Download C – An Overview of the Opportunities for Genomics in the Kingdom

Saudi Human Genome Project
Overview
C – An Overview of the Opportunities for Genomics in the Kingdom
Genomics is the Ideal Investment for a Nation
Looking across all areas of science and technology, investment in Genomics is a unique and wise
investment based on the guaranteed potential for life changing impact. Genomics generally refers to all
applications that come from reading the entire DNA blueprint of organisms – humans, plants or animals.
It is certain this industry will be at the heart of major advances in healthcare, as well as in public health,
agriculture and energy. The tremendous future value of Genomics is clear – far clearer than for other
emerging technologies – and the countries that make the aggressive investments in infrastructure and
applications will be positioned to reap the greatest rewards for decades to come.
The Critical Transition Moment is Now
Genomics is at the same point now as the computer industry was in the 1970’s, when the two previous
decades had created a foundation through research and large government projects. However, a shift in
technology triggered a migration from research to main stream application creating an era of massive
economic growth with far reaching societal impacts Specifically, the trigger was enabling disruptive
technologies of the microprocessor from Intel and personal computer from Apple introducing affordable
and easy to use computers sparking distributed deployment and utility. In much the same way, the past
two decades have developed the foundation for a genomics industry.
A Unique Global Flagship Opportunity for Saudi Arabia
For the Kingdom of Saudi Arabia, this presents a unique and extremely exciting opportunity to make
both a major, immediate impact on healthcare in the Kingdom, and to assume a world leading position
in the emerging era of Genomics. This can be achieved through a flagship initiative with two major
goals:
1. Eliminate the huge burden of recessive genetic disease from the population in 5 years, through a
process of discover, screening and pre-marital counseling
2. Assume a world leadership position in applied genomics, by being the first to leverage the
revolutionary technology
The Scope of Genomics
Genomics is the field of application based on reading the entire DNA blueprint of an organism (the
Genome), and using this information for a broad range of purposes, ranging from the most basic of
identification, to predicting or controlling outcomes as the organism interacts with its environment, in
addition to modifying the DNA blueprint itself to achieve desired ends. Genomics has valuable
applications across the entire spectrum of life, from humans, to animals, to plants and microorganisms.
In particular, the following are the major application areas:
 Healthcare:
o Recessive/Severe inherited genetics disease
o Common genetic disease
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Saudi Human Genome Project
Overview
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o Cancer
o Susceptibility to environmental exposures
Human Identification and Forensics
Public Health
o Infectious
o Food Safety
Animal Management
Agriculture
Energy/Bio Fuels
The Environment
Healthcare
In the area of human healthcare, genomics can be applied to help with prevention and treatment of the
diseases that result in major cost burdens to the national healthcare system, and deteriorated quality of
life for the people.
 Recessive Genetics Disease:
o This is the area where genomics can provide the most immediate, high impact for
healthcare in the kingdom, reducing costs and improving quality of life immediately
through a combination of pre-marital screening and pre-marital counseling. These high
impact changes can be made in a matter of just a few years, leveraging already existing
pre-marital counseling practices. The general potential is illustrated by the specific
example of how the incidence and suffering of inherited recessive blood disease
(Thalassemia) was rapidly and dramatically reduced in the population. In this case, the
process involved first and foremost development of a proper genomic screen to identify
carriers, followed by a population-scale program of pre-marital carrier screening and
pre-marital counseling to greatly reduce the number of children born with the disorder.
Over the course of just a few years, the benefits of he program are evident in promoting
healthy children born into families, and massive reductions in healthcare costs, with the
benefits starting immediately for the couples involved when the program was initiated,
and impacting all of society in just a few years.
o By taking advantage of the new breakthroughs in DNA analysis, it is possible to play out
this same scenario for all recessive genetic diseases, which collectively directly impact 510% of newborn children in the Kingdom. By first undertaking a large-scale genome
sequencing discovery phase, an affordable DNA test can be developed that screens for
carrier status of all recessive genetic diseases in a single, affordable test, including
Thalassemia. This test can be adopted into the existing healthcare system of pre-marital
screening and counseling, to achieve huge reductions – potentially even complete
elimination – in the numbers of newborns afflicted by these diseases in the 3-5 year
period.
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Saudi Human Genome Project
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Common Genetic Disease:
o For common diseases that have a strong genetic bases, genomics can be used to create
a risk screening test that can identify those people most at risk for developing the
disease. This critical information could be pivotal to guide early intervention and
prevention, to achieve lower healthcare costs for the country and improved quality of
life for the individual. The common, genetic-based diseases that impose the largest
burdens on the kingdom include Diabetes (affecting over 20% of the population) and
Obesity (affecting over 30% of the population), and thus there is tremendous potential
for saving healthcare costs and broadly improving quality of life through introducing risk
assessment testing.
