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CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets.
Kasaragod, Sandeep; Mohanty, Varshasnata; Tyagi, Ankur; Behera, Santosh Kumar; Patil, Arun H; Pinto, Sneha M; Prasad, T S Keshava; Modi, Prashant Kumar; Gowda, Harsha.
Affiliation
  • Kasaragod S; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
  • Mohanty V; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
  • Tyagi A; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
  • Behera SK; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
  • Patil AH; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
  • Pinto SM; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
  • Prasad TSK; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
  • Modi PK; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
  • Gowda H; Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
F1000Res ; 9: 344, 2020.
Article in En | MEDLINE | ID: mdl-33274046
Cancer genome sequencing studies have revealed a number of variants in coding regions of several genes. Some of these coding variants play an important role in activating specific pathways that drive proliferation. Coding variants present on cancer cell surfaces by the major histocompatibility complex serve as neo-antigens and result in immune activation. The success of immune therapy in patients is attributed to neo-antigen load on cancer cell surfaces. However, which coding variants are expressed at the protein level can't be predicted based on genomic data. Complementing genomic data with proteomic data can potentially reveal coding variants that are expressed at the protein level. However, identification of variant peptides using mass spectrometry data is still a challenging task due to the lack of an appropriate tool that integrates genomic and proteomic data analysis pipelines. To overcome this problem, and for the ease of the biologists, we have developed a graphical user interface (GUI)-based tool called CusVarDB. We integrated variant calling pipeline to generate sample-specific variant protein database from next-generation sequencing datasets. We validated the tool with triple negative breast cancer cell line datasets and identified 423, 408, 386 and 361 variant peptides from BT474, MDMAB157, MFM223 and HCC38 datasets, respectively.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Computational Biology / Databases, Protein / High-Throughput Nucleotide Sequencing Limits: Humans Language: En Journal: F1000Res Year: 2020 Document type: Article Affiliation country: India Country of publication: United kingdom

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Computational Biology / Databases, Protein / High-Throughput Nucleotide Sequencing Limits: Humans Language: En Journal: F1000Res Year: 2020 Document type: Article Affiliation country: India Country of publication: United kingdom