Halima Alnaqbi’s PhD research addresses the gap in Arab representation in global genome data and establishes preliminary framework for organ and bone marrow transplantation in the UAE. 

Organ transplantation is one of the greatest advances in modern medicine and is the only life-saving strategy for patients with end-stage organ failure. Unfortunately, the need for organ donors is much greater than the number of people who donate.

The human immune system, however, poses a significant barrier to success when organs are transplanted from one individual to another. Rejection is caused by the immune system identifying the transplant as foreign, triggering a response that will ultimately destroy the transplanted organ. Donor and recipient are carefully matched prior to transplantation to minimize the risk of rejection, using tissue typing and blood group markers, but research into the population-specific genome can also play a larger role.

Dr. Halima Alnaqbi has successfully completed her PhD in Immunogenetics with her thesis focusing on enhancing the existing organ transplantation system to include Arab ethnic groups. This was the first research to identify conserved extended haplotypes (CEHs) in Arabs using high-resolution HLA pedigree-phased haplotypes. Dr. Alnaqbi, Dr. Guan Tay, Dr. Sarah Chehadeh, and Dr. Habiba Alsafar, Director of the KU Biotechnology Center, published this research in.

The human leukocyte antigen (HLA) complex, also known as the major histocompatibility complex (MHC), is a set of genes that code for cell surface proteins essential for the acquired immune system to recognize foreign molecules. It is the set of genes that determines compatibility for organ transplant, among many other things, and has garnered attention for its high level of allele variety among populations.

With more than 7000 alleles, the HLA complex is the most polymorphic region of the human genome. Studies have already examined the HLA complexes of various populations for many medical purposes, including populations where particular HLA types are very common and could potentially be identified as hot spots for severe disease, endemic persistence, or pathogen emergence. Proper understanding of the population-specific HLA complex is instrumental for making informed medical decisions.

“Unfortunately, there is a dearth of information about the structure of the MHC in Arab populations, especially for those who reside in Gulf countries,” Dr. Alnaqbi said. “The structure and content of the MHC region in Arab populations remain poorly characterized, posing challenges when establishing disease association studies in ethnic groups that inhabit the region and reducing the capacity to translate genetic research into clinical practice. We wanted to address the knowledge gap and characterize CEHs in the United Arab Emirates population.”

Conserved extended haplotypes refer to the conserved, long stretches of DNA that occur in people from the same population or ancestry. A haplotype is a physical grouping of genomic variants that tend to be inherited together and extended haplotypes provide most of the markers for HLA-associated autoimmune diseases. Previous disease association studies have been dominated by analyses based on populations of European ancestries, but this is gradually changing, allowing researchers to fill the knowledge gaps in disease risk predictions in some ethnic groups. The genome structure of Arab populations from the Middle East, however, remains poorly characterized.

“Although often grouped for their shared language, history, and culture, the populations of the Arabian Peninsula represent a genetically diverse group,” Dr. Alnaqbi said. “With the United Arab Emirates recently establishing its national organ registry program, this study provides insights on the MHC of the UAE population, which is important for matching recipients to appropriate donors.”

To contribute to the available data on Arab populations, Dr. Alnaqbi analyzed MHC alleles and haplotype frequencies in consenting volunteers from the UAE. Families were randomly recruited from different parts of the UAE and all participants were UAE nationals. The research found sections of genetic code were shared between the participants, identifying conserved extended HLA haplotypes in the population.

Dr. Alnaqbi said. “We need more effort into studying the MHC region of the Arabian population to offer better healthcare and benefit from the new paradigm of healthcare represented by personalized and precision medicine.”

Jade Sterling
Science Writer
15 June 2022

The post PhD Research Helps Reduce Organ Transplant Risk Using New Insights to Emirati Genome appeared first on Khalifa University.

Research to Support Accurate Classification of Genome Variants for Development of Preventative Healthcare System

A team of scientists from Khalifa University of Science and Technology has completed a significant local genome study that will contribute to nationwide efforts to build a high-quality, comprehensive reference genome for the UAE population.

The first phase of the study — the description of the first whole genome sequences of UAE nationals — was completed in 2019. Subsequently, in 2020, the researchers completed the second phase which described the nature of the genetic diversity found among UAE nationals. This year, the researchers completed the third phase of the UAE reference genome, which supports a broader understanding of the genome composition of the nation.

Following advancements in DNA sequencing and analysis techniques since renowned scientist Craig Venter and his colleagues published the first whole human genome sequence at the turn of this century, the genome study has become part of a major area of research at Khalifa University.

