Future of Next Generation Sequencing for life sciences 2021
Merogenomics had the pleasure to be invited by Group Futurista to cover their virtual summit on the future of Next Generation Sequencing (NGS) as a media partner. Group Futurista organizes events dedicated to futuristic trends shaping the world; and the trends in Next Generation Sequencing technologies are just one of the many topics they promote.
We gladly jumped on the opportunity because conferences are always a fun window into seeing current developments in a given field. These are driven by many factors: the curiosity to solve difficult problems; the changing popularity of certain topics; the accumulation of past discoveries into new ideas or by the latest existential need, such as in response to the current pandemic. The Next Generation Sequencing field is moving very rapidly - so rapidly, in fact, that what technology can actually deliver versus what is available for current medical treatment to patients seems “light years away” and so we will try to give you some good examples in this post. Altogether the biggest question of the day was, where are we in terms of clinical utility of these powerful technologies? The collective consensus of the presenters was that despite massive advances, this technology is still far out of reach of every-day doctors, and nowhere near the norm for standard clinical use. There are many contributing factors to that end, an all-important one being the prohibitive costs.
In the meantime, technology is not waiting for clinical practice to adjust itself to what is already available to doctors - the research is always continuously evolving to deliver ever increasing benefits.
One exciting new benefit, never realized before, is use of genome sequencing to monitor in great detail the evolution of the SARS-CoV-2 virus as millions of virus samples throughout the entire world have been sequenced to be able to track how the SARS-CoV-2 virus is constantly mutating, and what variants are becoming prevalent around the world. This is why we have such a good understanding of so many different variants.
Not surprising, COVID-19 and virus genome sequencing took center stage at this summit, and was the opening talk of the day.
The opening talk was by Dr. Michael Oberholzer, an associate director for product management at Illumnia, the largest provider of sequencing machines in the world. Dr. Oberholzer reminded us that Next Generation Sequencing played centre role in this pandemic from the start, with the SARS-CoV-2 genome sequence becoming nearly instantly available since the first identification of an outbreak in China in December 2019. As mentioned, not only has it been used to track the emergence of new variants ever since, the technology has also been used to probe patients for an enhanced understanding of the genetic predisposition to COVID-19 disease, and even tracking of co-infecting pathogens.
Often being the leader in the industry, Illumina developed a diagnostic test for SARS-CoV-2. Taking advantage of the power of sequencing being able to decode many different pathogen species at a same time, the test is also designed to obtain genetic sequence of a broad array of respiratory pathogens. According to some data, up to a fifth of COVID-19 patients have co-infections. The test is called COVIDSeq (what else?) With such detailed information captured, the test can also be used for wide surveillance of pathogen outbreaks around the world. This will be especially important due to “immune vacuum”, unusual time period where we were not building as adequate immune protection as usual, which has led to spikes in pediatric RSV outbreaks and is expected to result in a strong influenza season.
One strong theme of the day was that cancer pathologists are about to be armed with exceedingly powerful tools to analyze the samples that are studied under their microscopes with additional powerful molecular information. Pathology analysis towards diagnosis will continue to grow in importance. No other medical field appears to attract more attention from genomics advancing technologies than cancer.
For example, Dr. Pranil Chandra, a chief medical officer and vice president of PathGroup, discussed the company’s comprehensive tools for simultaneous anatomical and molecular analysis that enhance the diagnostic powers of cancer biopsies. As part of the total biopsy data collected is sequencing of more than 500 different genes involved in cancer, a genetic test that aims to aid in cancer therapy selection. This test called PGDx elio Tissue Complete, would not be first of its kind tests on the market, but it is great that the repertoire of options is growing, as this indicates expanding expertise in screening cancer biopsies for the best potential treatments.
Dr. Koen De Gelas, a science and tech advisor at 10x Genomics company was the first one of the day to breach the topic of single cell genomics. Another company that is also a leader in single cell genomics, Mission Bio, was highlighted by Dr. Yue Wang. As we will see right away, single cell genomics allows probing the genetics of individual cell lineages within samples, gaining insight of the individual use of the genes of every single cell in the tissue. You can then correlate how different types of cells use genes encoded by the DNA differently. This is referred to as gene expression. You can map these gene expression relationships like some stars in a constellation. The closer the stars to each other in a constellation, the closer the relationship between cells and what genes they used. The further the stars are apart in this constellation, the more unrelated the pattern of genetic behaviour between these cell types.