Cancer:
o Cancer is a disease that results when damage to DNA produces uncontrolled cell growth,
resulting in a tumor. Cancer treatment relies on general measures such as surgery,
radiation, and a limited number of chemotherapies that may inhibit tumor growth.
Genomics offers the potential to personalize cancer therapy, by first directly reading the
mutations that resulted in the tumor growth, and then targeting the therapy based on
the patients’ specific mutations. This is a major area of current research, and
breakthroughs in these areas are happening and will be happening frequently as the
international biomedical research community focuses in this area in the coming decade.
As the required knowledge to guide treatment is accumulated, clinical use will always
rely on the fundamental genomic assay that measures the cancer mutations. To take
greatest advantage of the advances in treatment based on genomic knowledge of the
tumor, establishment of this diagnostic capability is critical for immediate access to
breakthrough discoveries in this field. The Kingdom can position itself to both
participate in the discoveries, and make the most rapid advance in clinical applications
by developing the basic diagnostic tumor analysis. In particular, this can be used to be
sure there is a research and treatment focus on the cancer types most relevant to the
Kingdom.
Susceptibility to Environmental Exposures:
o Many disorders are the result of exposure to environmental factors, and thus while the
ultimate cause of the disease is not genetic; the particular individual’s susceptibility can
be strongly genetic, with some individuals able to withstand the factor, while others
succumb. Genomics can be applied to develop risk screening tests for susceptibility,
which can be used for prevention by ensuring those at risk avoid exposure. One such
example of special importance to the Kingdom would be susceptibility to heat stroke,
which is particularly important for pilgrims participating in the Hajj, as well as soldiers
stationed in the desert. It is possible there are strong genetic susceptibility factors that
could be identified and screened for, to provide special protection to those at greatest
risk.
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Saudi Human Genome Project
Overview
Human Identification and Forensics:
 Genomic methods of DNA “fingerprinting” can be used to rapidly and uniquely identify people.
Human Identification applications could include a National ID card based on the individual’s genomic
information, used in identifying immigrants, identifying bodies in accidental deaths, homicides or
military or police action, determining paternity or degree of relatedness, determining who was
present at a crime scene, and in convicting or exonerating suspects in crime. In the Kingdom, this
could in particular be used to establish a comprehensive DNA ID database for the citizens to
enhance national security, and for the pilgrims who enter the country for Hajj.
Public Health:
There are a variety of ways in which genomic methods can be immediately applied to enhance public
health. Infectious disease monitoring and food safety are cited as examples of Public Health application
as follows:
 Infectious Disease:
o Rapid and sensitive DNA analysis can be for monitoring, early detection, diagnosis and
to guide treatment in order to have comprehensive, population scale program for
dealing with infectious disease outbreaks in the population, as well as the more focused
application of controlling infection in hospitals. In particular, the latest DNA reading
technologies allow for rapid identification of novel infectious strains, as illustrated in the
recent cases of the SARS virus outbreak in Asia which killed hundreds of people, and the
German E Coli outbreak in April 2011 which killed 45 people and hospitalized nearly
4,000. In particular, for the Kingdom, a comprehensive infectious disease monitoring
and rapid response capability would be of great value in protecting the public health
during the Hajj pilgrimages in which there is large potential for infectious diseases to be
transmitted.
 Food Safety:
o Food supplies and food processing facilities can be monitored for the presence of
harmful bacteria by using rapid genomic screening methods. This results in a safer food
supply, and limits the harm to the population when food contamination does occur.
Animal Management:
Genomic methods can be used to uniquely identify specific animals by their individual DNA
“fingerprints”, which can be used to determine ownership, verify identity, or to trace diseased or stolen
animal products back to the points of origin. Genomic methods can also be used to monitor and guide
animal breeding, or to allow selective breeding for specific traits. For examples, this can be applied to
the breeding of horses, to verify lineages or preselect offspring with desirable genetic traits.
Agriculture:
Genomic methods can be used to assist in breeding more desirable or robust strains, or in mitigating
disease that attack plants. In particular in the Kingdom, the Date Palm genome has just recently been
fully analyzed by a team at KACST, and this is a foundation for a larger program in date palm genomics
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Saudi Human Genome Project
Overview
that can be used to identify male from female plants, in breeding more desirable strains, and in
developing strains resistant to common or novel diseases or pests. Genomic methods in agriculture can
also be used to create plant strains that can tolerate salt-water, or tolerate desert conditions, which
could be used to prevent or reverse desertification of reduce needs for desalinated water for irrigation.
