Cancer Target Gene Screening: a web application for breast cancer target gene screening using multi-omics data analysis.

Breast cancer comprises several molecular subtypes with distinct clinical features and treatment responses, and a substantial portion of each subtype remains incurable. A comprehensive analysis of multi-omics data and clinical profiles is required in order to better understand the biological complexity of this cancer type and to identify new prognostic and therapeutic markers. Thus, there arises a need for useful analytical tools to assist in the investigation and clinical management of the disease. We developed Cancer Target Gene Screening (CTGS), a web application that provides rapid and user-friendly analysis of multi-omics data sets from a large number of primary breast tumors. It allows the investigation of genomic and epigenomic aberrations, evaluation of transcriptomic profiles and performance of survival analyses and of bivariate correlations between layers of omics data. Notably, the genome-wide screening function of CTGS prioritizes candidate genes of clinical and biological significance among genes with copy number alteration, DNA methylation and dysregulated expression by the integrative analysis of different types of omics data in customized subgroups of breast cancer patients. These features may help in the identification of druggable cancer driver genes in a specific subtype or the clinical condition of human breast cancer. CTGS is available at http://ctgs.biohackers.net.

Metabolite and Transcriptome Profiles of Proanthocyanidin Biosynthesis in the Development of Litchi Fruit.

The fruit of Litchi chinensis contains high levels of proanthocyanidins (PAs) in the pericarp. These substances can serve as substrates of laccase-mediated rapid pericarp browning after the fruit is harvested. In this study, we found that the major PAs in litchi pericarp were (-)-epicatechin (EC) and several procyanidins (PCs), primarily PC A2, B2, and B1, and the EC and the PC content decreased with the development of the fruit. RNA-seq analysis showed that 43 early and late structure genes related to flavonoid/PA biosynthesis were expressed in the pericarp, including five ANTHOCYANIDIN REDUCTASE (ANR), two LEUCOANTHOCYANIDIN REDUCTASE (LAR), and two ANTHOCYANIDIN SYNTHASE (ANS) genes functioning in the PA biosynthesis branch of the flavonoid pathway. Among these nine PA biosynthesis-related genes, ANR1a, LAR1/2, and ANS1 were highly positively correlated with changes in the EC/PC content, suggesting that they are the key PA biosynthesis-related genes. Several transcription factor (TF) genes, including MYB, bHLH, WRKY, and AP2 family members, were found to be highly correlated with ANR1a, LAR1/2, and ANS1, and their relevant binding elements were detected in the promoters of these target genes, strongly suggesting that these TF genes may play regulatory roles in PA biosynthesis. In summary, this study identified the candidate key structure and regulatory genes in PA biosynthesis in litchi pericarp, which will assist in understanding the accumulation of high levels of browning-related PA substances in the pericarp.

Screening of frequent variants associated with congenital hypothyroidism: a comparison with next generation sequencing.

Congenital hypothyroidism (CH) is considered the most common congenital endocrine disorder of genetic origin. Next generation sequencing (NGS) is the standard method for identifying genetic mutations, but it is an expensive and complex technique. Therefore, we propose to use Sanger sequencing to identify selected variants of the four most common CH-causative genes: DUOX2, TG, TSHR, and PAX8. To analyze the performance of Sanger sequencing, we compared its variant detection ability with that of a CH NGS panel containing 53 genes. We performed Sanger sequencing of selected variants and panel NGS analysis of 25 Japanese patients with CH. Sanger sequencing identified nine variants in seven patients, while NGS identified 24 variants in 14 patients. Of these, eight, five, eight, two, and one were found to be potentially pathogenic in DUOX2, TSHR, TG, UBR1, and TPO genes, respectively. The percentage of detectable variants using Sanger sequencing compared with NGS was 37.5% (9/24 variants), whereas the percentage of detectable cases carrying variants using Sanger sequencing compared with NGS was 50% (7/14 patients). We proposed a system for screening commonly identified CH-related variants by Sanger sequencing. Sanger sequencing could therefore identify about a third of CH-causative variants, so is considered an effective and efficient form of pre-screening before NGS.

Two New Unspecific Peroxygenases from Heterologous Expression of Fungal Genes in Escherichia coli.