Likewise, you can map comparisons between genetic mutations within tissues, which can be especially valuable in cancer. Currently with a tissue such as cancer biopsy, we get genetic sequences of everything that makes up the selected slice of the biopsy for DNA isolation. But that can actually include many cell types not related to cancer plus within cancer itself there can be a population of different cells with different mutations. In the end, you obtain very powerful genetic information, but still, it is a complicated mixture of signals. As Dr. Wang pointed out, the danger is that clinically relevant insights can be lost in averages.
But now when the technology allows us to probe individual cells molecularly, more intricate details emerge that enhance our understanding, and ability to respond. You can probe for specific genetic information of interest in every individual cell that is captured in a tissue. Not surprisingly, there are cancer panels available which probe for this information in pre-selected genes!
But it is the next tech that Dr. De Gelas talked about that was really cool, especially for pathologists. In essence the single cell technology can be applied to the same cancer biopsy slices that are stained for biological interpretation by pathologists. This field is permeated by powerful imaging technologies already, and having the ability to combine this information with how different cancer mutations show up in different cell lines is so amazingly futuristic. A field that is decades old is augmented with latest tech.
It is not just the ever-increasing ability to identify how complicated the cancer genetics can be that is moving forward. So is the technology that sorts and interprets the data for best treatment recommendations, which is more and more frequently powered by artificial intelligence.
Dr. Razelle Kurzrock, a co-founder and chief medical advisor of CureMatch, discussed the company’s artificial intelligence modality that helps select an ideal therapy based on the molecular data of numerous molecular tests for cancer patients. In other words, the program helps to select a closely personalized therapy. CureMatch aims to be the optimal treatment match. This is important that such sophisticated options are becoming available, as ironically the sudden explosion of this massive amount of patients’ data being available has paralyzed doctors to some degree from knowing exactly how to best to use the overwhelming amount of information properly. The hope is that emerging technologies like these will continue the adoption of life-saving technologies for cancer patients. After all, Dr. Kurzrock reminded us, that only 2% of patients are currently receiving targeted therapies. CureMatch can even select for drug combinations for up to three medications - best matched to abnormalities found in a patient’s tumour landscape. This is rapid movement in the field of cancer medicine. The ideal use for such technologies would be in hospitals so every oncologist should be peeking into this direction as it is worth looking at where the trends are heading when they are this powerful. Personalized medicine is becoming more real every day.
Dr. Daria Salyakina, a director of personalized medicine research at Nicklaus Children’s Hospital gave the first talk dedicated to the clinical outcomes of genomic testing. Specifically, it referred to the use of genome testing to help diagnose children with rare diseases that could not otherwise be diagnosed with other available tools. In essence we are referring to undiagnosed patients. It is very satisfying what great success they are having with that program. Of the approximate 3% of babies with a disease that could not be identified, the use of genome sequencing offered faster diagnosis, averaging 3-14 days, thus shortening the diagnostic time span by approximately 5 months in comparison to patients without genomic analysis! On top of that, the diagnosis was obtained for nearly half of tested patients, and even more importantly, of those, ~44% benefited from a personalized change in management. The most common benefits are: access to additional tests, reaching the appropriate specialists, adjustment in medication use, or finding a therapy for a metabolic condition.
But what was especially valuable from Dr. Salyakina’s talk, was that a cost analysis was also performed. These are always just mind blowing to see, especially since the disparity between the financial gains of whole genome sequencing use versus not using it, is growing. The average cost of a patient who underwent full genome sequencing for an undiagnosed condition was just over $11,000. But that paled in comparison to the cost for the other children who did not undergo genomics testing. The average cost of care exceeded $111,000, so another $100,000 per child! That amounted to several millions in savings in yearly healthcare costs from just that single Nicklaus Children Hospital alone!
