Human Cancer Genomic Research
About
The researchers at the Human Cancer Genomic Research (HCGR) continue to pursue the challenges in the field of Cancer Research and working on their mission which is to conduct translational research on concerns that are more prevalent in the Kingdom of Saudi Arabia. In the year 2014, the program continued to be an integral part of the International Cancer Genome Consortium (ICGC) for analyzing papillary thyroid cancer in the Kingdom of Saudi Arabia. They were able to investigate the role of mTOR signaling pathway in PYC and finally, they found a very low level of BRAF mutation in colorectal carcinoma in this region.
Research Activities
The main goal of the Human Cancer Genomic Research (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 that may be playing a role in the pathogenesis of these cancers by also using latest techniques to investigate the function of genes that have been implicated in the pathogenesis of various malignancies.
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 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.
- 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 down-regulated 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 inhibitors, 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 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 archival frozen tumor and normal tissue samples. In addition, DNA and RNA extraction from these frozen samples is also done 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 TMA punches of paraffin blocks) for various research projects.
- Cell blocks prepared from human cancer samples and cell lines used for Immunohistochemistry.
- Preparation of the tissue microarray that holds up to hundreds of tumor samples on one slide
- Processing of fresh tissue for frozen sections and formalin fixed paraffin embedded (FFPE) tissues from archival paraffin blocks for routine H&E staining and immunohistochemistry.
- Storing biomaterial under controlled temperature.
