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Next-generation genomics

Next Generation Genomics

Next Generation Genomics

 

The science of genomics is at the beginning of a new era of innovation. The rapidly declining cost of gene sequencing is making huge amounts of genetic data available, and the full power of information technology is being applied to vastly speed up the process of analyzing these data to discover how genes determine traits or mutate to cause disease. Armed with this information, scientists and companies are developing new techniques to directly write DNA and insert it into cells, building custom organisms and developing new drugs to treat cancer and other diseases. Over the coming decade, next-generation genomics technology could power rapid acceleration in the field of biology and further alter health care. Desktop gene-sequencing machines are not far off, potentially making gene sequencing part of every doctor’s diagnostic routine.
Longer term, these advances could lead to radical new possibilities, including fully tailoring or enhancing organisms (including humans) by precisely manipulating genes. This could lead to novel disease treatments and new types of genetically engineered products (such as genetically engineered biofuels), while enabling the nascent field of synthetic biology—designing DNA from scratch to produce desired traits.

The potential economic impact of next-generation gene sequencing in the applications that we have sized in health care, agriculture, and the production of substances such as biofuels could be $700 billion to $1.6 trillion a year by 2025. About 80 percent of this potential value would be realized through extending and enhancing lives through faster disease detection, more precise diagnoses, new drugs, and more tailored disease treatments (customized both to the patient and to the disease). In agriculture, analyzing plant genomes could lead to more advanced genetically modified (GM) crops and further optimize the process of farming by tailoring growing conditions and farming processes to a seed’s genetic characteristics. Furthermore, it may be possible to create high-value substances such as biofuels by modifying simple organisms such as E. coli bacteria. Easy access to gene-sequencing machines could not only put powerful genetic technology in the hands of researchers and physicians, but could also create a global community of co-creators that might advance biotechnology in unforeseeable ways, as hobbyists propelled the microcomputer revolution.
The technical challenges inherent in next-wave genetic engineering technology are great but may be less formidable than the social, ethical, and regulatory concerns it may generate. While this technology has the potential to create huge benefits for society, it comes with an equally impressive set of risks. Genetically modified organisms could interfere with natural ecosystems, with potentially disastrous results including loss of species and habitats. Genomic technology
raises privacy and security concerns related to the potential theft or misuse of personal genetic information stored on computers. And while the potential for widespread access to sequencing and, eventually, DNA synthesis technology will create opportunities for innovators, it also raises the specter of bioterrorism.Moreover, this technology could well unfold in a regulatory vacuum: governments have yet to address major questions concerning who should own genetic
information, what it can be used for, and who should have access to next generation
genomic capabilities.

DEFINITION

Next-generation genomics can be described as the combination of next-generation sequencing technologies, big data analytics, and technologies with the ability to modify organisms, which include both recombinant techniques and DNA synthesis (that is, synthetic biology). Next-generation sequencing represents newer, lower-cost methods for sequencing—or decoding—DNA. It encompasses the second- and third-generation sequencing systems now coming into widespread use, both of which can sequence many different parts of a genome in parallel.

The rate of improvement in gene-sequencing technology over the past decade has been astonishing. When the first human genome was sequenced in 2003, it cost nearly $3 billion and took 13 years of work by teams of scientists from all over the world collaborating on the Human Genome Project. Now a $1,000 sequencing machine could soon be available that will be able to sequence a human genome in a few hours. In fact, over the past decade, the rate of improvement in sequencing speed has exceeded Moore’s law, the famously fast rate of performance improvement achieved by computer processors. This improvement in performance has been achieved by creating highly parallel systems that can sequence millions of DNA base pairs in a very short time. As the DNA is read, the process generates massive data, which are passed on to powerful computers for decoding. Thus, progress in genomics and computing speed are evolving in tandem—a development that has been referred to as “wet” science meeting “dry” science.

This advance in DNA sequencing speed (along with simultaneous reductions in cost) promises to accelerate the process of biological discovery. Historically, biological research has relied largely on hypothesis-driven, trial-and-error testing. This approach is very time-consuming and difficult, so scientists’ understanding of which genes drive specific outcomes (such as diseases) remains very limited. With growing access to large samples of fully sequenced genomes, researchers can employ more broad-based methods, performing correlation analysis on big data sets of sequenced genomes together with patient data, and testing combinations of genes, diseases, and organism characteristics to determine which genes drive which outcomes. These big data experiments can include data on genealogy, clinical studies, and any other statistics that could help link genotype (DNA) to phenotype (organism characteristics or behavior). Armed with this information, it could be possible to better identify and diagnose people at high risk for conditions such as heart disease or diabetes, allowing earlier, more effective intervention.

Next-generation sequencing also makes personalized medicine possible. Individual patients possess unique genomes and can be affected differently by the same disease or therapy. The ability to genetically sequence all patients, along with the viruses, bacteria, and cancers that affect them, can allow for better matching of therapy to the patient. Sequencing can also help physicians understand whether a set of symptoms currently treated as a single disease is, in fact, caused by multiple factors.

