乳腺癌预后基因集
主要是靠基因表达数据得到 prognostic gene signatures
In addition to cell of origin and somatic mutation events, studies over the past 10 years have demonstrated that genetic polymorphism can significantly affect gene expression.
using a genetically engineered mouse mammary tumor model we demonstrate that the PAM50 subtype signature of tumors driven by a common oncogenic event can be significantly influenced by the genetic background on which the tumor arises.
虽然 genefu 这个R包收集了非常多，但是毕竟是2012年发表的了。
Signature | Description | Validation | Training platform | Coverage (%) |
|---|---|---|---|---|
Intrinsic [1, 21] | Intrinsic subtype | Ref. [2, 3] | Stanford cDNA array | 410/549 (75%) |
PAM50 [9] | PAM50 subtype | Ref. [9] | Agilent Human oligo array | 42/50 (84%) |
70gene [4] | MammaPrint | Ref. [5, 22, 23, 24] | Agilent 25 k Human oligo array | 46/70 (65.7%) |
76gene [6] | Veridex | Ref. [25, 26] | Affymetrix u133a GeneChip | 76/76 (100%) |
Hypoxia [30] | Hypoxia signature | Ref. [15, 30] | Stanford cDNA array | 117/253 (46.2%)a |
WR [28] | Wound response | Ref. [15, 29] | Stanford cDNA array | 298/380 (78.4%) |
GGI [7] | Genomic Grade Index | Ref. [17, 27] | Affymetrix u133a GeneChip | 128/128 (100%) |
RS [12] | OncoType DX Recurrent Score | Ref. [12, 31] | qRT-PCR | 21/21 (100%) |
EP [32] | EndoPredict risk score | Ref. [32, 40] | qRT-PCR | 11/11 (100%) |
一篇2012年的评价文章；Systematic assessment of prognostic gene signatures for breast cancer shows distinct influence of time and ER status
而且即使有那么多的基因集，它们之间的重合情况很差，却都能在各自的数据集表现优异。
所以2017年的文章 Prognostic cancer gene signatures share common regulatory motifs 分析了这个现象。
一篇社评也提到了 Gene-Expression Signature in Breast Cancer—Where Did It Start and Where Are We Now? 那些基因集都有各自的局限性。
一篇综述：Multigene prognostic tests in breast cancer: past, present, future
这些观点同时也适用于其它癌症，所有的基因集都是基于自己特殊的数据集得到的，样本量也不够，研究的病人本身异质性很大，虽然都是同样的癌症，但是可能是不同的分类，不同的进展时期，病人有着不同的遗传背景。
T. Sorlie and R. Tibshirani and J. Parker and T. Hastie and J. S. Marron and A. Nobel and S. Deng and H. Johnsen and R. Pesich and S. Geister and J. Demeter and C. Perou and P. E. Lonning and P. O. Brown and A. L. Borresen-Dale and D. Botstein (2003) "Repeated Observation of Breast Tumor Subtypes in Independent Gene Expression Data Sets", Proceedings of the National Academy of Sciences, 1(14):8418–8423
Hu, Zhiyuan and Fan, Cheng and Oh, Daniel and Marron, JS and He, Xiaping and Qaqish, Bahjat and Livasy, Chad and Carey, Lisa and Reynolds, Evangeline and Dressler, Lynn and Nobel, Andrew and Parker, Joel and Ewend, Matthew and Sawyer, Lynda and Wu, Junyuan and Liu, Yudong and Nanda, Rita and Tretiakova, Maria and Orrico, Alejandra and Dreher, Donna and Palazzo, Juan and Perreard, Laurent and Nelson, Edward and Mone, Mary and Hansen, Heidi and Mullins, Michael and Quackenbush, John and Ellis, Matthew and Olopade, Olufunmilayo and Bernard, Philip and Perou, Charles (2006) "The molecular portraits of breast tumors are conserved across microarray platforms", BMC Genomics, 7(96)
Parker, Joel S. and Mullins, Michael and Cheang, Maggie C.U. and Leung, Samuel and Voduc, David and Vickery, Tammi and Davies, Sherri and Fauron, Christiane and He, Xiaping and Hu, Zhiyuan and Quackenbush, John F. and Stijleman, Inge J. and Palazzo, Juan and Marron, J.S. and Nobel, Andrew B. and Mardis, Elaine and Nielsen, Torsten O. and Ellis, Matthew J. and Perou, Charles M. and Bernard, Philip S. (2009) "Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes", Journal of Clinical Oncology, 27(8):1160–1167
Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, and Sotiriou C (2008) "Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes", Clinical Cancer Research, 14(16):5158–5165.
Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, Haibe-Kains B, Desmedt C, Ignatiadis M, Sengstag T, Schutz F, Goldstein DR, Piccart MJ and Delorenzi M (2008) "Meta-analysis of Gene-Expression Profiles in Breast Cancer: Toward a Unified Understanding of Breast Cancer Sub-typing and Prognosis Signatures", Breast Cancer Research, 10(4):R65.
Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C. (2012) "A three-gene model to robustly identify breast cancer molecular subtypes.", J Natl Cancer Inst., 104(4):311–325.
Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Graf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group, Langerod A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Borresen-Dale AL, Brenton JD, Tavare S, Caldas C, Aparicio S. (2012) "The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.", Nature, 486(7403):346–352.
Paquet ER, Hallett MT. (2015) "Absolute assignment of breast cancer intrinsic molecular subtype.", J Natl Cancer Inst., 107(1):357.
Aleix Prat, Joel S Parker, Olga Karginova, Cheng Fan, Chad Livasy, Jason I Herschkowitz, Xiaping He, and Charles M. Perou (2010) "Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer", Breast Cancer Research, 12(5):R68