GeneFuse: detection and visualization of target gene fusions from DNA sequencing data

Chen, Shifu; Liu, Ming; Huang, Tanxiao; Liao, Wenting; Xu, Mingyan; Gu, Jia

doi:10.7150/ijbs.24626

“…N base) is ignored. This k-mer representation has been used widely in our previous works, such as GeneFuse [ 28 ]. A progressive method for k-mer calculation is applied to accelerate k-mer generation.…”

Section: Methodsmentioning

confidence: 99%

A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data

Chen

¹

,

He

²

,

Li

³

et al. 2020

Briefings in Bioinformatics

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In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset. UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction and other preprocessing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, Middle East respiratory syndrome and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv.

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“…N base) is ignored. This k-mer representation has been used widely in our previous works, such as GeneFuse [24]. A progressive method for k-mer calculation is applied to accelerate k-mer generation.…”

Section: K-mer Generation and Representationmentioning

confidence: 99%

A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data

Chen

¹

,

He

²

,

Li

³

et al. 2020

Preprint

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In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms, and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset.UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input, and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction, and other pre-processing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid SARS-CoV-2 identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, MERS, and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv. As part of the OpenGene projects, fastv and UniqueKMER are open-sourced through the MIT license.Fastv is available at https://github.com/OpenGene/fastv, and UniqueKMER is available at https://github.com/OpenGene/UniqueKMER. The pre-computed unique k-mer resources are also provided in these repositories. Key PointsThis tool presents a new tool fastv for rapid identification of SARS-Cov-2, other viruses and microorganisms. Another tool UniqueKMER is presented for generation of high-quality unique k-mers.Unique k-mer resources for tens of thousands of viruses and microorganisms have been precomputed, and uploaded to the tools' repositories. Supplementary DataA pipeline for alignment-based SARS-CoV-2 identification was provided in Supplementary file 1.

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“…However, several studies have reported opposite data regarding the protumor effect of the microenvironment in BC. In particular, carcinoma-associated fibroblasts (CAFs), MSCs, TAMs, Breg, Treg, and Th2 lymphocytes may contribute to the development of metastases 39–41. Litviakov et al reported the lack of clinical response to neoadjuvant anthracycline therapy in BC patients that was associated with the presence of M2 macrophages (YKL-39 – CCL18 + or YKL-39 + CCL18 – ) in the tumor 42…”

Section: Nact Modulates Immune Responses In the Tumor Microenvironmentmentioning

confidence: 99%

<p>Mechanisms behind prometastatic changes induced by neoadjuvant chemotherapy in the breast cancer microenvironment</p>

Перельмутер

¹

,

Таширева

²

,

Savelieva

³

et al. 2019

BCTT

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Chemotherapy, along with surgery and radiotherapy, is a key treatment option for malignant tumors. Neoadjuvant chemotherapy (NACT) reduces the tumor size and enables total tumor resection. In addition, NACT is believed to be more effective in destroying micrometastases than the same chemotherapy performed after surgery. To date, various NACT regimens have been tested and implemented, which provide a favorable outcome in primary tumors and reduce the risk of progression. However, there is increasing evidence of the NACT ability to increase the risk of cancer progression. This review discusses potential mechanisms by which NACT promotes distant metastasis of breast cancer through changes in the microenvironment of tumor cells. We describe prometastatic NACT-mediated changes in angiogenesis, immuno-inflammatory reactions in the stroma, intravasation, and amount of circulating tumor cells. The role of NACT-related cellular stress in cancer metastasis is also discussed.

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GeneFuse: detection and visualization of target gene fusions from DNA sequencing data

Cited by 42 publications

References 22 publications

A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data

A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data

A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data

<p>Mechanisms behind prometastatic changes induced by neoadjuvant chemotherapy in the breast cancer microenvironment</p>

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