1 Head and Neck Cancer Research Team, Cancer Research Malaysia, Subang Jaya, Malaysia.
2 Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
J Dent Res. 2018 Jul;97(8):909-916. doi: 10.1177/0022034518759038. Epub 2018 Mar 7.
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/ .
头颈部癌症（HNC）衍生细胞系是研究癌症发展和精准治疗相关生物学机制的基本模型。然而，从现有数据库中挖掘 HNC 细胞的基因组信息需要具备生物信息学和计算技能。在这里，我们开发了一个用户友好的网络资源，用于探索、可视化和分析常用 HNC 细胞系的基因组信息。我们在 GENIPAC 中填充了来自 3 项研究的 44 种 HNC 细胞系的信息：ORL 系列、OPC-22 和 H 系列。具体来说，所有 3 项研究的 mRNA 表达均采用 RNA-seq 获得。ORL 系列的拷贝数改变分析在全基因组人类 Cytoscan HD 阵列上进行，而 OPC-22 的拷贝数改变则来自全外显子组测序。ORL 系列和 H 系列的突变源自 RNA-seq 信息，而 OPC-22 则基于全外显子组测序。所有基因组信息均使用定制脚本进行预处理，并通过 cBioPortal 提供的数据集验证工具进行数据验证和校正。在 GENIPAC 中，可以轻松评估 44 种 HNC 细胞系的临床和基因组信息。我们通过一些常见于 HNC 的基因组改变，如 TP53、EGFR、CCND1 和 PIK3CA，演示了 GENIPAC 的功能实用性。我们表明，这些在癌症基因组图谱数据库中报道的基因组改变在 GENIPAC 中的 HNC 细胞系中得到了再现。重要的是，通路内的基因组改变可以同时可视化。我们开发 GENIPAC 是为了提供对 HNC 细胞系基因组信息的访问。这一癌症组学倡议将帮助研究界加速对头颈部癌症的理解，并为头颈部癌症的治疗开发新的精准治疗选择。GENIPAC 可在 http://genipac.cancerresearch.my/ 免费获取。
