Abstract:
BACKGROUND:Fusion genes are known to be drivers of many common cancers, so they are potential markers for diagnosis, prognosis or therapy response. The advent of paired-end RNA sequencing enhances our ability to discover fusion genes. While there are available methods, routine analyses of large number of samples are still limited due to high computational demands. RESULTS:We develop FuSeq, a fast and accurate method to discover fusion genes based on quasi-mapping to quickly map the reads, extract initial candidates from split reads and fusion equivalence classes of mapped reads, and finally apply multiple filters and statistical tests to get the final candidates. We apply FuSeq to four validated datasets: breast cancer, melanoma and glioma datasets, and one spike-in dataset. The results reveal high sensitivity and specificity in all datasets, and compare well against other methods such as FusionMap, TRUP, TopHat-Fusion, SOAPfuse and JAFFA. In terms of computational time, FuSeq is two-fold faster than FusionMap and orders of magnitude faster than the other methods. CONCLUSIONS:With this advantage of less computational demands, FuSeq makes it practical to investigate fusion genes in large numbers of samples. FuSeq is implemented in C++ and R, and available at https://github.com/nghiavtr/FuSeq for non-commercial uses.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Vu TN,Deng W,Trac QT,Calza S,Hwang W,Pawitan Ydoi
10.1186/s12864-018-5156-1subject
Has Abstractpub_date
2018-11-01 00:00:00pages
786issue
1issn
1471-2164pii
10.1186/s12864-018-5156-1journal_volume
19pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Sugarcane is an economically important crop contributing about 80% and 40% to the world sugar and ethanol production, respectively. The complicated genetics consequential to its complex polyploid genome, however, have impeded efforts to improve sugar yield and related important agronomic traits. Modern sugar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-314
更新日期:2013-05-10 00:00:00
abstract:BACKGROUND:The astounding regenerative abilities of planarian flatworms prompt steadily growing interest in examining their molecular foundation. Planarian regeneration was found to require hundreds of genes and is hence a complex process. Thus, RNA interference followed by transcriptome-wide gene expression analysis b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6292-y
更新日期:2019-11-29 00:00:00
abstract:BACKGROUND:Identification of genes with ascending or descending monotonic expression patterns over time or stages of stem cells is an important issue in time-series microarray data analysis. We propose a method named Monotonic Feature Selector (MFSelector) based on a concept of total discriminating error (DEtotal) to i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S2-S2
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the pa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5214-8
更新日期:2018-11-29 00:00:00
abstract:BACKGROUND:Colon cancer occurrence is increasing worldwide, making it the third most frequent cancer. Although many therapeutic options are available and quite efficient at the early stages, survival is strongly decreased when the disease has spread to other organs. The identification of molecular markers of colon canc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4139-y
更新日期:2017-09-30 00:00:00
abstract:BACKGROUND:Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visuali...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3195-z
更新日期:2016-11-07 00:00:00
abstract:BACKGROUND:Genotyping-by-sequencing (GBS) is becoming an attractive alternative to array-based methods for genotyping individuals for a large number of single nucleotide polymorphisms (SNPs). Costs can be lowered by reducing the mean sequencing depth, but this results in genotype calls of lower quality. A common analys...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2252-3
更新日期:2015-12-09 00:00:00
abstract:BACKGROUND:The origin and importance of exon-intron architecture comprises one of the remaining mysteries of gene evolution. Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. However, there is little study about the structural variation of exons an...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-47
更新日期:2009-01-24 00:00:00
abstract:BACKGROUND:Carolacton is a newly identified secondary metabolite causing altered cell morphology and death of Streptococcus mutans biofilm cells. To unravel key regulators mediating these effects, the transcriptional regulatory response network of S. mutans biofilms upon carolacton treatment was constructed and analyze...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-362
更新日期:2014-05-12 00:00:00
abstract:BACKGROUND:The capsular polysaccharide is the principal virulence factor of Streptococcus pneumoniae and a target for current pneumococcal vaccines. However, some pathogenic pneumococci are serologically nontypeable [nontypeable pneumococci (NTPn)]. Due to their relative rarity, NTPn are poorly characterized, and, as s...