Unspecific peroxygenases (UPOs) constitute a new family of fungal heme-thiolate enzymes in which there is high biotechnological interest. Although several thousand genes encoding hypothetical UPO-type proteins have been identified in sequenced fungal genomes and other databases, only a few UPO enzymes have been experimentally characterized to date. Therefore, gene screening and heterologous expression from genetic databases are a priority in the search for ad hoc UPOs for oxyfunctionalization reactions of interest. Very recently, Escherichia coli production of a previously described basidiomycete UPO (as a soluble and active enzyme) has been reported. Here, we explored this convenient heterologous expression system to obtain the protein products from available putative UPO genes. In this way, two UPOs from the ascomycetes Collariella virescens (syn., Chaetomium virescens) and Daldinia caldariorum were successfully obtained, purified, and characterized. Comparison of their kinetic constants for oxidation of model substrates revealed 10- to 20-fold-higher catalytic efficiency of the latter enzyme in oxidizing simple aromatic compounds (such as veratryl alcohol, naphthalene, and benzyl alcohol). Homology molecular models of these enzymes showed three conserved and two differing residues in the distal side of the heme (the latter representing two different positions of a phenylalanine residue). Interestingly, replacement of the C. virescens UPO Phe88 by the homologous residue in the D. caldariorum UPO resulted in an F88L variant with 5- to 21-fold-higher efficiency in oxidizing these aromatic compounds.IMPORTANCE UPOs catalyze regio- and stereoselective oxygenations of both aromatic and aliphatic compounds. Similar reactions were previously described for cytochrome P450 monooxygenases, but UPOs have the noteworthy biotechnological advantage of being stable enzymes requiring only H2O2 to be activated. Both characteristics are related to the extracellular nature of UPOs as secreted proteins. In the present study, the limited repertoire of UPO enzymes available for organic synthesis and other applications is expanded with the description of two new ascomycete UPOs obtained by Escherichia coli expression of the corresponding genes as soluble and active enzymes. Moreover, directed mutagenesis in E. coli, together with enzyme molecular modeling, provided relevant structure-function information on aromatic substrate oxidation by these two new biocatalysts.

Case report: Analysis of BRCA1 and BRCA2 gene mutations in a hereditary ovarian cancer family.

OBJECTIVE: Breast cancer susceptibility gene 1/2 (BRCA1/2) is the most important susceptibility gene associated with hereditary ovarian cancer (HOC). We aimed to screen BRAC1 and BRAC2 gene mutations in a member of a hereditary ovarian cancer family in China, and to analyze the structure and function of the mutant protein. METHODS: A typical HOC family was selected. Blood samples and pathological tissue samples were taken from the female members of the family. Blood samples from two patients with sporadic ovaries of the same pathological type were taken as a control group. After RNA extraction, PCR amplification was applied and the PCR products were directly sequenced and aligned, prediction and analysis of protein structure and molecular conformation that may be caused by BRCA1/2 mutation. RESULTS: The whole gene analysis of BRCA1 and BRCA2 in ovarian cancer patients in the family showed that there were 8 mutations in BRCA1 whole gene sequencing, including 3 nonsense mutations (2314C>T, 2543T>C, 4540T>C); two mutations have been recorded, which are associated with cervical cancer (2844C>T) and endometriosis (3345A>G); three newly discovered mutations (3780A>G, 5069A>G, 3326A>T). Among them, 3780A>G and 5069A>G caused amino acid changes, while 3326A>T mutation caused Arg mutation to stop codon. A total of 7 mutations were detected in BRCA2 whole-genome sequencing, including 5 non-significant mutations (3623A>G, 4034T>C, 4790A>G, 6740G>C, 7469A>G); one no-record mutation (1716T>A), and 1 recorded mutation (1342A>C), which was associated with breast cancer and ovarian cancer. BRCA1 (3326A>T) and BRCA2 (1342A>C) mutations were co-existing in patients (II1, II3, and II5) identified as serous adenocarcinoma grade II. Two cases of ovarian serous cystadenocarcinoma with no history of family tumors were normalized for BRCA1/2 gene sequencing. In the gene detection of III generation female, four females with BRCA2 (1342A>C) mutation were found, and one of them also carried the BRCA1 (3326A>T) mutation, who can be considered a high-risk group of HOC in this family. Online protein structure predictions revealed that BRCA1 (3326A>T) mutations mutated AGA at this site to TGA resulting in a translated Arg (arginine) mutation as a stop codon, while BRCA2 (1342A>C) mutated AAT at this site to CAT resulting in a translated Asn mutation to His. CONCLUSION: The BRCA1 (3326A>T) and BRCA2 (1342A>C) were detected in the HOC family, which may be the susceptibility gene of the family's HOC. The BRCA1/2 gene screening may be possible to obtain high-risk populations in this family.

