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Product, Agrigenomics, Complex Disease Genomics, Microbial Genomics

Making a Difference in the World Through Genomics

Illumina Applied Genomics business focuses on areas where the biggest impact is possible

Making a Difference in the World Through Genomics
08 September 2016

“The limit of what’s possible with next-generation sequencing (NGS) and our genotyping technologies is the creativity of our customers to bring the future into existence,” said Rob Brainin, Vice President and General Manager of the Applied Genomics business at Illumina. The business unit develops products that harness the strengths of Illumina sequencing and microarray technologies in ways that make an impact. It currently focuses on microbiology, agrigenomics, forensics, transplant diagnostics and HLA typing, complex disease, consumer, and education and awareness around whole-genome sequencing. We caught up with Rob Brainin to understand how his group identifies opportunities and builds new markets.

What do you see as your biggest area of opportunity?

We have so many great opportunities that it is hard to pick just one. Right now, I’m excited about the potential applications in microbiology. The opportunity set within that is so diverse, and there are so many facets that are interesting from a market development perspective. The human microbiome, for example, is emerging as critical to our health. Beyond microbes’ role in making us sick, there is research being done to understand the interaction between microbes and our health in areas ranging from obesity to cancer, to complex diseases like Parkinson’s and Alzheimer’s.

Environmental metagenomics is another large area. NGS can be used to study all the organisms and their abundance in a given environment or sample. This offers tremendous opportunities in areas like environmental ecology, water quality, and even bioterrorism. There are more clinical applications of NGS in microbiology including infectious disease, pathogen identification, and areas like public health/outbreak monitoring.

And there’s a significant opportunity as well in food science and safety. Microbes in the soil can influence crop yields and potentially even the flavor of many foods.  Yet at the same time, other microbes can be sources of contamination.   

Speaking of food, what do you see as drivers of growth in the agrigenomics business?

It’s going to take a lot of food to feed a global population of 9 billion people by 2050, especially considering how urbanization, development, and global warming will affect how and where we grow crops and graze livestock. We see a large market opportunity in agrigenomics where Illumina technologies can play an important role in solving global food challenges. We hope to grow the market to have every high value animal such as cows and even pigs genetically tested at birth. Similarly, we would love to see seed companies using genomics across all their crops. We’re investing heavily in this market to deliver solutions that meet the needs of these customers. Our new Infinium® XT microarray solution is an example—the higher throughput, lower density BeadChips were developed because our customers told us they had a need for this type of a product.

What movement are you seeing towards the adoption of Illumina solutions for forensic genomics and what barriers are you trying to overcome?

We find that the forensics community is very excited for the potential of using NGS in their work. This is a group of dedicated criminal justice professionals who want nothing more than access to technology that can help solve the cases that can’t be solved today. That said, formal accreditation by the National DNA Index System (NDIS) and similar governance bodies around the world is needed to drive broader acceptance of this new technology. 

What about Complex Disease research? What is it and what is going on in that market?

We think of complex diseases as diseases where there are many genes believed to be involved, or a complex interplay of genetics and other factors like environment and lifestyle. Cardiovascular disease, neurodegenerative disease, and autoimmune disease are examples. This is an area where there is interesting research happening using both sequencing and arrays. We’ve developed several array products including the PsychArray, Immunoarray, and Global Screening Array, which will have a lasting impact on the field by enabling large genome-wide association studies (GWAS) to occur. But we found that researchers in this field are increasingly using single-cell analysis to try to understand as much as they can about disease genetics and processes. Earlier this year we announced partnerships with Bio-Rad Laboratories Inc. and FlowJo, LLC, to co-develop a new product for isolating and barcoding single cells and enable researchers with software that wraps around our technologies.

What about consumer applications?

Consumers are becoming increasingly savvy about genomics as the mainstream media continues to report on applications and opportunities. This awareness is making people more curious about the contents of their own DNA and the DNA around them. We’re continuing to see great demand for our array products from customers like 23andMe and Ancestry, whose customers are interested in learning about their genetic traits and biogeographical ancestry. Consumers are also showing an interest in other research projects using Illumina technology, like the American Gut Project, which is using sequencing to map and study the diversity of gut microbiota from samples sent in by consumers.

It’s been about a year and a half since you launched the TruSight® HLA Sequencing Panel. How is the product doing and what’s next for that market?

The human leukocyte antigen (HLA) system is so important to so many aspects of our health and the body’s ability to mount an immune response. We’ve seen tremendous adoption of TruSight HLA because our customers are finding that NGS is a critical tool for understanding this difficult-to-study region of the genome. In the future, NGS-based products could be routinely used in transplant diagnostics. As a technology, NGS is ideally suited not only for HLA typing to help determine whether an organ, tissue, or bone marrow donor is matched with a recipient, but also for post-transplant monitoring, which often today is done by doing a punch biopsy into the transplanted organ.  NGS can detect DNA in a recipient’s blood stream and distinguish between DNA from the donor and recipient. In this scenario, a higher concentration of DNA from the donor could signal to the clinical team that the recipient’s body is rejecting the organ. A much less invasive way to do this test, but it will require demonstration of clinical utility for uptake to occur in the market.

Tell me about the Understand Your Genome® program. In the four years you’ve been doing it, what’s been the impact and how has it evolved?

Understand Your Genome is a special program for us. It’s about transforming the perception of genomics among physicians, thought leaders, and those poised to implement genomics in clinical settings. We do that through an experiential education model that fosters cross-disciplinary conversations about genomic medicine. Participants go through the process of having physician-mediated genome sequencing, they get genetic counseling, they learn from thought leaders in the field who have seen the benefits of genomics in clinical settings, they interact with their peers, and ultimately, they get to explore their genomes using the MyGenome App on an iPad. 

We’ve grown the program over the last few years, and we’ve instituted a sponsorship program for partners. The partners have helped us expand the reach of the program. By doing that, we’ve become the leading source of clinically interpreted personal genomes. This has enabled us to learn a lot and we are beginning to publish on interesting aspects of clinical genomics, such as informed consent and return of results, clinical findings, and engagement in a healthy population with whole-genome sequencing.  Along these lines, we recently piloted a demonstration project with the San Diego Blood Bank to expand our work on community engagement in genomics research. This work has also opened doors to make us part of conversations about national and large-scale programs (White House Precision Medicine Initiative, Genomics England, etc.).

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