RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2011 
FD May 01 
VO 21 
IS 5 
SP 665 
OP 675 
DO 10.1101/gr.113555.110 
UL http://genome.cshlp.org/content/21/5/665.abstract 
AB 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.