Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes.
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes.
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DOI：
10.1534/g3.116.033514
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发表时间：
2016-12-07
期刊：
影响因子：
--
通讯作者：
Doherty JA
中科院分区：
文献类型：
--
作者：
Way GP;Rudd J;Wang C;Hamidi H;Fridley BL;Konecny GE;Goode EL;Greene CS;Doherty JA
高级别浆液性卵巢癌（HGSC）的四种基因表达亚型先前已被描述。在这些早期研究中，排除了一部分不适合四种亚型分类的样本。因此，我们试图在不去除任何样本的情况下系统地确定人群中转录组HGSC亚型的一致性。我们创建了一个生物信息学管道，使用k-means和非负矩阵因子分解（NMF）独立地对五个最大的mRNA表达数据集进行聚类。我们总结了差异表达模式，以比较研究中的聚类。虽然以前的研究报告了四种亚型，但我们的跨人群比较不支持四种亚型。由于这些结果与以前的报告形成对比，我们试图重现这些研究中进行的分析。我们的研究结果表明，早期结果有利于四个亚型可能已被驱动列入浆液性交界性肿瘤。总之，我们的分析表明，两个或三个，而不是四个，基因表达亚型在数据集之间是最一致的。
Four gene expression subtypes of high-grade serous ovarian cancer (HGSC) have been previously described. In these early studies, a fraction of samples that did not fit well into the four subtype classifications were excluded. Therefore, we sought to systematically determine the concordance of transcriptomic HGSC subtypes across populations without removing any samples. We created a bioinformatics pipeline to independently cluster the five largest mRNA expression datasets using k-means and nonnegative matrix factorization (NMF). We summarized differential expression patterns to compare clusters across studies. While previous studies reported four subtypes, our cross-population comparison does not support four. Because these results contrast with previous reports, we attempted to reproduce analyses performed in those studies. Our results suggest that early results favoring four subtypes may have been driven by the inclusion of serous borderline tumors. In summary, our analysis suggests that either two or three, but not four, gene expression subtypes are most consistent across datasets.
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影响因子：
11.1
作者：
Tan, Tuan Zea;Miow, Qing Hao;Huang, Ruby Yun-Ju;Wong, Meng Kang;Ye, Jieru;Lau, Jieying Amelia;Wu, Meng Chu;Hadi, Luqman Hakim Bin Abdul;Soong, Richie;Choolani, Mahesh;Davidson, Ben;Nesland, Jahn M.;Wang, Ling-Zhi;Matsumura, Noriomi;Mandai, Masaki;Konishi, Ikuo;Goh, Boon-Cher;Chang, Jeffrey T.;Thiery, Jean Paul;Mori, Seiichi
通讯作者：
Mori, Seiichi
影响因子：
12.3
作者：
Celik S;Logsdon BA;Battle S;Drescher CW;Rendi M;Hawkins RD;Lee SI
通讯作者：
Lee SI
DOI：
10.1097/pas.0b013e3181cf3d79
发表时间：
2010-03
期刊：
The American journal of surgical pathology
影响因子：
--
作者：
Kurman RJ;Shih IeM
通讯作者：
Shih IeM
DOI：
10.1073/pnas.091062498
发表时间：
2001-04-24
影响因子：
11.1
作者：
Tusher, VG;Tibshirani, R;Chu, G
通讯作者：
Chu, G
影响因子：
10.3
作者：
Konecny, Gottfried E.;Wang, Chen;Goode, Ellen L.
通讯作者：
Goode, Ellen L.