journal_title:BMC genomics
pub_type: 历史文章,杂志文章
doi:10.1186/s12864-016-2808-x
更新日期:2016-06-22 00:00:00
abstract:BACKGROUND:Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6736-4
更新日期:2020-04-20 00:00:00
abstract:BACKGROUND:Although primarily known as the site of ribosome subunit production, the nucleolus is involved in numerous and diverse cellular processes. Recent large-scale proteomics projects have identified thousands of human proteins that associate with the nucleolus. However, in most cases, we know neither the fraction...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-74
更新日期:2011-01-27 00:00:00
abstract:BACKGROUND:An estimated 15,000 children and adolescents under the age of 19 years are diagnosed with leukemia, lymphoma and other tumors in the USA every year. All children and adolescent acute leukemia patients will undergo chemotherapy as part of their treatment regimen. Fortunately, survival rates for most pediatric...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2965-y
更新日期:2016-08-15 00:00:00
abstract:BACKGROUND:Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs) of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-214
更新日期:2007-07-04 00:00:00
abstract:BACKGROUND:Genome-wide expression profiles are altered during biological aging and can describe molecular regulation of tissue degeneration. Age-regulated mRNA expression trends from cross-sectional studies could describe how aging progresses. We developed a novel statistical methodology to identify age-regulated expre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-132
更新日期:2014-02-14 00:00:00
abstract:BACKGROUND:Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-536
更新日期:2012-10-06 00:00:00
abstract:BACKGROUND:There is interest in improving the flavor of commercial strawberry (Fragaria × ananassa) varieties. Fruit flavor is shaped by combinations of sugars, acids and volatile compounds. Many efforts seek to use genomics-based strategies to identify genes controlling flavor, and then designing durable molecular mar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-217
更新日期:2014-04-17 00:00:00
abstract:BACKGROUND:Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a respiratory disease which causes great economic losses worldwide. Many virulence factors are involved in the pathogenesis, namely capsular polysaccharides, RTX toxins, LPS and many iron acquisition systems. In order to ide...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-98
更新日期:2010-02-08 00:00:00
abstract:BACKGROUND:A fundamental requirement for genomic studies is the availability of genetic material of good quality and quantity. The desired quantity and quality are often hard to obtain when target DNA is composed of complex mixtures of relatively short DNA fragments. Here, we sought to develop a method to representativ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-415
更新日期:2008-09-15 00:00:00
abstract:BACKGROUND:Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of the key genes and pathways that involved in CIMS were important to understand the underlying molecu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5203-y
更新日期:2018-11-07 00:00:00
abstract:BACKGROUND:Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less we...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-948
更新日期:2014-11-01 00:00:00
abstract:BACKGROUND:Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recent...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4876-6
更新日期:2018-06-25 00:00:00
abstract:BACKGROUND:Increased focus surrounds identifying patients with advanced non-small cell lung cancer (NSCLC) who will benefit from treatment with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI). EGFR mutation, gene copy number, coexpression of ErbB proteins and ligands, and epithelial to mesenchy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-289
更新日期:2006-11-10 00:00:00
abstract:BACKGROUND:Controlling and managing the breeding of bluefin tuna (Thunnus spp.) in captivity is an imperative step towards obtaining a sustainable supply of these fish in aquaculture production systems. Germ cell transplantation (GCT) is an innovative technology for the production of inter-species surrogates, by transp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2397-8
更新日期:2016-03-10 00:00:00
abstract:BACKGROUND:Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential production of NR will contribute to elucidate which genes are involved in the synthesis, regulation and a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5287-4
更新日期:2018-12-04 00:00:00
abstract:BACKGROUND:The complex genome of rapeseed (Brassica napus) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-281
更新日期:2012-06-24 00:00:00
abstract:BACKGROUND:Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus) using Illumina short-read sequencing data, by comparing our lab data for 38 goats from three Chi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07267-6
更新日期:2020-11-27 00:00:00
abstract:BACKGROUND:Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: elements of different families do not cooperate, but they independently fight for their survival in ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-219
更新日期:2008-05-14 00:00:00
abstract:BACKGROUND:Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a la...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-149
更新日期:2006-06-13 00:00:00
abstract:BACKGROUND:Linkage disequilibrium (LD) plays a fundamental role in population genetics and in the current surge of studies to screen for subtle genetic variants affecting complex traits. Methods widely implemented in LD analyses require samples to be randomly collected, which, however, are usually ignored and thus rais...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-328
更新日期:2010-05-26 00:00:00