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Background: Due to experimental batch effects, the application of a quantitative transcriptional signature for disease diagnoses commonly requires inter-sample data normalization, which would be hardly applicable under common clinical settings. Many cancers might have qualitative differences with the non-cancer states in the gene expression pattern. Therefore, it is reasonable to explore the power of qualitative diagnostic signatures which are robust against experimental batch effects and other random factors. Results: Firstly, using data of technical replicate samples from the MicroArray Quality Control (MAQC) project, we demonstrated that the low-throughput PCR-based technologies also exist large measurement variations for gene expression even when the samples were measured in the same test site. Then, we demonstrated the critical limitation of low stability for classifiers based on quantitative transcriptional signatures in applications to individual samples through a case study using a support vector machine and a naïve Bayesian classifier to discriminate colorectal cancer tissues from normal tissues. To address this problem, we identified a signature consisting of three gene pairs for discriminating colorectal cancer tissues from non-cancer (normal and inflammatory bowel disease) tissues based on within-sample relative expression orderings (REOs) of these gene pairs. The signature was well verified using 22 independent datasets measured by different microarray and RNA_seq platforms, obviating the need of inter-sample data normalization. Conclusions: Subtle quantitative information of gene expression measurements tends to be unstable under current technical conditions, which will introduce uncertainty to clinical applications of the quantitative transcriptional diagnostic signatures. For diagnosis of disease states with qualitative transcriptional characteristics, the qualitative REO-based signatures could be robustly applied to individual samples measured by different platforms. [ABSTRACT FROM AUTHOR]

Background: Wingspan stenting for the treatment of complex intracranial atherosclerotic stenosis (ICAS), i.e., that involving tortuous vascular pathways, long (>15 mm) lesions or arterial bifurcations, has a relatively high risk of complications. This retrospective study assessed the safety and efficacy of undersized balloon angioplasty followed by deployment of the more flexible Enterprise stent for the treatment of complex symptomatic ICAS.Methods: Forty-four patients on combined antiplatelet therapy and intensive risk factor management and a symptomatic 70-99% stenosis of a major intracranial artery in complex settings that was treated with balloon angioplasty and Enterprise stent deployment between July 2009 and August 2013 were enrolled. Primary outcome was occurrence of ischemic or hemorrhagic stroke or death within 30 days after intervention. Secondary outcomes included procedural success (defined as achievement of <50% immediate residual stenosis), and follow-up clinical and angiographic outcomes.Results: With a procedural success rate of 100%, stenosis was reduced from 79.3 ± 8.1-14.9 ± 2.3%. Three (6.8%) ischemic and 1 (2.2%) hemorrhagic strokes occurred during the periprocedural period, with no further transient ischemic attacks or strokes in the 42 patients available at median 25.6 (range, 12-57) months follow-up. Of the 38 (86.4%) patients who underwent angiographic follow-up, 3 (6.81%) developed >50% in-stent restenosis after mean 22 months follow-up.Conclusion: In this retrospective, single-center experience, undersized balloon angioplasty followed by Enterprise stent deployment appears technically feasible with a relatively low rate of complications for the treatment of complex symptomatic ICAS. Prospective, multicenter, randomized controlled trials against optimal medical management are warranted. [ABSTRACT FROM AUTHOR]

Background: Deregulations of long non-coding RNAs (lncRNAs) have been implicated in cancer initiation and progression. Current methods can only capture differential expression of lncRNAs at the population level and ignore the heterogeneous expression of lncRNAs in individual patients., Methods: We propose a method (LncRIndiv) to identify differentially expressed (DE) lncRNAs in individual cancer patients by exploiting the disrupted ordering of expression levels of lncRNAs in each disease sample in comparison with stable normal ordering. LncRIndiv was applied to lncRNA expression profiles of lung adenocarcinoma (LUAD). Based on the expression profile of LUAD individual-level DE lncRNAs, we used a forward selection procedure to identify prognostic signature for stage I-II LUAD patients without adjuvant therapy., Results: In both simulated data and real pair-wise cancer and normal sample data, LncRIndiv method showed good performance. Based on the individual-level DE lncRNAs, we developed a robust prognostic signature consisting of two lncRNA (C1orf132 and TMPO-AS1) for stage I-II LUAD patients without adjuvant therapy (P = 3.06 × 10 -6 , log-rank test), which was confirmed in two independent datasets of GSE50081 (P = 1.82 × 10 -2 , log-rank test) and GSE31210 (P = 7.43 × 10 -4 , log-rank test) after adjusting other clinical factors such as smoking status and stages. Pathway analysis showed that TMPO-AS1 and C1orf132 could affect the prognosis of LUAD patients through regulating cell cycle and cell adhesion., Conclusions: LncRIndiv can successfully detect DE lncRNAs in individuals and be applied to identify prognostic signature for LUAD patients.

Background: Wingspan stenting for the treatment of complex intracranial atherosclerotic stenosis (ICAS), i.e., that involving tortuous vascular pathways, long (>15 mm) lesions or arterial bifurcations, has a relatively high risk of complications. This retrospective study assessed the safety and efficacy of undersized balloon angioplasty followed by deployment of the more flexible Enterprise stent for the treatment of complex symptomatic ICAS., Methods: Forty-four patients on combined antiplatelet therapy and intensive risk factor management and a symptomatic 70-99% stenosis of a major intracranial artery in complex settings that was treated with balloon angioplasty and Enterprise stent deployment between July 2009 and August 2013 were enrolled. Primary outcome was occurrence of ischemic or hemorrhagic stroke or death within 30 days after intervention. Secondary outcomes included procedural success (defined as achievement of <50% immediate residual stenosis), and follow-up clinical and angiographic outcomes., Results: With a procedural success rate of 100%, stenosis was reduced from 79.3 ± 8.1-14.9 ± 2.3%. Three (6.8%) ischemic and 1 (2.2%) hemorrhagic strokes occurred during the periprocedural period, with no further transient ischemic attacks or strokes in the 42 patients available at median 25.6 (range, 12-57) months follow-up. Of the 38 (86.4%) patients who underwent angiographic follow-up, 3 (6.81%) developed >50% in-stent restenosis after mean 22 months follow-up., Conclusion: In this retrospective, single-center experience, undersized balloon angioplasty followed by Enterprise stent deployment appears technically feasible with a relatively low rate of complications for the treatment of complex symptomatic ICAS. Prospective, multicenter, randomized controlled trials against optimal medical management are warranted.

Background: Hundreds of genes that are causally implicated in oncogenesis have been found and collected in various databases. For efficient application of these abundant but diverse data sources, it is of fundamental importance to evaluate their consistency., Results: First, we showed that the lists of cancer genes from some major data sources were highly inconsistent in terms of overlapping genes. In particular, most cancer genes accumulated in previous small-scale studies could not be rediscovered in current high-throughput genome screening studies. Then, based on a metric proposed in this study, we showed that most cancer gene lists from different data sources were highly functionally consistent. Finally, we extracted functionally consistent cancer genes from various data sources and collected them in our database F-Census., Conclusions: Although they have very low gene overlapping, most cancer gene data sources are highly consistent at the functional level, which indicates that they can separately capture partial genes in a few key pathways associated with cancer. Our results suggest that the sample sizes currently used for cancer studies might be inadequate for consistently capturing individual cancer genes, but could be sufficient for finding a number of cancer genes that could represent functionally most cancer genes. The F-Census database provides biologists with a useful tool for browsing and extracting functionally consistent cancer genes from various data sources.