Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

AbstractAdvances in whole genome sequencing promise to enable the accurate and comprehensive structural variant (SV) discovery. Dissecting SVs from whole genome sequencing (WGS) data presents a substantial number of challenges and a plethora of SV-detection methods have been developed. Currently, there is a paucity of evidence which investigators can use to select appropriate SV-detection tools. In this paper, we evaluated the performance of SV-detection tools using a comprehensive PCR-confirmed gold standard set of SVs. In contrast to the previous benchmarking studies, our gold standard dataset included a complete set of SVs allowing us to report both precision and sensitivity rates of SV-detection methods. Our study investigates the ability of the methods to detect deletions, thus providing an optimistic estimate of SV detection performance, as the SV-detection methods that fail to detect deletions are likely to miss more complex SVs. We found that SV-detection tools varied widely in their performance, with several methods providing a good balance between sensitivity and precision. Additionally, we have determined the SV callers best suited for low and ultra-low pass sequencing data.

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Towards online anomaly detection by combining multiple detection methods and Storm

NOMS 2016 - 2016 IEEE/IFIP Network Operations and Management Symposium ◽

10.1109/noms.2016.7502903 ◽

2016 ◽

Cited By ~ 2

Author(s):

Ziyu Wang ◽

Jiahai Yang ◽

Hui Zhang ◽

Chenxi Li ◽

Shize Zhang ◽

...

Keyword(s):

Anomaly Detection ◽

Detection Methods ◽

Multiple Detection ◽

Online Anomaly Detection

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A lack of evidence for down-modulation of CD3ζ expression in colorectal carcinoma and pregnancy using multiple detection methods

Clinical & Experimental Immunology ◽

10.1046/j.1365-2249.1999.01044.x ◽

1999 ◽

Vol 118 (2) ◽

pp. 197-204 ◽

Cited By ~ 5

Author(s):

Deakin ◽

Singh ◽

Crowe ◽

Ellis ◽

Dalgleish ◽

...

Keyword(s):

Colorectal Carcinoma ◽

Detection Methods ◽

Multiple Detection

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Application of Repair and Anti-Corrosion Technology on Reinforced Concrete Structures of a Domestic Wharf

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.189-193.165 ◽

2011 ◽

Vol 189-193 ◽

pp. 165-168

Author(s):

Xiao Dong Zhao ◽

Xi Qiu Fan ◽

Mei Ling Tian

Keyword(s):

Reinforced Concrete ◽

Research Work ◽

Concrete Structures ◽

Detection Methods ◽

Reinforced Concrete Structures ◽

Reinforced Concrete Structure ◽

The Status ◽

Multiple Detection ◽

Technical Discussion ◽

Technical Basis

According to the status and service environment of a domestic wharf, the corrosion of reinforced concrete structure was evaluated by multiple detection methods, on the base of which the corresponding repair and anti-corrosion program were adopted, thus good preservative effect was achieved. The research work and demonstration project are expected to provide technical discussion and reference for peer experts, as well as technical basis for the corrosion protection of reinforced concrete structures in similar marine environment.

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N4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana

Genome Biology ◽

10.1186/s13059-021-02578-7 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Shuai Wang ◽

Hairong Xie ◽

Fei Mao ◽

Haiyan Wang ◽

Shu Wang ◽

...

Keyword(s):

Gene Expression ◽

Genomic Dna ◽

Gene Expression Regulation ◽

Detection Methods ◽

Dna Modification ◽

Protein Coding ◽

Transcription Start Sites ◽

Genome Wide ◽

Multiple Detection ◽

Cellular Dna

Abstract Background Direct analogs of chemically modified bases that carry important epigenetic information, such as 5-methylcytosine (m5C)/5-methyldeoxycytosine (5mC), 5-hydroxymethylcytosine (hm5C)/5-hydroxymethyldeoxycytosine (5hmC), and N6-methyladenosine (m6A)/N6-methyldeoxyadenosine (6mA), are detected in both RNA and DNA, respectively. The modified base N4-acetylcytosine (ac4C) is well studied in RNAs, but its presence and epigenetic roles in cellular DNA have not been explored. Results Here, we demonstrate the existence of N4-acetyldeoxycytosine (4acC) in genomic DNA of Arabidopsis with multiple detection methods. Genome-wide profiling of 4acC modification reveals that 4acC peaks are mostly distributed in euchromatin regions and present in nearly half of the expressed protein-coding genes in Arabidopsis. 4acC is mainly located around transcription start sites and positively correlates with gene expression levels. Imbalance of 5mC does not directly affect 4acC modification. We also characterize the associations of 4acC with 5mC and histone modifications that cooperatively regulate gene expression. Moreover, 4acC is also detected in genomic DNA of rice, maize, mouse, and human by mass spectrometry. Conclusions Our findings reveal 4acC as a hitherto unknown DNA modification in higher eukaryotes. We identify potential interactions of this mark with other epigenetic marks in gene expression regulation.

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