[Overview of research in ginsenosides glycosyltransferase].

Glycosyltransferases(UGTs) are key enzymes in the biosynthesis of ginsenosides, which can catalyze the transfer of glycans from donor molecules to acceptor molecules, and form a variety of biologically active glycoside compounds. With the development of high-throughput sequencing technology, a large number of medicinal plant genome and transcriptome sequences have been catalyzed, while more and more UGT genes have been discovered and verified. The methods of discovering UGT genes include differential expression analysis, homologous sequence screening, gene cluster screening, chemical proteome screening. This paper summarized the research progress of UGT genes screening and functional verification of three valuable Panax medicinal materials P. notoginseng, P. ginseng, and P. quinquefolius, so as to provide a reference for the study of UGT genes in natural products.

De novo transcriptome sequencing and differential gene expression analysis of two parasitic human Demodex species.

Demodex are among the tiniest organisms in Acari and are important mammalian parasites. However, differences in pathogenicity between two human parasites, Demodex folliculorum and Demodex brevis, remain unknown. Related genetic studies are limited by RNA extraction difficulties and molecular data deficiencies. In this study, RNA extraction, de novo sequencing, functional annotation, and differential gene expression analyses were performed to compare D. folliculorum and D. brevis. This yielded 67.09 and 65.10 million clean reads, respectively, with similar annotations. Bioinformatics analyses and manual alignments identified 237 coding sequences comprising 48 genes from 29 families, including five important functional classes. Of these, 30 genes from 20 families related to metabolism, motion, detoxification and stress response, and allergic reaction were differentially expressed between the two species. Cathepsin type 1, serine protease inhibitor, arginine kinase, triosephosphate isomerase, muscle-specific protein 20-2, myosin alkaline light chain, troponin C, tropomyosin, and heat shock protein 90 were highly expressed in D. folliculorum, whereas cathepsin type 2, aspartic protease, serine protease, myosin heavy chain type 2, and alpha tubulin type 1C were highly expressed in D. brevis. Verified coding sequences were nearly consistent with unigene clusters. Further, absolute quantification results demonstrated that differentially expressed genes followed the predicted expression trend. Therefore, the first RNA sequencing and functional annotation analysis of two Demodex species was successful. Differential expression of important functional genes is likely implicated in pathogenicity disparities between these two species. Our study provides molecular data and technical support for further studies on human Demodex pathogenicity and functional genes.

Multi-subgroup gene screening using semi-parametric hierarchical mixture models and the optimal discovery procedure: Application to a randomized clinical trial in multiple myeloma.

This article proposes an efficient approach to screening genes associated with a phenotypic variable of interest in genomic studies with subgroups. In order to capture and detect various association profiles across subgroups, we flexibly estimate the underlying effect size distribution across subgroups using a semi-parametric hierarchical mixture model for subgroup-specific summary statistics from independent subgroups. We then perform gene ranking and selection using an optimal discovery procedure based on the fitted model with control of false discovery rate. Efficiency of the proposed approach, compared with that based on standard regression models with covariates representing subgroups, is demonstrated through application to a randomized clinical trial with microarray gene expression data in multiple myeloma, and through a simulation experiment.

[Screening of the SETX gene in sporadic amyotrophic lateral sclerosis patients of Chinese origin].

Objective: To investigate all coding regions of amyotrophic lateral sclerosis (ALS)-related gene Senataxin (SETX) in sporadic amyotrophic lateral sclerosis patients of Chinese origin. Methods: From January 2010 to December 2014, the peripheral venous blood samples and clinical data were collected from 311 patients with sporadic amyotrophic lateral sclerosis (SALS) and 311 healthy controls who were of Chinese ancestry from the Department of Neurology, Chinese PLA General Hospital.Genomic DNA was extracted from peripheral venous blood of all participants using standard methods. The coding regions of SETX were amplified by polymerase chain reaction (PCR) and screened for mutations using next-generation sequencing technology. The online software SIFT and PolyPhen-2 were used to analyze the conservation of an altered amino acid and predict the potential pathogenicity of identified mutations. The SPSS 22.0 software was used to analyze the clinical feature of all participants. Results: Tenkinds of rare and one novel nonsynonymous mutations were identified and were absent in 311 controls. Twelve (3.86%) patients carried one SETX gene mutation. Five (1.61%) out of above-mentioned 12 patients carried highly pathogenic mutations including p. Pro1868Leu (c.5603G>A), p. Pro1331Leu (c.3992G>A), p. Glu756Val (c.2267T>A), p. Leu564Val (c.1690A>C), and p. Asn144Ser (c.431T>C). Patients carried SETX mutations were not different from other patients in onset age. Conclusion: Mutations in SETX are likely to be a pathogenesis for Chinese sporadic amyotrophic lateral sclerosis.

