abstract: Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10-20 kb and compared their characteristics with short insert (1 kb) libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer.
authors.affiliation: Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.
authors.forename: Fei
authors.initials: F
authors.lastname: Yao
authors.forename: Pramila N
authors.initials: PN
authors.lastname: Ariyaratne
authors.forename: Axel M
authors.initials: AM
authors.lastname: Hillmer
authors.forename: Wah Heng
authors.initials: WH
authors.lastname: Lee
authors.forename: Guoliang
authors.initials: G
authors.lastname: Li
authors.forename: Audrey S M
authors.initials: AS
authors.lastname: Teo
authors.forename: Xing Yi
authors.initials: XY
authors.lastname: Woo
authors.forename: Zhenshui
authors.initials: Z
authors.lastname: Zhang
authors.forename: Jieqi P
authors.initials: JP
authors.lastname: Chen
authors.forename: Wan Ting
authors.initials: WT
authors.lastname: Poh
authors.forename: Kelson F B
authors.initials: KF
authors.lastname: Zawack
authors.forename: Chee Seng
authors.initials: CS
authors.lastname: Chan
authors.forename: See Ting
authors.initials: ST
authors.lastname: Leong
authors.forename: Say Chuan
authors.initials: SC
authors.lastname: Neo
authors.forename: Poh Sum D
authors.initials: PS
authors.lastname: Choi
authors.forename: Song
authors.initials: S
authors.lastname: Gao
authors.forename: Niranjan
authors.initials: N
authors.lastname: Nagarajan
authors.forename: Hervé
authors.initials: H
authors.lastname: Thoreau
authors.forename: Atif
authors.initials: A
authors.lastname: Shahab
authors.forename: Xiaoan
authors.initials: X
authors.lastname: Ruan
authors.forename: Valère
authors.initials: V
authors.lastname: Cacheux-Rataboul
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bourque
authors.forename: Wing-Kin
authors.initials: WK
authors.lastname: Sung
authors.forename: Edison T
authors.initials: ET
authors.lastname: Liu
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D015894:Genome, Human; D015698:Genomic Library; D056914:Genomic Structural Variation; D006801:Humans; D016254:Mutagenesis, Insertional; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D016366:Open Reading Frames; D017422:Sequence Analysis, DNA / Q000379:methods*