Human Cancer Genomic Research

Human Cancer Genomic Research (HCGR) laboratory is actively involved in identifying dysregulation in various genes and signaling pathways in those cancer that are more prevalent in the Kingdom of Saudi Arabia, such as Papillary Thyroid Carcinoma, Colorectal carcinoma, Breast Cancer and Epithelial Ovarian Carcinoma. The researchers at HCGR continue to pursue these challenges by performing translational studies to identify molecular and genetic variations that may play a role in pathogenesis of these cancers. Once these molecular and genetic variations are identified, intensive data analysis using clinical history is done to determine the role of these alterations in the pathogenesis of cancers. Targeting these identified molecular and genetic alterations using either molecular inhibitors, small interference RNA (siRNA) or antibodies are also performed to identify genes that can be therapeutically targeted for the improvement of cancer therapy. We are active member of the ICGC-ARGO international project, presenting thyroid cancer. The Consortium is dedicated to produce high-quality genomic data on more than 25,000 tumors for up to 50 types of cancer that are of clinical and societal importance across the globe. As a part of the ICGC-ARGO project, we continue to identify new genomic drivers in thyroid cancer, to help improve understanding and clinical management of this disease in Saudi Arabia. Therefore, the main mission of HCGR is to design better strategies to diagnose, prognosticate and treat neoplasm that are specifically relevant to Saudi Arabia.

Focus areas
The main goal of the HCGR is to recognize or categorize the dysregulation in various genes and signaling pathways in those cancers that are most prevalent in the Kingdom of Saudi Arabia. The other main focus of HCGR is also to perform high-quality translational research using state-of-the-art technologies, including high-throughput, third-generation sequencing analysis. The scientists and other researchers of HCGR lab continue their research in pursuing these challenges by performing translation studies to identify molecular and genetic markers that may be playing a role in the pathogenesis of these cancers by using the latest techniques to investigate the function of genes that have been implicated in the pathogenesis of various malignancies.

List of sections
Experimental Pathology and Molecular Oncology: The section focuses on translational studies, towards developing new diagnostic and therapeutic strategies aimed at improving the management of cancer. This is a unique facility and provides unprecedented tools for translational research in the region. The main functions of this lab are as follows:

•High-throughput sequencing analysis of DNA samples to identify mutations and deletions that may be playing a pivotal role in the pathogenesis of cancers.
•Identification of various dysregulated proteins that is either overexpressed or downregulated by Immunohistochemistry (IHC) in different tumor tissue in a tissue microarray format.
•In vitro studies conducted to identify dysregulated survival pathways and molecules in cancer that can be targeted using either small molecular inhibitor, peptides, naturally occurring drugs and •siRNA transfection strategies using cancer cell lines.
•Finally, further confirmation of in vitro data by inoculating tumor cells in either SCID or Nude mice and then treat them with the specific inhibitors and follow the progress of these tumors over several weeks in vivo to determine tumor regression, protein down-regulation and at the same time identify any toxicity associated with the inhibitors in animals

Bioinformatics
The section provides bioinformatics support to the department with the main focus on management, integration and analysis of next-generation sequencing data. The section has state of the art tools, software and computational facility for catering to the needs of the department besides having large storage servers for data safety and backup. With our inbuilt pipelines, methods and expertise, we mine the useful knowledge from high-throughput data.

The section is well equipped with the following types of bioinformatics and high-throughput sequencing analyses:

•De novo genome assembly
•Reference genome mapping
•Variant analysis
•Transcriptome analysis
•Copy number and structural variation analysis
•Custom pipeline development
•Whole genome sequencing
•Targeted sequencing
•RNA-seq
 

Biological Repository Center:
The main function of the Biological Repository Centre (BRC) is the proper preservation & storage of fresh frozen tumor and normal tissue samples. In addition, DNA and RNA extraction from these frozen samples is also performed that are utilized for mutational analysis and differential expression studies in various projects. The functions of the BRC include:

Processing biomaterial (DNA and/or RNA extraction from fresh frozen or formalin-fixed paraffin embedded tissues) for various research projects.
Cell blocks prepared from human cancer samples and cell lines used for Immunohistochemistry.
•Preparation of the tissue microarray that holds hundreds of tumor samples on a single slide
•Storing biomaterial under controlled temperature.

Career Opportunities 
Human Cancer Genomic Research (HCGR) is carried out by a talented and specialized collaborative team.