Identification and functional analysis of a new glyphosate resistance gene from a fungus cDNA library.

Glyphosate is a widely used broad spectrum herbicide; however, this limits its use once crops are planted. If glyphosate-resistant crops are grown, glyphosate can be used for weed control in crops. While several glyphosate resistance genes are used in commercial glyphosate tolerant crops, there is interest in identifying additional genes for glyphosate tolerance. This research constructed a high-quality cDNA library form the glyphosate-resistant fungus Aspergillus oryzae RIB40 to identify genes that may confer resistance to glyphosate. Using a medium containing glyphosate (120mM), we screened several clones from the library. Based on a nucleotide sequence analysis, we identified a gene of unknown function (GenBank accession number: XM_001826835.2) that encoded a hypothetical 344-amino acid protein. The gene was named MFS40. Its ORF was amplified to construct an expression vector, pGEX-4T-1-MFS40, to express the protein in Escherichia coli BL21. The gene conferred glyphosate tolerance to E. coli ER2799 cells.

Next Generation Sequencing Data Analysis in Primary Immunodeficiency Disorders - Future Directions.

Primary immunodeficiency diseases (PIDs) comprise a group of highly heterogeneous immune system diseases and around 300 forms of PID have been described to date. Next Generation Sequencing (NGS) has recently become an increasingly used approach for gene identification and molecular diagnosis of human diseases. Herein we summarize the practical considerations for the interpretation of NGS data and the techniques for searching disease-related PID genes, and suggest future directions for research in this field.

Mutation spectrum in BBS genes guided by homozygosity mapping in an Indian cohort.

Bardet-Biedl syndrome (BBS), a ciliopathy disorder with pleiotropic effect manifests primarily as retinal degeneration along with renal insufficiency, polydactyly and obesity. In this study, we have performed homozygosity mapping using NspI 250K affymetrix gene chip followed by mutation screening of the candidate genes located in the homozygous blocks. These regions are prioritized based on the block length and candidature of the genes in BBS and other ciliopathies. Gene alterations in known BBS (22) and other ciliopathy genes such as ALMS1 (2) were seen in 24 of 30 families (80%). Mutations in BBS3 gene, inclusive of a novel recurrent mutation (p.I91T) accounted for 18% of the identified variations. Disease associated polymorphisms p.S70N (BBS2), rs1545 and rs1547 (BBS6) were also observed. This is the first study in Indian BBS patients and homozygosity mapping has proved to be an effective tool in prioritizing the candidate genes in consanguineous pedigrees. The study reveals a different mutation profile in the ciliopathy genes in Indian population and implication of novel loci/genes in 20% of the study group.

Genetic variation analysis of Guanling cattle based on whole-genome resequencing.

Objective: The objective of this study was to unravel the genetic traits of Guanling cattle, pinpoint genes advantageous for muscle growth, and lay a foundation for the preservation of genetic diversity and further analysis of regulation mechanism of important economic traits in local cattle breed. Methods: In this study, we sequenced the whole genome of 3 Guanling cattle in Guizhou province using the Illumina HiSeq cBo sequencing platform. And, high- multiplex PCR technology was employed to detect high-quality SNP sites of other 55 Guanling cattle. Results: Our study identified 166,411 non-synonymous SNPs (nsSNPs) and 42,423 insertions and deletions (indels). Through SNP annotation, gene function enrichment analysis, and comparing with Simmental, Angus, and Limousin cattle, we identified six genes (LEPR, AKAP9, SIX4, SPIDR, PRG4, FASN) which are potentially influential on meat quality traits, playing crucial roles in muscle growth, fat metabolism, and bodily support. We also examined polymorphisms at seven SNP sites in Guanling cattle and found that all seven were in Hardy-Weinberg equilibrium. Conclusion: These findings suggested that these gene sites are stable and widespread in the Guanling cattle population. Our research lays the groundwork for future genetic enhancement and variety identification of Guanling cattle.

