Whole genome and transcriptome sequencing of a B3 thymoma.
Whole genome and transcriptome sequencing of a B3 thymoma.
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DOI：
10.1371/journal.pone.0060572
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Giaccone G
中科院分区：
文献类型：
--
作者：
Petrini I;Rajan A;Pham T;Voeller D;Davis S;Gao J;Wang Y;Giaccone G
胸腺瘤的分子病理学尚不清楚。在肿瘤中经常发现基因组畸变，但胸腺瘤中没有广泛的测序报道。在这里，我们提出了B3胸腺瘤在全基因组和转录组水平的第一个全面的观点。一位55岁的白人女性接受了IVA B3期胸腺瘤的完全切除。从癌细胞超过80%的快速冷冻肿瘤样本中提取RNA和DNA。我们使用Agilent平台进行阵列比较基因组杂交，使用HiSeq 2000 （Illumina）进行转录组测序，使用Complete Genomics Inc平台进行全基因组测序。全基因组测序确定了95%以上肿瘤和正常对照基因组中这两个等位基因的序列（NCBI Build 37）。拷贝数（CN）畸变与先前描述的B3胸腺瘤相似，染色体1q、5、7和X的CN增加，以及3p、6、11q42.2 qter和q13的CN丢失。1个易位t（11；X）通过全基因组测序鉴定，PCR和Sanger测序证实。鉴定出10个单核苷酸变异（SNVs）和2个插入/缺失（INDELs）；这些突变导致非同义氨基酸改变或剪接位点受到影响。该患者缺乏常见的癌症相关突变，这表明胸腺瘤可能通过与其他肿瘤类型不同的机制进化，并支持额外的高通量测序筛选的基本原理，以更好地了解胸腺瘤的体细胞遗传结构。
Molecular pathology of thymomas is poorly understood. Genomic aberrations are frequently identified in tumors but no extensive sequencing has been reported in thymomas. Here we present the first comprehensive view of a B3 thymoma at whole genome and transcriptome levels. A 55-year-old Caucasian female underwent complete resection of a stage IVA B3 thymoma. RNA and DNA were extracted from a snap frozen tumor sample with a fraction of cancer cells over 80%. We performed array comparative genomic hybridization using Agilent platform, transcriptome sequencing using HiSeq 2000 (Illumina) and whole genome sequencing using Complete Genomics Inc platform. Whole genome sequencing determined, in tumor and normal, the sequence of both alleles in more than 95% of the reference genome (NCBI Build 37). Copy number (CN) aberrations were comparable with those previously described for B3 thymomas, with CN gain of chromosome 1q, 5, 7 and X and CN loss of 3p, 6, 11q42.2-qter and q13. One translocation t(11;X) was identified by whole genome sequencing and confirmed by PCR and Sanger sequencing. Ten single nucleotide variations (SNVs) and 2 insertion/deletions (INDELs) were identified; these mutations resulted in non-synonymous amino acid changes or affected splicing sites. The lack of common cancer-associated mutations in this patient suggests that thymomas may evolve through mechanisms distinctive from other tumor types, and supports the rationale for additional high-throughput sequencing screens to better understand the somatic genetic architecture of thymoma.
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影响因子：
64.8
作者：
Ellis, Matthew J.;Ding, Li;Shen, Dong;Luo, Jingqin;Suman, Vera J.;Wallis, John W.;Van Tine, Brian A.;Hoog, Jeremy;Goiffon, Reece J.;Goldstein, Theodore C.;Ng, Sam;Lin, Li;Crowder, Robert;Snider, Jacqueline;Ballman, Karla;Weber, Jason;Chen, Ken;Koboldt, Daniel C.;Kandoth, Cyriac;Schierding, William S.;McMichael, Joshua F.;Miller, Christopher A.;Lu, Charles;Harris, Christopher C.;McLellan, Michael D.;Wendl, Michael C.;DeSchryver, Katherine;Allred, D. Craig;Esserman, Laura;Unzeitig, Gary;Margenthaler, Julie;Babiera, G. V.;Marcom, P. Kelly;Guenther, J. M.;Leitch, Marilyn;Hunt, Kelly;Olson, John;Tao, Yu;Maher, Christopher A.;Fulton, Lucinda L.;Fulton, Robert S.;Harrison, Michelle;Oberkfell, Ben;Du, Feiyu;Demeter, Ryan;Vickery, Tammi L.;Elhammali, Adnan;Piwnica-Worms, Helen;McDonald, Sandra;Watson, Mark;Dooling, David J.;Ota, David;Chang, Li-Wei;Bose, Ron;Ley, Timothy J.;Piwnica-Worms, David;Stuart, Joshua M.;Wilson, Richard K.;Mardis, Elaine R.
通讯作者：
Mardis, Elaine R.
影响因子：
14.8
作者：
Kumar, Prateek;Henikoff, Steven;Ng, Pauline C.
通讯作者：
Ng, Pauline C.
影响因子：
21.3
作者：
Fan, Zhipeng;Yamaza, Takayoshi;Lee, Janice S.;Yu, Jinhua;Wang, Songlin;Fan, Guoping;Shi, Songtao;Wang, Cun-Yu
通讯作者：
Wang, Cun-Yu
影响因子：
20.3
作者：
Grossmann, Vera;Tiacci, Enrico;Falini, Brunangelo
通讯作者：
Falini, Brunangelo
影响因子：
4.8
作者：
Feng, K;Zhou, XH;F채ssler, R
通讯作者：
F채ssler, R