Pangenome has emerged as a powerful frontier in the field of genomics, providing insights that are vital for understanding genetic diversity and functions across various species. Traditionally, when studying a species' genome, researchers relied on a single reference genome to represent the species. However, as sequencing technologies advanced, scientists began uncovering significant genetic variations across individuals within the same species. This led to the realization that no single genome can capture the entire genetic diversity of a species.
What is a pangenome?
A pangenome is the full complement of genes within a species, encompassing the core genome (genes present in all individuals of the species) and the accessory genome (genes that vary between individuals, including those arising from horizontal gene transfer, structural variations or environmental adaptations). By studying pangenomes, researchers can better understand genetic diversity, uncover novel genes and identify associations between genotypes and phenotypes.
For microbial species, pangenomes reveal the genetic repertoire enabling adaptation to different environments, while in humans, pangenomes shed light on the intricate variations that influence health, disease susceptibility and evolution.
Applications where pangenome can provide more insights
1. Comparative genomics: Pangenome analysis allows researchers to compare genomes across multiple individuals or species. For example, in microbial genomics, it helps identify genes responsible for antibiotic resistance, pathogenicity or environmental adaptation. Understanding accessory genes can guide drug development or vaccine design.
2. Evolutionary insights: By analysing core and accessory genomes, scientists can trace evolutionary relationships and population dynamics. Pangenome analysis reveals how species adapt to changing environments, shedding light on processes like gene duplication, horizontal gene transfer and natural selection.
3. Crop improvement: In agriculture, pangenomes are used to identify genetic variations associated with desirable traits, such as disease resistance, drought tolerance or higher yields. For example, the rice pangenome has enabled breeders to develop varieties suited to specific environmental conditions.
4. Structural variation analysis: Traditional genomic analyses often miss large structural variations (SVs), such as insertions, deletions or inversions. Pangenome analysis captures these SVs, providing a more complete understanding of genetic diversity and its functional impact.
5. Functional genomics: Pangenomes can guide functional studies by identifying novel genes or regulatory elements. This approach has been critical in characterising the accessory genome of bacteria to understand pathogenicity mechanisms.
6. Metagenomics and microbiome studies: In metagenomics, pangenomes help deconvolute complex microbial communities, enabling researchers to study interactions between microorganisms and their hosts.
Breakthroughs and technical solutions
The Human Pangenome Reference Consortium
The Human Pangenome Reference Consortium (HPRC) is an ambitious global effort, launched in 2022, to capture the full range of genetic diversity across human populations. For decades, scientists have relied on a single-reference genome, GRCh38, to represent humanity. While groundbreaking, this reference genome is based on the DNA of one person, meaning it cannot reflect the variations found in different populations. This limits our understanding of human genetics and the development of personalised healthcare.
The HPRC aims to address this gap by sequencing and assembling the genomes of individuals from diverse ancestries. This work creates a pangenome that includes not just the common genetic sequences shared by all humans but also the unique differences specific to individuals or populations. For example, early results showed that around 10% of new genetic sequences discovered in the pangenome are specific to people of African descent, highlighting how much genetic diversity was missed before.
Google AI
One of the key players in advancing the HPRC is Google AI. Google's cutting-edge artificial intelligence tools are speeding up the project and making it more efficient. Here’s how:
1. Faster and better genome assembly: Google's AI systems helped scientists piece together DNA data more quickly and accurately than traditional methods. By using machine learning models, the process of building complete, high-quality genomes was both faster and more reliable.
2. Finding hidden genetic differences: AI tools from Google are especially good at detecting genetic differences that are harder to spot, like large insertions or deletions of DNA. These differences can have a big impact on traits, diseases and how people respond to treatments.
3. A smarter way to study genomes: Instead of using a single genome as a reference, the HPRC uses graph-based genomes—a way of representing multiple genomes together. Google AI provided tools to help scientists analyse these complex networks of genetic data, making it easier to compare genomes and find patterns.
4. Handling huge amounts of data: The HPRC generates massive amounts of DNA data that need to be stored and analysed. Google’s cloud technology and AI systems ensure this data is processed efficiently and securely, allowing researchers around the world to collaborate seamlessly.
5. Promoting diversity in genomics: Google AI is helping the project focus on genetic diversity. Its tools can identify genetic differences unique to certain populations, ensuring the pangenome reflects the full variety of human life.
Thanks to Google AI’s support, the Human Pangenome Project is breaking new ground in understanding human genetics. It is creating a resource that will help develop personalised treatments and improve healthcare for everyone, no matter where they come from. This work not only makes science more inclusive but also moves us closer to a future where medicine is tailored to the unique needs of every individual.
NVIDIA Parabricks
Another powerful tool accelerating pangenome analysis is NVIDIA Parabricks. Built on GPU-accelerated computing, Parabricks dramatically speeds up genomic data processing—reducing tasks that once took days to just hours or even minutes. This is especially useful in large-scale projects like the Human Pangenome Project, where thousands of genomes need to be analysed.
Parabricks helps researchers assemble genomes faster, detect genetic variations more efficiently, and handle complex datasets with high accuracy—all while reducing computational costs and time.
1. Ultra-fast genome processing: Accelerates tasks like read alignment, variant calling and base recalibration by up to 30x–50x using GPU power
2. Efficient structural variant detection: Speeds up detection of large-scale variations crucial to pangenome analysis
3. Scalability for large datasets: Ideal for processing hundreds or thousands of genomes simultaneously—critical for building pangenomes
4. Integration with common pipelines: Compatible with GATK, DeepVariant and other industry-standard tools, ensuring smooth adoption
5. Reduced computational costs: Minimises time and energy consumption, making large-scale pangenome projects more sustainable and cost-effective
6. High accuracy with speed: Maintains equivalent or better accuracy compared to CPU-based workflows while cutting runtime drastically
Cognizant’s edge
At Cognizant, we bring a unique edge to pangenome analysis through hands-on experience with real-world applications. We recently supported a client project focused on vaccine development, leveraging advanced bioinformatics tools. Our expertise lies in integrating robust workflows with a deep understanding of biological data, enabling targeted insights without compromising data confidentiality. This makes us deliver impactful, research-driven solutions in the evolving field of pangenomics.
Conclusion
Pangenome analysis is redefining the way we understand genetic diversity, moving beyond the limitations of single-reference genomes. With applications spanning human health, agriculture and microbial genomics, it has become a cornerstone of modern bioinformatics. Industry trends, such as graph-based genomes and third-generation sequencing, are driving innovation in the field, while AI integration promises to unlock even greater potential. As the field evolves, ethical considerations and equitable access to genomic data will remain paramount, ensuring that the benefits of pangenome research are shared across global populations.
