Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.
Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.
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DOI：
10.1016/j.cancergen.2011.07.009
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发表时间：
2011-08
期刊：
影响因子：
1.9
通讯作者：
Milosavljevic A
中科院分区：
文献类型：
--
作者：
Hampton OA;Koriabine M;Miller CA;Coarfa C;Li J;Den Hollander P;Schoenherr C;Carbone L;Nefedov M;Ten Hallers BF;Lee AV;De Jong PJ;Milosavljevic A
癌症基因组经常经历基因组不稳定，导致染色体重排的积累。迄今为止，主要的挑战之一是使用短读大规模平行测序自信而准确地识别这些重排。我们能够通过结合两种不同的大规模平行测序策略来提高癌症重排检测：中等大小（平均36千碱基）和标准5千碱基配对文库。我们将这一策略应用于两种乳腺癌细胞系MCF7和HCC1954的重排图谱。我们检测并验证了MCF7中的91个体细胞重排和HCC1954中的25个体细胞重排，包括与这两个细胞系中先前报道的转录畸变相对应的基因组改变。每个基因组包含两种类型的断点——聚集和分散。在这两种细胞系中，分散的断点显示低拷贝重复的富集，而聚集的断点与高拷贝数扩增有关。比较两个基因组，我们观察到影响不同基因集的高度相似的结构突变谱，指出在非常不同的基因网络扰动背景下相似的基因组不稳定性历史。
Cancer genomes frequently undergo genomic instability resulting in accumulation of chromosomal rearrangement. To date, one of the main challenges has been to confidently and accurately identify these rearrangements using short-read massively parallel sequencing. We were able to improve cancer rearrangement detection by combining two distinct massively parallel sequencing strategies: fosmid-sized (36 Kilobases on average) and standard 5 Kilobase mate pair libraries. We applied this strategy to map rearrangements in two breast cancer cell lines, MCF7 and HCC1954. We detect and validate a total of 91 somatic rearrangements in MCF7 and 25 in HCC1954, including genomic alterations corresponding to previously reported transcript aberrations in these two cell lines. Each of the genomes contains two types of breakpoints – clustered and dispersed. In both cell lines, the dispersed breakpoints show enrichment for low copy repeats, while the clustered breakpoints associate with high-copy number amplifications. Comparing the two genomes, we observe highly similar structural mutational spectra affecting different sets of genes, pointing to similar histories of genomic instability against the background of very different gene network perturbations.
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影响因子：
4.2
作者：
Huang, Guan-Li;Zhang, Xiao-Hua;Hu, Xiao-Qu
通讯作者：
Hu, Xiao-Qu
影响因子：
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作者：
Bashir, Ali;Liu, Yu-Tsueng;Bafna, Vineet
通讯作者：
Bafna, Vineet
影响因子：
64.8
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Berger, Michael F.;Lawrence, Michael S.;Demichelis, Francesca;Drier, Yotam;Cibulskis, Kristian;Sivachenko, Andrey Y.;Sboner, Andrea;Esgueva, Raquel;Pflueger, Dorothee;Sougnez, Carrie;Onofrio, Robert;Carter, Scott L.;Park, Kyung;Habegger, Lukas;Ambrogio, Lauren;Fennell, Timothy;Parkin, Melissa;Saksena, Gordon;Voet, Douglas;Ramos, Alex H.;Pugh, Trevor J.;Wilkinson, Jane;Fisher, Sheila;Winckler, Wendy;Mahan, Scott;Ardlie, Kristin;Baldwin, Jennifer;Simons, Jonathan W.;Kitabayashi, Naoki;MacDonald, Theresa Y.;Kantoff, Philip W.;Chin, Lynda;Gabriel, Stacey B.;Gerstein, Mark B.;Golub, Todd R.;Meyerson, Matthew;Tewari, Ashutosh;Lander, Eric S.;Getz, Gad;Rubin, Mark A.;Garraway, Levi A.
通讯作者：
Garraway, Levi A.
影响因子：
30.8
作者：
Campbell, Peter J.;Stephens, Philip J.;Pleasance, Erin D.;O'Meara, Sarah;Li, Heng;Santarius, Thomas;Stebbings, Lucy A.;Leroy, Catherine;Edkins, Sarah;Hardy, Claire;Teague, Jon W.;Menzies, Andrew;Goodhead, Ian;Turner, Daniel J.;Clee, Christopher M.;Quail, Michael A.;Cox, Antony;Brown, Clive;Durbin, Richard;Hurles, Matthew E.;Edwards, Paul A. W.;Bignell, Graham R.;Stratton, Michael R.;Futreal, P. Andrew
通讯作者：
Futreal, P. Andrew
影响因子：
56.9
作者：
Kim, Hongtae;Chen, Junjie;Yu, Xiaochun
通讯作者：
Yu, Xiaochun