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Gene signature

About: Gene signature is a(n) research topic. Over the lifetime, 2957 publication(s) have been published within this topic receiving 103471 citation(s). The topic is also known as: gene expression signature & gene signatures. more


Open accessJournal ArticleDOI: 10.1073/PNAS.0506580102
Abstract: Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets. more

26,320 Citations

Open accessJournal ArticleDOI: 10.1093/JNCI/DJJ329
Marc Buyse, Sherene Loi1, Laura J. van't Veer, Giuseppe Viale  +16 moreInstitutions (9)
Abstract: Background: A 70-gene signature was previously shown to have prognostic value in patients with node-negative breast cancer. Our goal was to validate the signature in an independent group of patients. Methods: Patients (n = 307, with 137 events after a median follow-up of 13.6 years) from fi ve European centers were divided into high- and low-risk groups based on the gene signature classifi cation and on clinical risk classifi cations. Patients were assigned to the gene signature low-risk group if their 5-year distant metastasis – free survival probability as estimated by the gene signature was greater than 90%. Patients were assigned to the clinicopathologic low-risk group if their 10-year survival probability, as estimated by Adjuvant! software, was greater than 88% (for estrogen receptor [ER] – positive patients) or 92% (for ERnegative patients). Hazard ratios (HRs) were estimated to compare time to distant metastases, disease-free survival, and overall survival in high- versus low-risk groups. Results: The 70-gene signature outperformed the clinicopathologic risk assessment in predicting all endpoints. For time to distant metastases, the gene signature yielded HR = 2.32 (95% confi dence interval [CI] = 1.35 to 4.00) without adjustment for clinical risk and hazard ratios ranging from 2.13 to 2.15 after adjustment for various estimates of clinical risk; clinicopathologic risk using Adjuvant! software yielded an unadjusted HR = 1.68 (95% CI = 0.92 to 3.07). For overall survival, the gene signature yielded an unadjusted HR = 2.79 (95% CI = 1.60 to 4.87) and adjusted hazard ratios ranging from 2.63 to 2.89; clinicopathologic risk yielded an unadjusted HR = 1.67 (95% CI = 0.93 to 2.98). For patients in the gene signature high-risk group, 10-year overall survival was 0.69 for patients in both the low – and high – clinical risk groups; for patients in the gene signature low-risk group, the 10-year survival rates were 0.88 and 0.89, respectively. Conclusions: The 70-gene signature adds independent prognostic information to clinicopathologic risk assessment for patients with early breast cancer. [J Natl Cancer Inst 2006;98: 1183 – 92 ] more

Topics: Gene signature (61%), Hazard ratio (53%), Survival analysis (51%) more

1,146 Citations

Open accessJournal ArticleDOI: 10.1016/J.CCR.2009.12.041
Neta Erez1, Morgan L. Truitt1, Peter Olson1, Sarah T. Arron1  +1 moreInstitutions (1)
17 Feb 2010-Cancer Cell
Abstract: Cancer-associated fibroblasts (CAFs) support tumorigenesis by stimulating angiogenesis, cancer cell proliferation, and invasion. We demonstrate that CAFs also mediate tumor-enhancing inflammation. Using a mouse model of squamous skin carcinogenesis, we found a proinflammatory gene signature in CAFs isolated from dysplastic skin. This signature was maintained in CAFs from subsequent skin carcinomas and was evident in mammary and pancreatic tumors in mice and in cognate human cancers. The inflammatory signature was already activated in CAFs isolated from the initial hyperplastic stage in multistep skin tumorigenesis. CAFs from this pathway promoted macrophage recruitment, neovascularization, and tumor growth, activities that are abolished when NF-kappaB signaling was inhibited. Additionally, we show that normal dermal fibroblasts can be "educated" by carcinoma cells to express proinflammatory genes. more

Topics: Cancer-Associated Fibroblasts (55%), Proinflammatory cytokine (54%), Carcinogenesis (51%) more

