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Open Access Highly Accessed Methodology article

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

Charles Cole1, Konstantinos Krampis2, Konstantinos Karagiannis1, Jonas S Almeida3, William J Faison1, Mona Motwani1, Quan Wan1, Anton Golikov4, Yang Pan1, Vahan Simonyan4 and Raja Mazumder15*

Author Affiliations

1 Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA

2 J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

3 Division of Informatics of the Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA

4 Center for Biologics Evaluation and Research, US Food and Drug Administration, 1451 Rockville Pike, HFM-470, Rockville, MD 20852, USA

5 McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA

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BMC Bioinformatics 2014, 15:28  doi:10.1186/1471-2105-15-28

Published: 27 January 2014

Abstract

Background

Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it.

Results

To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr webcite).

Conclusions

Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides.

Keywords:
SRA; TCGA; nsSNV; SNV; SNP; Next-gen; NGS; Phylogenetics; Cancer