How a new type of reference genome is a gamechanger for biomedical research
The first human genome, published 20 years ago, revolutionized biomedical research, but did not capture the full genetic diversity of the human population. This led to bias and the possibility of missing out on important discoveries in other regions of the human genome. However, a new type of reference genome called a pangenome, is changing that. Representing 47 individuals from diverse regions such as Asia, Africa, and the Caribbean, the pangenome allows scientists to integrate new and unique information in the reference and, eventually, have the potential to develop targeted medical treatments associated with individual or population-specific DNA sequences.
Pangenome-Based Discoveries
Every time human genomes are sequenced, scientists discover previously unknown pieces of human DNA that are unique to each individual. The pangenome captures this new information, making it possible to identify regions of the genome that are present in some individuals but are missing from the reference. Using the pangenome to study new regions of the genome that differ between individuals can lead to a deeper understanding of how diseases affect different individuals. This can lead to the development of targeted medical treatments, as the work of Cristian Groza, a PhD student, demonstrated that there are 2-3% more active regions in the human genome that were previously overlooked. An example study published in Cellular Genomics shows that new regions that differ between individuals in response to influenza infection were also detected.
Adapting Genomic Methods
As more groups study the implications of pangenome references, scientists will need to adapt genomic methods to this new reference genome tool. “The full consequences of the reference to the pangenome remain unclear,” however, the use of the pangenome is crucial for the success of McGill University’s new D2R programme. The programme aims to mobilize the university’s research expertise, in an inclusive manner, to advance the development of the next generation of RNA drugs for infections, viral diseases, cancer and rare diseases.
Pangenomes: Unlocking the Potential of Gene Editing
The potential of pangenomes goes beyond medical treatments. The wealth of new information provided by pangenomes can be used in gene editing, which has the potential to fundamentally alter the human genome. Pangenomes, working in tandem with gene editing, could help eliminate genetic diseases. However, this technology raises ethical questions, including the possibility of developing “designer babies”. Advances in pangenomes and gene editing will undoubtedly lead to many debates and discussions.
Summary:
A pangenome is a new type of reference genome created as a response to the limitations of the first human genome, published 20 years ago. A pangenome is composed of 47 individuals from diverse regions that capture unique and new information on each human genome. By studying specific individuals and populations, pangenomes will lead to a deeper understanding of how certain diseases affect certain individuals or populations. Pangenomes are the key to developing personalized medical treatments in the future. Furthermore, pangenomes in tandem with gene-editing will transform the study of genetics and medical treatments. Ethical questions remain, however, over the possibility of designer babies.
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The first human genome, which has served as a reference up to now, was published approximately 20 years ago. It was a landmark achievement that had a major impact on biomedical research and changed the way scientists study human biology. But it was based on just a few individuals and did not capture the full genetic diversity of the human population.
An important step forward for both biology and biomedical research
“Since this reference has been at the core of most genomic analyses, it leads to bias and we may miss important things happening in regions of the human genome that are not present in the reference,” says Guillaume Bourque, department professor. of Human Genetics at McGill University and the Director of Bioinformatics at the McGill Genome Center. He is among a large group of scientists who recently published a paper in Natureon the first generation of a new type of reference genome, called a pangenome, representing 47 individuals as genetically diverse as possible, from Africa, Asia, and the Caribbean, to name just a few regions.
The researchers revealed that every time they sequenced a human genome, they found pieces of human DNA that were unique to each individual. The pangenome allows the integration of this new information in the reference. Eventually, this may have significant impacts in terms of the development of targeted medical treatments associated with these unique or population-specific DNA sequences.
Pangenome should lead to a deeper understanding of disease responses
Bourque adds: “This is very exciting because we can now look at regions of the genome that are present in some individuals but are missing from the reference. The work of my PhD student Cristian Groza showed that we can detect 2-3% more active regions.” in the human genome that were previously overlooked.While the 2-3% may seem insignificant, those are regions that differ from individual to individual and therefore could be important in explaining differences in disease responses For example, in fact, in a study published in Cellular Genomics, we detected new regions that differ between individuals and are potentially important in the response to influenza infection. This is just the tip of the iceberg in terms of confirming that things are actually happening in these new regions of the genome.”
The full consequences of the reference to the pangenome remain unclear.
Some of the benefits of this new pangenome reference have already been demonstrated. But the full implications of this new genetic reference tool have yet to be determined, as scientists can now study regions of the human genome that they couldn’t before. Understanding its potential role and its consequences will be the work of hundreds of groups for years to come. A major challenge is that many genomic methods currently rely on a linear reference genome, they will need to be adapted to use a pangenome instead.
The use of the pangenome will also be important in the context of McGill University’s new D2R programme, which aims to mobilize the university’s research expertise to advance, in an inclusive manner, the development of the next generation of RNA drugs for infections. viral, cancer, and rare diseases.
https://www.sciencedaily.com/releases/2023/06/230605181322.htm
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