A Gene Selection Method Considering Measurement Errors.

The analysis of gene expression data has made significant contributions to understanding disease mechanisms and developing new drugs and therapies. In such analysis, gene selection is often required for identifying informative and relevant genes and removing redundant and irrelevant ones. However, this is not an easy task as gene expression data have inherent challenges such as ultra-high dimensionality, biological noise, and measurement errors. This study focuses on the measurement errors in gene selection problems. Typically, high-throughput experiments have their own intrinsic measurement errors, which can result in an increase of falsely discovered genes. To alleviate this problem, this study proposes a gene selection method that takes into account measurement errors using generalized liner measurement error models. The method consists of iterative filtering and selection steps until convergence, leading to fewer false positives and providing stable results under measurement errors. The performance of the proposed method is demonstrated through simulation studies and applied to a lung cancer data set.

Screening for metastasis-related genes in mouse melanoma cells through sequential tail vein injection.

Tumor metastasis, responsible for approximately 90% of cancer-associated mortality, remains poorly understood. Here in this study, we employed a melanoma lung metastasis model to screen for metastasis-related genes. By sequential tail vein injection of mouse melanoma B16F10 cells and the subsequently derived cells from lung metastasis into BALB/c mice, we successfully obtained highly metastatic B16F15 cells after five rounds of in vivo screening. RNA-sequencing analysis of B16F15 and B16F10 cells revealed a number of differentially expressed genes, some of these genes have previously been associated with tumor metastasis while others are novel discoveries. The identification of these metastasis-related genes not only improves our understanding of the metastasis mechanisms, but also provides potential diagnostic biomarkers and therapeutic targets for metastatic melanoma.

Prioritization of risk genes in colorectal cancer by integrative analysis of multi-omics data and gene networks.

Genome-wide association studies (GWASs) have identified over 140 colorectal cancer (CRC)-associated loci; however, target genes at the majority of loci and underlying molecular mechanisms are poorly understood. Here, we utilized a Bayesian approach, integrative risk gene selector (iRIGS), to prioritize risk genes at CRC GWAS loci by integrating multi-omics data. As a result, a total of 105 high-confidence risk genes (HRGs) were identified, which exhibited strong gene dependencies for CRC and enrichment in the biological processes implicated in CRC. Among the 105 HRGs, CEBPB, located at the 20q13.13 locus, acted as a transcription factor playing critical roles in cancer. Our subsequent assays indicated the tumor promoter function of CEBPB that facilitated CRC cell proliferation by regulating multiple oncogenic pathways such as MAPK, PI3K-Akt, and Ras signaling. Next, by integrating a fine-mapping analysis and three independent case-control studies in Chinese populations consisting of 8,039 cases and 12,775 controls, we elucidated that rs1810503, a putative functional variant regulating CEBPB, was associated with CRC risk (OR=0.90, 95%CI=0.86-0.93, P=1.07×10-7). The association between rs1810503 and CRC risk was further validated in three additional multi-ancestry populations consisting of 24,254 cases and 58,741 controls. Mechanistically, the rs1810503 A to T allele change weakened the enhancer activity in an allele-specific manner to decrease CEBPB expression via long-range promoter-enhancer interactions, mediated by the transcription factor, REST, and thus decreased CRC risk. In summary, our study provides a genetic resource and a generalizable strategy for CRC etiology investigation, and highlights the biological implications of CEBPB in CRC tumorigenesis, shedding new light on the etiology of CRC.

Ambient temperature regulates root circumnutation in rice through the ethylene pathway: transcriptome analysis reveals key genes involved.

Plant roots are constantly prepared to adjust their growth trajectories to avoid unfavorable environments, and their ability to reorient is particularly crucial for survival. Under laboratory conditions, this continuous reorientation of the root tip is manifested as coiling or waving, which we refer to as root circumnutation. However, the effect of ambient temperature (AT) on root circumnutation remains unexplored. In this study, rice seedlings were employed to assess the impact of varying ATs on root circumnutation. The role of ethylene in mediating root circumnutation under elevated AT was examined using the ethylene biosynthesis inhibitor aminooxyacetic acid (AOA) and the ethylene perception antagonist silver thiosulfate (STS). Furthermore, transcriptome sequencing, weighted gene co-expression network analysis, and real-time quantitative PCR were utilized to analyze gene expressions in rice root tips under four distinct treatments: 25°C, 35°C, 35°C+STS, and 35°C+AOA. As a result, genes associated with ethylene synthesis and signaling (OsACOs and OsERFs), auxin synthesis and transport (OsYUCCA6, OsABCB15, and OsNPFs), cell elongation (OsEXPAs, OsXTHs, OsEGL1, and OsEXORDIUMs), as well as the inhibition of root curling (OsRMC) were identified. Notably, the expression levels of these genes increased with rising temperatures above 25°C. This study is the first to demonstrate that elevated AT can induce root circumnutation in rice via the ethylene pathway and proposes a potential molecular model through the identification of key genes. These findings offer valuable insights into the growth regulation mechanism of plant roots under elevated AT conditions.

Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing.

Although per-base sequencing costs have decreased during recent years, library preparation for targeted massively parallel sequencing remains constrained by high reagent cost, limited design flexibility, and protocol complexity. To address these limitations, we previously developed Hi-Plex, a polymerase chain reaction (PCR) massively parallel sequencing strategy for screening panels of genomic target regions. Here, we demonstrate that Hi-Plex applied with hybrid adapters can generate a library suitable for sequencing with both the Ion Torrent and the TruSeq chemistries and that adjusting primer concentrations improves coverage uniformity. These results expand Hi-Plex capabilities as an accurate, affordable, flexible, and rapid approach for various genetic screening applications.

An efficient and robust method for analyzing population pharmacokinetic data in genome-wide pharmacogenomic studies: a generalized estimating equation approach.

Powerful array-based single-nucleotide polymorphism-typing platforms have recently heralded a new era in which genome-wide studies are conducted with increasing frequency. A genetic polymorphism associated with population pharmacokinetics (PK) is typically analyzed using nonlinear mixed-effect models (NLMM). Applying NLMM to large-scale data, such as those generated by genome-wide studies, raises several issues related to the assumption of random effects as follows: (i) computation time: it takes a long time to compute the marginal likelihood; (ii) convergence of iterative calculation: an adaptive Gauss-Hermite quadrature is generally used to estimate NLMM; however, iterative calculations may not converge in complex models; and (iii) random-effects misspecification leads to slightly inflated type-I error rates. As an alternative effective approach to resolving these issues, in this article, we propose a generalized estimating equation (GEE) approach for analyzing population PK data. In general, GEE analysis does not account for interindividual variability in PK parameters; therefore, the usual GEE estimators cannot be interpreted straightforwardly, and their validities have not been justified. Here, we propose valid inference methods for using GEE even under conditions of interindividual variability and provide theoretical justifications of the proposed GEE estimators for population PK data. In numerical evaluations by simulations, the proposed GEE approach exhibited high computational speed and stability relative to the NLMM approach. Furthermore, the NLMM analysis was sensitive to the misspecification of the random-effects distribution, and the proposed GEE inference is valid for any distributional form. We provided an illustration by using data from a genome-wide pharmacogenomic study of an anticancer drug.

Gene Screening for Prognosis of Non-Muscle-Invasive Bladder Carcinoma under Competing Risks Endpoints.

Background: Discovering clinically useful molecular markers for predicting the survival of patients diagnosed with non−muscle-invasive bladder cancer can provide insights into cancer dynamics and improve treatment outcomes. However, the presence of competing risks (CR) endpoints complicates the estimation and inferential framework. There is also a lack of statistical analysis tools and software for coping with the high-throughput nature of these data, in terms of marker screening and selection. Aims: To propose a gene screening procedure for proportional subdistribution hazards regression under a CR framework, and illustrate its application in using molecular profiling to predict survival for non-muscle invasive bladder carcinoma. Methods: Tumors from 300 patients diagnosed with bladder cancer were analyzed for genomic abnormalities while controlling for clinically important covariates. Genes with expression patterns that were associated with survival were identified through a screening procedure based on proportional subdistribution hazards regression. A molecular predictor of risk was constructed and examined for prediction accuracy. Results: A six-gene signature was found to be a significant predictor associated with survival of non−muscle-invasive bladder cancer, subject to competing risks after adjusting for age, gender, reevaluated WHO grade, stage and BCG/MMC treatment (p-value < 0.001). Conclusion: The proposed gene screening procedure can be used to discover molecular determinants of survival for non−muscle-invasive bladder cancer and in general facilitate high-throughput competing risks data analysis with easy implementation.