1,113 Citations

Journal ArticleDOI: 10.1056/NEJMOA063994
Rui Liu1, Xinhao Wang2, Grace Y. Chen, Piero Dalerba1  +8 moreInstitutions (3)
Abstract: BACKGROUND Breast cancers contain a minority population of cancer cells characterized by CD44 expression but low or undetectable levels of CD24 (CD44+CD24-/low) that have higher tumorigenic capacity than other subtypes of cancer cells. METHODS We compared the gene-expression profile of CD44+CD24-/low tumorigenic breast-cancer cells with that of normal breast epithelium. Differentially expressed genes were used to generate a 186-gene "invasiveness" gene signature (IGS), which was evaluated for its association with overall survival and metastasis-free survival in patients with breast cancer or other types of cancer. RESULTS There was a significant association between the IGS and both overall and metastasis-free survival (P<0.001, for both) in patients with breast cancer, which was independent of established clinical and pathological variables. When combined with the prognostic criteria of the National Institutes of Health, the IGS was used to stratify patients with high-risk early breast cancer into prognostic categories (good or poor); among patients with a good prognosis, the 10-year rate of metastasis-free survival was 81%, and among those with a poor prognosis, it was 57%. The IGS was also associated with the prognosis in medulloblastoma (P=0.004), lung cancer (P=0.03), and prostate cancer (P=0.01). The prognostic power of the IGS was increased when combined with the wound-response (WR) signature. CONCLUSIONS The IGS is strongly associated with metastasis-free survival and overall survival for four different types of tumors. This genetic signature of tumorigenic breast-cancer cells was even more strongly associated with clinical outcomes when combined with the WR signature in breast cancer. more

Topics: CA15-3 (62%), Cancer (62%), Breast cancer (62%) more

990 Citations

Open accessJournal ArticleDOI: 10.1056/NEJMOA1602253
Fatima Cardoso1, Laura J. van't Veer2, Jan Bogaerts3, Leen Slaets3  +30 moreInstitutions (16)
Abstract: BackgroundThe 70-gene signature test (MammaPrint) has been shown to improve prediction of clinical outcome in women with early-stage breast cancer. We sought to provide prospective evidence of the clinical utility of the addition of the 70-gene signature to standard clinical–pathological criteria in selecting patients for adjuvant chemotherapy. MethodsIn this randomized, phase 3 study, we enrolled 6693 women with early-stage breast cancer and determined their genomic risk (using the 70-gene signature) and their clinical risk (using a modified version of Adjuvant! Online). Women at low clinical and genomic risk did not receive chemotherapy, whereas those at high clinical and genomic risk did receive such therapy. In patients with discordant risk results, either the genomic risk or the clinical risk was used to determine the use of chemotherapy. The primary goal was to assess whether, among patients with high-risk clinical features and a low-risk gene-expression profile who did not receive chemotherapy, the... more

  • Table 1. Characteristics of the Patients and Tumors at Baseline, According to Risk Group.*
    Table 1. Characteristics of the Patients and Tumors at Baseline, According to Risk Group.*
  • Table 1. Characteristics of the Patients and Tumors at Baseline, According to Risk Group.*
    Table 1. Characteristics of the Patients and Tumors at Baseline, According to Risk Group.*
  • Table 2. Outcome According to Discordant Risk Group and Treatment Strategy (Per-Protocol Population).*
    Table 2. Outcome According to Discordant Risk Group and Treatment Strategy (Per-Protocol Population).*
Topics: MammaPrint (60%), Breast cancer (57%), Gene signature (54%) more

977 Citations

No. of papers in the topic in previous years

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Topic's top 5 most impactful authors

Lajos Pusztai

8 papers, 436 citations

Shu-Dong Zhang

7 papers, 142 citations

Yujin Hoshida

4 papers, 398 citations

Josep M. Llovet

4 papers, 519 citations

Naoto T. Ueno

4 papers, 46 citations

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