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J Dent Res. 2018 Jul;97(8):909-916. doi: 10.1177/0022034518759038. Epub 2018 Mar 7.

GENIPAC: A Genomic Information Portal for Head and Neck Cancer Cell Systems.

Author information

1
1 Head and Neck Cancer Research Team, Cancer Research Malaysia, Subang Jaya, Malaysia.
2
2 Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
3
3 Data Intensive Computing Centre, Research Management and Innovation Complex, University of Malaya, Kuala Lumpur, Malaysia.
4
4 Department of Computer System and Technology, Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur, Malaysia.
5
5 Faculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, Malaysia.
6
6 Centre for Clinical and Diagnostic Oral Sciences, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
7
7 Moores Cancer Center, University of California San Diego, San Diego, CA, USA.
8
8 Centre for Data Science, University of Malaya, Kuala Lumpur, Malaysia.
9
9 Institute of Mathematical Sciences, University of Malaya, Kuala Lumpur, Malaysia.
10
10 Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.

Abstract

Head and neck cancer (HNC)-derived cell lines represent fundamental models for studying the biological mechanisms underlying cancer development and precision therapies. However, mining the genomic information of HNC cells from available databases requires knowledge on bioinformatics and computational skill sets. Here, we developed a user-friendly web resource for exploring, visualizing, and analyzing genomics information of commonly used HNC cell lines. We populated the current version of GENIPAC with 44 HNC cell lines from 3 studies: ORL Series, OPC-22, and H Series. Specifically, the mRNA expressions for all the 3 studies were derived with RNA-seq. The copy number alterations analysis of ORL Series was performed on the Genome Wide Human Cytoscan HD array, while copy number alterations for OPC-22 were derived from whole exome sequencing. Mutations from ORL Series and H Series were derived from RNA-seq information, while OPC-22 was based on whole exome sequencing. All genomic information was preprocessed with customized scripts and underwent data validation and correction through data set validator tools provided by cBioPortal. The clinical and genomic information of 44 HNC cell lines are easily assessable in GENIPAC. The functional utility of GENIPAC was demonstrated with some of the genomic alterations that are commonly reported in HNC, such as TP53, EGFR, CCND1, and PIK3CA. We showed that these genomic alterations as reported in The Cancer Genome Atlas database were recapitulated in the HNC cell lines in GENIPAC. Importantly, genomic alterations within pathways could be simultaneously visualized. We developed GENIPAC to create access to genomic information on HNC cell lines. This cancer omics initiative will help the research community to accelerate better understanding of HNC and the development of new precision therapeutic options for HNC treatment. GENIPAC is freely available at http://genipac.cancerresearch.my/ .

KEYWORDS:

bioinformatics; biomarkers; cancer biology; gene expression; genomics; oral carcinogenesis

PMID:
29512401
DOI:
10.1177/0022034518759038

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