The Khalifa University scientists recently published a report titled ‘A population-specific Major Allele Reference Genome from the United Arab Emirates population’ in the international journal, Frontiers in Genetics. The study was authored by Dr. Habiba Alsafar, Associate Professor, Department of Genetics and Molecular Biology, Dr. Andreas Henschel, Associate Professor, Electrical Engineering and Computer Science, with Dr. Gihan Daw Elbait and Dr. Guan Tay, from the Center for Biotechnology.

Dr. Arif Sultan Al Hammadi, Executive Vice-President, Khalifa University, said: “Our researchers have published the first whole genome of a UAE national and have followed it up with this reference genome.  This will advance our understanding of the genomes of the UAE population, improving the ability of researchers and clinicians to identify genetic causes of diseases that are common in the UAE and the region. This is a stellar achievement in the field of medicine and healthcare, as this will become a fundamental tool that will advance genome and public health research in the UAE, and contribute to nationwide efforts, being led by the recently formed UAE Genomics Council to incorporate genomics into the healthcare ecosystem of the UAE.” 

The ethnic composition of the population of a nation contributes to its genetic uniqueness.  Consequently, it is important to define national reference genomes of its people to avoid any confounding effects which are linked to the use of reference genomes from other national genome sequencing efforts. A total of 1,028 UAE nationals were recruited for this study, as part of the 1,000 UAE genome project that was conceived by the research team when the Center of Biotechnology was founded in 2015. Of these, 129 samples were selected as individuals that are most representative of the genetic diversity of the UAE for construction of the UAERG.

“Despite achieving this major milestone in a relatively short period of time, our work to improve our understanding of how genes contribute to health continues,” said Dr. Alsafar and added, “Our next challenge is to decode the genome data to identify genetic markers that better predict the likelihood of disease.”

Precision medicine has the potential to profoundly improve the practice of medicine. The goal is to enable clinicians to quickly, efficiently and accurately predict the most appropriate course of action for a patient; a pre-emptive strike to prevent or delay the onset of disease.  However, the practice of precision medicine and personalized healthcare is a complex science as it is influenced by a range of factors such as the environment and the inherent characteristics within an individual. Genetics is an important contributor to this complexity and genome science will play a key role in the rollout of future national health programs.

Since the establishment of the Center for Biotechnology (BTC), its primary mission sought to address a gap in knowledge relating to the specific genomic features of the UAE population.  In 2018, the BTC team outlined a vision for a National Arab Genome project for the UAE in the Journal of Human Genetics. The aim was to address the deficiency in genome data on the UAE population to improve our understanding of genome variants that are unique to the population of the nation.  The team led by eminent geneticist Dr. Alsafar, proceeded with the bold ambition to sequence Emirati nationals to provide a reference upon which clinical decisions can be made.

In 2019, Dr. Alsafar led the team that described the first Whole Genomes Sequences (WGS) of two UAE nationals in Nature Publishing Group’s Scientific Report.  “It was important to achieve this milestone, as the whole genome sequences provided a starting point for construction of a UAE reference panel which will lead to improvements in the delivery of precision medicine, which we hope will eventually lead to improvements in the quality of life of UAE nationals” said Dr Alsafar.

Despite reporting on the first genome of a UAE national, the Khalifa University team continued to sequence samples provided by UAE nationals for research. In mid-2020, the team followed up the report of the first UAE Whole Genome Sequence with two papers in Frontiers in Genetics. These studies showed that the contemporary population of the UAE arose from gradual admixture through complex and long term interactions between local communities of the area that is now the UAE and the people of neighbouring regions.

The seven emirates that formed the UAE in 1971 were once sheikhdoms that were homes of communities that existed for centuries. These communities lived on the southern routes of human migration within the Arabian Peninsula. Some of the inhabitants of the region encountered people who led a nomadic lifestyle, travelling widely into and out of neighbouring African, Asian and European states. As these nomadic communities passed through this region, traces of genetic impressions of the populations that they encountered in their travels were left behind.

As researchers continue to probe the secrets entwined in the genome of the UAE population, the construction of this reference genome is intended to drive the developing paradigm that is precision medicine, specifically clinical practice that embraces prevention rather than treating disease once it has taken hold.

Clarence Michael
English Editor Specialist
5 July 2021

The post Khalifa University Researchers Complete Reference Genome Study for the UAE appeared first on Khalifa University.