It is such real-life examples that we need to help increase the awareness of the incredible value of medical genomics, which importantly includes helping with the overall economics of healthcare. The higher initial cost of the genome test is worth it to help reduce much greater total costs otherwise spread over a long period of time, as the patients go through a complicated, lengthy investigation process to figure out what is wrong with them on their diagnostic odyssey. This process can be very draining and overwhelming for affected family.
Srinivas Sashidhar, head of the clinical research services at myOnsite Healthcare, discussed the clinical studies landscape. myOnsite Healthcare aids in onboarding Next Generation Sequencing clinical trials. They observed that the use of their system not only helps doctors increase patient participation in clinical trials, but also increases patient retention. Clinical trials around sequencing technologies are definitely of high interest, but not without their challenges. Properly stratifying patients remains one of the biggest. Limited infrastructure access, high costs and establishing valid payors for tests are some of the others. But progress is definitely being made.
Advances in tech
Many talks were dedicated to advances in existing technologies that help improve the quality of data obtained through Next Generation Sequencing. Many of these relate to enhancing the purity of sample.
Martin Pieprzyk, the CEO of LevitasBio, demoed another cool technology - the selection of specific cell types within a population of cells. Cells are sorted in a sample, by applying a magnetic field where cells of different types react differently to the applied magnetic field, and thus migrate according to a specific strength of magnetic field. It is one easy way to select live and viable cells from all of the dead ones in the sample. It appears that cleaning up a sample from such debris improves the quality of subsequent molecular information such as genetic sequencing. And the system looked like it could handle any cell type!
Dr. Lewis Marshall, vice president of R&D at Purigen Biosystems showed how the company’s tech can be utilized to purify genetic material away from any cellular debris through segregation of cellular material responding to an electrical current. Since all biological material has a certain electric charge, the electric current segregates different biological material based on that charge. The result is a cleaner quality of genetic material for subsequent sequencing with higher yield, increasing the quality of captured data.
Advances have also been made in determining the quality of what genetic information is captured specifically for downstream analysis.
Bellal Moghis, a director of NGS product marketing of Agilent Technologies provided a window into enhanced ways of capturing information of interest out of a human genome sample. Agilent has been going at it for a while so they are one of the industry leaders, with everyone in the genomic world familiar with their capture systems called Sure Select. But what made the discussion of the latest improvement of that system interesting, is its improved design was developed through artificial intelligence. AI helped to streamline how the genomic fragments of interest are being captured. These capture methods are specific to an area of interest, and once again, cancer specific kits are available to probe cancer genes to help with therapy selection. Oncologists seriously are gaining options rapidly!
Dr. Pedro Echave, NGS products expert at PerkinElmer, discussed an additional way of how the RNA of cells can be analyzed, with a specific focus on overcoming the challenges of the isolation of short length RNA fragments to more accurately represent their realistic abundance inside cells. RNA not only plays a role as a blueprint to produce proteins (mRNA) but can also play many regulatory effects, and much of that influence still awaits to be fully deciphered. Dr. Echave also discussed the first kit to allow simultaneous isolation and identification of both the transcriptome RNA (again, this refers to mRNA used to produce proteins) and also the shorter regulatory RNAs. Previously you would have to perform two independent experiments to get to all of that information.
The final theme was the continuous enhancement of the technology that allows for full automation in handing samples, while fully preparing them for sequencing without any need of human interaction. With this type of tech available, human interaction time would be shaved to a mere few minutes while currently, sample preparation for any large scale genetic sequencing is very human labour intensive.
Dr. Chaithanya Ponnaluri, a development scientist at New England Biolabs introduced a new way of analysing how DNA is epigenetically manipulated. He discussed a completely new enzymatic method to detect where the DNA was methylated (the epigenetic change). Data suggest this novel tactic is outperforming the standard approach in probing epigenetics. Epigenetics is a fast growing and still emerging field, so new sequencing technology is definitely welcome.
Dr. James Cooley, senior marketing manager at HTG Molecular Diagnostics, introduced new technology to analyze what type of RNA is produced by the cells, as an alternative to currently employed RNA sequencing methods. Specifically, this technology uses capture probes of DNA that display a complimentary sequence of interest that ends up binding to the RNA. But these probes are chemically modified so that in a subsequent step, destructive enzymes remove all of the genetic material except those probes bound to the RNA. It is these tiny surviving fragments that are then decoded for sequence, allowing identification of what RNA was produced in a given biological sample. In a way, this looks like genotyping your RNA (probing for very specific mutations of interest inside someone’s genetic material).