Energy:
Energy production for bio-fuel is a major emerging area of genomics research, where genomic methods
are used to modify the DNA of plants or algae to make them better suited for bio-fuel production.
The Environment:
Genomic methods can be very powerful for monitoring and protecting the environment. For example,
genome analysis can determine the full spectrum and relative abundances of different animals; insects
or microorganisms that inhabit a particular ecosystem, and can provide a warning when environmental
changes are underway. This can, for example, be used to monitor bacteria levels in seawater bordering
the Kingdom. In another extreme, there is research on modifying bacterial genomes to enable them to
efficiently consume oil, which can be used to clean up oil leakage that can foul coast waters near the
Kingdom.
Focus on Human Health and Immediate Social Impact:
The greatest immediate impact of Genomics on the Kingdom is in the elimination of recessive genetic
disease. Recessive genetic disease impacts an estimated 8% of newborns, placing great personal
burdens on families, and a great cost burden on the national healthcare system. Genomic methods
allow for a nearly complete elimination of rare recessive disease through a three phase process:
 Discovery:
o Reading the genomes of affected individuals can be used to find the causal gene
mutations. If sufficient number (tens of thousands) is properly analyzed, all the major
disease risk factors in the population can be identified.
 Creation of Comprehensive Carrier Screening Diagnostic:
o The discovered genes can be read out in a highly cost effective way using a targeted
diagnostic sequencing assay, which is used to screen the population for carriers who are
therefore at risk for having affected children.
 Pre-marital Screening and Counseling:
o Couples contemplating marriage in the Kingdom already undergo mandatory carrier
screening and counseling to prevent Thalassemia, by using the comprehensive DNA
diagnostic, they can at the same time be screened for carrier status on all recessive
genetic disorders impacting the population, and counseled accordingly, thereby doing
for all recessive diseases what has been accomplished for Thalassemia, which has been
greatly reduced in occurrence in the Kingdom.
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Saudi Human Genome Project
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Newborn Screening and Early Intervention:
o The Kingdom has a national newborn screening program to assess risk for ~20 metabolic
disorders, and this program could be extended to screen for risk for the full array of
genetic disorders, to enable early diagnosis, intervention and treatment options.
Major Value Proposition for Genomics in Healthcare: Screening and Prevention:
The flagship initiative that will have the greatest immediate impact on quality of life and healthcare
savings is a major initiative to eliminate recessive genetic disease through comprehensive pre-marital
screening. This effort has immediate impact as soon as the screening begins, and this can begin as soon
as the risk factors are discovered, since the population-scale screening and counseling procedures are
already fully established by the campaign to eliminate Thalassemia. In this way it is quite possible that
in less than 5 years, the incidence of newborns with severe genetic disorders can be greatly reduced
towards the point of complete elimination. This would be the first time in history a country has
deployed genomics to substantially improve its healthcare.
The Grand 202 Vision: Sequence the Entire Kingdom in this Decade:
The Kingdom could become the first nation in the world to fully know its fundamental biological
makeup. This in turn will drive direct and indirect advances in medical care for decades to come, by
relating the genome information to the national healthcare records to determine genetic risk and
causality for all health-related conditions.
Establishing Genomic Personalized Medicine at a Population Scale:
Genomic personalized medicine for an entire population will consist primarily of having the ability to
screen individuals for all forms of genetic disease risk. This can then be used for pre-natal screening,
newborn screening, pre-marital screening, and general population screening, either to identify at risk
individuals early and apply proper preventative options, or to confirm diagnosis and ensure the proper
selection of treatments.
In order to achieve the deployment of Personalized Medicine into a population, a series of steps must be
performed, beginning with the collection and bio-banking of subjects for research, and ending with
deployment of a clinical diagnostic screen at the population scale.
The Concept of the Saudi Human Genome Project:
The Saudi Human Genome Project is meant to encompass the first major portion of the process of
realizing personalized genomic medicine in the kingdom. This requires the ability to collect many
subjects fully representing normal and disease states of the Saudi population, sequence their genomes,
interpret and validate the results to solve for the disease causing genes and variants, and store the
results in an accessible knowledgebase for future use. The concept of what must be done is clear, and
the individual elements of it have all be thoroughly demonstrated by the global scientific community
over the previous decades, although the work required here is on a scale never yet undertaken in the
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Saudi Human Genome Project
Overview
global genetics community. Nonetheless, the goal of eliminating genetic disease is worthy of the
tremendous effort required.
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