TY  - JOUR
A1  - Hillmer, Axel M.
A1  - Yao, Fei
A1  - Inaki, Koichiro
A1  - Lee, Wah Heng
A1  - Ariyaratne, Pramila N.
A1  - Teo, Audrey S.M.
A1  - Woo, Xing Yi
A1  - Zhang, Zhenshui
A1  - Zhao, Hao
A1  - Ukil, Leena
A1  - Chen, Jieqi P.
A1  - Zhu, Feng
A1  - So, Jimmy B.Y.
A1  - Salto-Tellez, Manuel
A1  - Poh, Wan Ting
A1  - Zawack, Kelson F.B.
A1  - Nagarajan, Niranjan
A1  - Gao, Song
A1  - Li, Guoliang
A1  - Kumar, Vikrant
A1  - Lim, Hui Ping J.
A1  - Sia, Yee Yen
A1  - Chan, Chee Seng
A1  - Leong, See Ting
A1  - Neo, Say Chuan
A1  - Choi, Poh Sum D.
A1  - Thoreau, Hervé
A1  - Tan, Patrick B.O.
A1  - Shahab, Atif
A1  - Ruan, Xiaoan
A1  - Bergh, Jonas
A1  - Hall, Per
A1  - Cacheux-Rataboul, Valère
A1  - Wei, Chia-Lin
A1  - Yeoh, Khay Guan
A1  - Sung, Wing-Kin
A1  - Bourque, Guillaume
A1  - Liu, Edison T.
A1  - Ruan, Yijun
T1  - Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
Y1  - 2011/05/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 665 
EP  - 675 
DO  - 10.1101/gr.113555.110 
VL  - 21 
IS  - 5 
UR  - http://genome.cshlp.org/content/21/5/665.abstract 
N2  - Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long-span paired-end-tag (PET) sequencing approach using 10-Kb genomic DNA inserts to study human genome structural variations (SVs). The use of a 10-Kb insert size allows the identification of breakpoints within repetitive or homology-containing regions of a few kilobases in size and results in a higher physical coverage compared with small insert libraries with the same sequencing effort. We have applied this approach to comprehensively characterize the SVs of 15 cancer and two noncancer genomes and used a filtering approach to strongly enrich for somatic SVs in the cancer genomes. Our analyses revealed that most inversions, deletions, and insertions are germ-line SVs, whereas tandem duplications, unpaired inversions, interchromosomal translocations, and complex rearrangements are over-represented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA–PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures that are compatible with breakage-fusion-bridge cycles, and we discover that large duplications are among the initial rearrangements that trigger genome instability for extensive amplification in epithelial cancers. 
ER  -