Last addition to this list is Dr. Jo Vandesompele, a professor at Ghent University who discussed how liquid biopsy mRNA can be probed for novel biomarkers. Liquid biopsy is all an encompassing term for analyzing molecules floating in the blood - a very powerful tool that allows for live monitoring of early warning signals. Identifying cancer specific mutations in genetic material floating in the blood is one such option already being used. Most frequently liquid biopsy is used in reference to analysis of DNA fragments floating freely, directly in the blood. But much investigation into RNA has also been published. So the concept of an RNA liquid biopsy is certainly not new though its emergence as a legitimate quality option for helping correlate RNA biomarker to health outcomes is refreshing. In essence, we are talking about discovering what our body says to its cells from a given RNA content in the blood.
Dr. Vandesompele presented a validated workflow of successful RNA sequencing of extracellular RNA (or cell free RNA, a term more frequently used in a DNA liquid biopsy). The technique demonstrates that different biofluids can range a thousand-fold in the amount of RNA, so these are vast differences. It not only varies by amount; it also varies dramatically by content. Some biofluids just have so much more to say than others. Like tears for example. Of all the biofluids, tears rank near the top for how many different mRNAs are represented. With over thirteen thousand different mRNAs, it is a whole book! You don’t want to know what ranked top. Or maybe you do?
The emergence of health information due to the ability to decode human genetic content is only the tip of the iceberg. On top of that we still have to enhance our awareness of the complex interplay of epigenetics, transcriptomics plus the microbial world’s metagenomics and how it influences the use of the human genome by human cells within our body (remember, you have fewer human cells in your body than non-human cells). And how does this complex relationship influence our health? These are still emerging studies that will eventually transform medicine in their own right, similar to the way genomics already has. We are still deciphering new layers of complexity.
Long read sequencing
Dr. Fritz Sedlazeck, an associate professor at Baylor College of Medicine brought another angle at looking at the future of genomics - that is grasping a greater appreciation of structural variants in the human population. Specifically, he discussed observed the structural variation in Han Chinese, the largest ethnicity in the world, using long read sequencing technology. This is another advanced technology that allows analysis of genomic code for very long stretches of DNA or RNA. It has been around for a while and its powerful advantages long-time appreciated. Reducing costs however, allow its more frequent use now. The human genome has finally been fully decoded only just recently, thanks to use of such long read sequencing technologies.
The power of decoding long reads was in fact nicely demonstrated in this scenario where sections of genome were identified that previously were not even thought to be a part of human genome at all. Similar sequences had only been observed in other Hominidae lineages. This demonstrates how diverse and heterogenous the human genome might be, which can potentially even vary substantially in size between different ethnicities. We might not be able to get away with one single reference template when analyzing all of the human genomes in the world. Human species have lived long enough in isolated pockets to allow a specific signature of variation to be imprinted on their genomes by random mutations throughout time. Currently we are only starting to assemble ethnicity specific reference genomes, but the trend is definitely growing. Long read sequencing technologies are absolutely essential for this process to capture the most accurate view of the genomic code. And we also have a growing appreciation of the use of this technology to uncover structural variants of medical importance as well.
Overall, the entire conference was cleverly designed to showcase the advances in Next Generation Sequencing from many different angles and appeared to be an appropriate representation of the current tangents driving the future of NGS. One area that might not have been represented but should commence being investigated carefully is the emergence of genetic manipulation of our species. There are many exciting areas of development in this field as well, while also needing to discuss the potential risks of certain technologies. But this was a pretty good snapshot and the future of sequencing technology definitely continues to bring more exciting revelations within not only our own world of biology, but also the world around us.
This article has been produced by Merogenomics Inc. and edited by Jason Chouinard, B.Sc. Reproduction and reuse of any portion of this content requires Merogenomics Inc. permission and source acknowledgment. It is your responsibility to obtain additional permissions from the third party owners that might be cited by Merogenomics Inc. Merogenomics Inc. disclaims any responsibility for any use you make of content owned by third parties without their permission.
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