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The Saudi Genome Project (SHGP)

By Benjamin Chong


Saudi Arabia is embarking on a new initiative known as the Saudi Human Genome Program (part of a larger project called Vision 2030), aimed at sequencing 100,000 human genomes over the next five years. This project seeks to solve the increasing amount of genetic diseases in the country, improve healthcare, and lead the way for personalized medicine. With a focus on the Saudi population, the SHGP aims to unlock the genetic secrets behind various diseases and revolutionize healthcare in the kingdom.

The Problem:

Saudi Arabia struggles with a significant burden of genetic diseases, likely because of blood related marriages. This prevalence leads to severe inherited disorders affecting 8% of births, as well as common genetic conditions like diabetes, affecting over 20% of the population. These diseases affect the lives of individuals and place a strain on the healthcare system, nearly $27 billion annually.

The Goals of the SHGP:

The primary objective of the Saudi Human Genome Program is to identify the genetic basis of both severe and common inherited diseases in the Saudi population. By employing cutting-edge genomics technologies, including genome sequencing and advanced bioinformatics analysis, the SHGP aims to establish a robust foundation for genomic medicine. This foundation encompasses the development of laboratory infrastructure, technical capacity, and the creation of a comprehensive genomic knowledge database.

Executing the SHGP:

The SHGP is led by the King Abdulaziz City for Science and Technology (KACST) in Saudi Arabia. It involves the establishment of ten genome centers across the country, tasked with recruiting subjects and conducting genome sequencing. These centers employ next-generation sequencing (NGS) technology, which enables quick and cost-effective reading of DNA sequences. To handle the large amounts of genomic data generated, the project also uses advanced computing infrastructure and bioinformatics workflows.

The Process:

The SHGP follows standard procedures for sample collection, banking, processing, and sequencing. The collected DNA samples undergo NGS including whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted gene sequencing. These approaches allow for a detailed analysis of genetic variations and the disease-causing genes. The genomic variant data are then analyzed and incorporated into a Saudi-specific database.

WGS, WES and Targeted Gene Sequencing

Whole-genome sequencing (WGS) is a technology that sequences an individual's entire genome, including genes and non-coding regions. It detects various genetic variants and is useful for studying complex diseases.


Whole-exome sequencing (WES) focuses on sequencing only the protein-coding regions of the genome, identifying disease-causing mutations in a cost-effective manner. It is commonly used for monogenic disorders. Targeted gene sequencing (gene panel sequencing) sequences specific genes associated with a disease or condition. It is efficient for clinical diagnostics and screening relevant genes.

The Role of Bioinformatics:

Bioinformatics plays a pivotal role in the SHGP due to the immense scale and complexity of the generated data. Managing big data, encompassing volume, velocity, variety, and veracity, presents a challenge that requires effective data management and analysis methods. The project leverages distributed IT infrastructure to optimize data transfers among different sites. Moreover, high-performance computing resources, such as the SANAM supercomputer, aid in the storage and analysis of genomic data, ensuring efficient processing and interpretation.

Global Impact and Future Prospects:

The Saudi Human Genome Program has garnered international recognition as a leading biomedical project, positioning Saudi Arabia as a trailblazer in disease genetics research and personalized medicine. It aligns with the global trend of national and regional genomics initiatives targeting larger cohorts and population-specific contexts. By leveraging next-generation sequencing technologies and establishing a comprehensive genomic database, the SHGP aims to drive breakthroughs in personalized medicine, improve disease prevention, and contribute to global efforts in combating genetic disorders.

Final Thoughts:

The Saudi Human Genome Program represents a pivotal step towards leveraging genomics to address the burden of genetic diseases in Saudi Arabia. The SHGP holds promise of revolutionizing healthcare and transforming it into a more personalized and effective approach. This landmark project, driven by cutting-edge technologies and comprehensive bioinformatics analysis, has the potential to aid the well-being of the Saudi people and significantly impact genomics research/medicine on a global scale.




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