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Ko G, Kim PG, Cho Y, Jeong S, Kim JY, Kim KH, Lee HY, Han J, Yu N, Ham S, Jang I, Kang B, Shin S, Kim L, Lee SW, Nam D, Kim JF, Kim N, Kim SY, Lee S, Roh TY, Lee B. Bioinformatics services for analyzing massive genomic datasets. Genomics Inform 2020; 18:e8. [PMID: 32224841 PMCID: PMC7120352 DOI: 10.5808/gi.2020.18.1.e8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/11/2020] [Indexed: 11/25/2022] Open
Abstract
The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www.bioexpress.re.kr/.
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Affiliation(s)
- Gunhwan Ko
- Korea Bioinformation Center (KOBIC), KRIBB, Daejeon 34141, Korea
| | - Pan-Gyu Kim
- Korea Bioinformation Center (KOBIC), KRIBB, Daejeon 34141, Korea
| | - Youngbum Cho
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | - Seongmun Jeong
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | | | - Ho-Yeon Lee
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | - Jiyeon Han
- Department of BioInformation Science, Ewha Womans University, Seoul 03760, Korea
| | - Namhee Yu
- Department of BioInformation Science, Ewha Womans University, Seoul 03760, Korea
| | - Seokjin Ham
- Department of Life Sciences and Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Insoon Jang
- Department of Life Sciences and Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Byunghee Kang
- Department of Life Sciences and Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Sunguk Shin
- Department of Systems, Biology Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Lian Kim
- Bioposh Inc., Daejeon 34016, Korea
| | | | - Dougu Nam
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jihyun F Kim
- Department of Systems, Biology Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.,Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seoul 03722, Korea
| | - Namshin Kim
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | - Seon-Young Kim
- Genome Structure Research Center, KRIBB, Daejeon 34141, Korea
| | - Sanghyuk Lee
- Department of BioInformation Science, Ewha Womans University, Seoul 03760, Korea
| | - Tae-Young Roh
- Department of Life Sciences and Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea.,SysGenLab Inc., Pohang 37613, Korea
| | - Byungwook Lee
- Korea Bioinformation Center (KOBIC), KRIBB, Daejeon 34141, Korea
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Nordentoft I, Lamy P, Birkenkamp-Demtröder K, Shumansky K, Vang S, Hornshøj H, Juul M, Villesen P, Hedegaard J, Roth A, Thorsen K, Høyer S, Borre M, Reinert T, Fristrup N, Dyrskjøt L, Shah S, Pedersen JS, Ørntoft TF. Mutational context and diverse clonal development in early and late bladder cancer. Cell Rep 2014; 7:1649-1663. [PMID: 24835989 DOI: 10.1016/j.celrep.2014.04.038] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 04/02/2014] [Accepted: 04/21/2014] [Indexed: 11/16/2022] Open
Abstract
Bladder cancer (or urothelial cell carcinoma [UCC]) is characterized by field disease (malignant alterations in surrounding mucosa) and frequent recurrences. Whole-genome, exome, and transcriptome sequencing of 38 tumors, including four metachronous tumor pairs and 20 superficial tumors, identified an APOBEC mutational signature in one-third. This was biased toward the sense strand, correlated with mean expression level, and clustered near breakpoints. A>G mutations were up to eight times more frequent on the sense strand (p<0.002) in [ACG]AT contexts. The patient-specific APOBEC signature was negatively correlated to repair-gene expression and was not related to clinicopathological parameters. Mutations in gene families and single genes were related to tumor stage, and expression of chromatin modifiers correlated with survival. Evolutionary and subclonal analyses of early/late tumor pairs showed a unitary origin, and discrete tumor clones contained mutated cancer genes. The ancestral clones contained Pik3ca/Kdm6a mutations and may reflect the field-disease mutations shared among later tumors.
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Affiliation(s)
- Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Karey Shumansky
- BC Cancer Research Centre, 675 West 10(th) Avenue, Vancouver, BC V5T4E6, Canada
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Malene Juul
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Palle Villesen
- Department of Bioinformatic Research, Aarhus University, Universitetsparken, 8000 Aarhus, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Andrew Roth
- BC Cancer Research Centre, 675 West 10(th) Avenue, Vancouver, BC V5T4E6, Canada
| | - Kasper Thorsen
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Søren Høyer
- Department of Pathology, Aarhus University Hospital, North Road Ringgade 8000 Aarhus, Denmark
| | - Michael Borre
- Department of Urology, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Niels Fristrup
- Department of Urology, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Sohrab Shah
- BC Cancer Research Centre, 675 West 10(th) Avenue, Vancouver, BC V5T4E6, Canada
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark
| | - Torben F Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 100, 8200 Aarhus, Denmark.
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Cohen-Eliav M, Golan-Gerstl R, Siegfried Z, Andersen CL, Thorsen K, Ørntoft TF, Mu D, Karni R. The splicing factor SRSF6 is amplified and is an oncoprotein in lung and colon cancers. J Pathol 2013; 229:630-9. [PMID: 23132731 DOI: 10.1002/path.4129] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 10/03/2012] [Accepted: 10/09/2012] [Indexed: 01/01/2023]
Abstract
An increasing body of evidence connects alterations in the process of alternative splicing with cancer development and progression. However, a direct role of splicing factors as drivers of cancer development is mostly unknown. We analysed the gene copy number of several splicing factors in colon and lung tumours, and found that the gene encoding for the splicing factor SRSF6 is amplified and over-expressed in these cancers. Moreover, over-expression of SRSF6 in immortal lung epithelial cells enhanced proliferation, protected them from chemotherapy-induced cell death and converted them to be tumourigenic in mice. In contrast, knock-down of SRSF6 in lung and colon cancer cell lines inhibited their tumourigenic abilities. SRSF6 up- or down-regulation altered the splicing of several tumour suppressors and oncogenes to generate the oncogenic isoforms and reduce the tumour-suppressive isoforms. Our data suggest that the splicing factor SRSF6 is an oncoprotein that regulates the proliferation and survival of lung and colon cancer cells.
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Affiliation(s)
- Michal Cohen-Eliav
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University - Hadassah Medical School, Jerusalem, Israel
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