Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons

Fei Yao, Pramila N. Ariyaratne, Axel M. Hillmer, Wah Heng Lee, Guoliang Li, Audrey S M Teo, Xing Yi Woo, Zhenshui Zhang, Jieqi P. Chen, Wan Ting Poh, Kelson F B Zawack, Chee Seng Chan, See Ting Leong, Say Chuan Neo, Poh Sum D Choi, Song Gao, Niranjan Nagarajan, Hervé Thoreau, Atif Shahab, Xiaoan Ruan & 6 others Valère Cacheux-Rataboul, Chia Lin Wei, Guillaume Bourque, Wing Kin Sung, Edison T. Liu, Yijun Ruan

Research output: Contribution to journalArticle

12 Citations (Scopus)

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.

LanguageEnglish
Article numbere46152
JournalPLoS ONE
Volume7
Issue number9
DOIs
Publication statusPublished - 28 Sep 2012

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Yao, Fei ; Ariyaratne, Pramila N. ; Hillmer, Axel M. ; Lee, Wah Heng ; Li, Guoliang ; Teo, Audrey S M ; Woo, Xing Yi ; Zhang, Zhenshui ; Chen, Jieqi P. ; Poh, Wan Ting ; Zawack, Kelson F B ; Chan, Chee Seng ; Leong, See Ting ; Neo, Say Chuan ; Choi, Poh Sum D ; Gao, Song ; Nagarajan, Niranjan ; Thoreau, Hervé ; Shahab, Atif ; Ruan, Xiaoan ; Cacheux-Rataboul, Valère ; Wei, Chia Lin ; Bourque, Guillaume ; Sung, Wing Kin ; Liu, Edison T. ; Ruan, Yijun. / Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. In: PLoS ONE. 2012 ; Vol. 7, No. 9.
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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.",
author = "Fei Yao and Ariyaratne, {Pramila N.} and Hillmer, {Axel M.} and Lee, {Wah Heng} and Guoliang Li and Teo, {Audrey S M} and Woo, {Xing Yi} and Zhenshui Zhang and Chen, {Jieqi P.} and Poh, {Wan Ting} and Zawack, {Kelson F B} and Chan, {Chee Seng} and Leong, {See Ting} and Neo, {Say Chuan} and Choi, {Poh Sum D} and Song Gao and Niranjan Nagarajan and Herv{\'e} Thoreau and Atif Shahab and Xiaoan Ruan and Val{\`e}re Cacheux-Rataboul and Wei, {Chia Lin} and Guillaume Bourque and Sung, {Wing Kin} and Liu, {Edison T.} and Yijun Ruan",
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Yao, F, Ariyaratne, PN, Hillmer, AM, Lee, WH, Li, G, Teo, ASM, Woo, XY, Zhang, Z, Chen, JP, Poh, WT, Zawack, KFB, Chan, CS, Leong, ST, Neo, SC, Choi, PSD, Gao, S, Nagarajan, N, Thoreau, H, Shahab, A, Ruan, X, Cacheux-Rataboul, V, Wei, CL, Bourque, G, Sung, WK, Liu, ET & Ruan, Y 2012, 'Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons', PLoS ONE, vol. 7, no. 9, e46152. https://doi.org/10.1371/journal.pone.0046152

Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. / Yao, Fei; Ariyaratne, Pramila N.; Hillmer, Axel M.; Lee, Wah Heng; Li, Guoliang; Teo, Audrey S M; Woo, Xing Yi; Zhang, Zhenshui; Chen, Jieqi P.; Poh, Wan Ting; Zawack, Kelson F B; Chan, Chee Seng; Leong, See Ting; Neo, Say Chuan; Choi, Poh Sum D; Gao, Song; Nagarajan, Niranjan; Thoreau, Hervé; Shahab, Atif; Ruan, Xiaoan; Cacheux-Rataboul, Valère; Wei, Chia Lin; Bourque, Guillaume; Sung, Wing Kin; Liu, Edison T.; Ruan, Yijun.

In: PLoS ONE, Vol. 7, No. 9, e46152, 28.09.2012.

Research output: Contribution to journalArticle

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AU - Yao, Fei

AU - Ariyaratne, Pramila N.

AU - Hillmer, Axel M.

AU - Lee, Wah Heng

AU - Li, Guoliang

AU - Teo, Audrey S M

AU - Woo, Xing Yi

AU - Zhang, Zhenshui

AU - Chen, Jieqi P.

AU - Poh, Wan Ting

AU - Zawack, Kelson F B

AU - Chan, Chee Seng

AU - Leong, See Ting

AU - Neo, Say Chuan

AU - Choi, Poh Sum D

AU - Gao, Song

AU - Nagarajan, Niranjan

AU - Thoreau, Hervé

AU - Shahab, Atif

AU - Ruan, Xiaoan

AU - Cacheux-Rataboul, Valère

AU - Wei, Chia Lin

AU - Bourque, Guillaume

AU - Sung, Wing Kin

AU - Liu, Edison T.

AU - Ruan, Yijun

PY - 2012/9/28

Y1 - 2012/9/28

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