Advanced genomics will also facilitate advances in agriculture. Farmers might be better able to optimize soil types, watering schedules, crop rotations, and other growing conditions based on a more complete understanding of crop genomes. It may also be possible to produce genetically modified crops that can grow in locations where soil conditions and access to water cannot be easily improved; crops that can thrive in colder, drier climates; or crops that generate a larger portion of their weight as food. Crops might also be modified to serve as better raw materials for the production of biofuels. Modified animals in our food supply might also be on the horizon. For example, one US company is seeking approval for an Atlantic salmon modified with an eel gene that enables it to reach maturity in half the normal time.

Finally, next-generation genomic technology could be used to modify the DNA of common organisms to produce valuable substances. Using synthetic biology or even standard, well-established recombinant techniques, the metabolic systems of certain organisms can be modified to produce specific substances, potentially including fuels, pharmaceuticals, and chemicals for cosmetics.

POTENTIAL FOR ACCELERATION

Next-generation genomics has the potential to give humans far greater power over biology, allowing us to cure diseases or customize organisms to help meet the world’s need for food, fuel, and medicine. With world population heading toward eight billion in 2025, there is a growing need for more efficient ways to provide fuel for heat, electricity generation, and transportation; to feed people; and to cure their ailments. Meanwhile, populations are aging in advanced economies. By 2025 approximately 15 percent of the world’s population will be 60 years of age or older, multiplying health-care challenges.

Next-generation genomics can address these needs. The falling cost of genome-sequencing technology will accelerate both knowledge and applications. In genomics, the relevant unit of performance measurement is the time and cost per sequenced base pair (the basic units of DNA). With newer generations of sequencing technology, the cost of sequencing a full human genome has fallen to around $5,000, but the $1,000 genome is widely expected to be achieved within the next few years. Counsyl, a Silicon Valley company, already offers a $600 genetic test that can screen children for more than 400 mutations and 100 genetic disorders.

Cancer is a genetic disease that is caused when mutated cells grow out of control. Sequencing is already being used to tailor treatments that are customized to the genome of the patient and the mutated genome of the tumor. Studies have shown how specific cancer-causing mutations correlate with responses to different cancer treatments and there is a healthy pipeline of bio treatment and diagnostic drugs. However, given the rate at which drugs fail during testing, it is not likely that the number of drugs used with companion diagnostics over the next five years will rise rapidly.

Oncology remains at the forefront of genetic research and development in medicine, but applications for other types of diseases are on the radar. Researchers are also focusing on mutation-based links to widespread diseases such as cardiovascular disease to identify how different genomes correspond to different responses to therapies.

GM crops are playing an increasingly important role in improving agriculture in developing economies. The total area planted in GM crops has risen from 1.7 million hectares in 1996 to more than 170 million hectares in 2012, and for the first time farmers in developing economies planted more hectares of GM crops than did farmers in advanced countries. Planting of GM crops grew 11 percent in developing economies in 2012, more than three times the rate of such planting in advanced economies. Next-generation genomics could enable the creation of even more advanced varieties with even greater potential value.

Synthetic biology is still in a very early stage of development, but could become a source of growth. If the process can be perfected, modifying organisms could become as simple as writing computer code. While the technology is new, there is already evidence for applications in science and business. For example, a research team at Ginko Bioworks in Boston is working on developing the biological equivalent of a high-level programming language with the goal of enabling large-scale production of synthetically engineered organisms.

Companies are beginning to invest in synthetic biology capabilities. Joule Unlimited and Algenol Biofuels, for example, have created demonstration plants that can produce high-value substances using synthetically engineered organisms—diesel fuel in the case of Joule Unlimited and ethanol at Algenol. However, synthetic biology remains challenging, with high up-front capital investments required and difficulties in economically scaling production.

ECONOMIC IMPACT

In the applications we assessed, we estimate that next-generation genomics have a potential economic impact of $700 billion to $1.6 trillion per year by 2025. We estimate the impact of disease prevention and treatment applications that we size could be $500 billion to $1.2 trillion per year in 2025, based on extended life expectancy stemming from better and faster disease diagnosis and more tailored treatments (Exhibit 9). In particular, new technology has the potential to improve treatment of genetically linked diseases such as cancer and cardiovascular diseases, which currently kill around 26 million patients per year.

Some 14 million new cases of life-threatening cancers can be expected to be diagnosed worldwide in 2025. Determining how many of these patients could have longer lives or better quality of life due to more effective treatment based on next-generation genomics is not straightforward. Most cancers still may not be curable even after sequencing identifies the genetic mutations that trigger disease. For some cancers, however, the process of identifying the mutations involved and then developing targeted therapy is moving ahead. For example, Herceptin, a breast cancer drug, acts only on tumors that contain cancer cells that, because of a gene mutation, make more of the HER2 tumor-creating protein than normal cells. Studies have shown that Herceptin can decrease fatalities by, for example, reducing the risk of recurring tumors. Some industry leaders believe that eventually most types of cancer could be treated with targeted therapies based on next-generation genetic sequencing.

Published in partnership with McKinsey & Company

To estimate the potential economic impact of these improved diagnostic and tailored treatment methods, we estimate the value to the patient of the extended life that might result. Based on the assessment of cancer experts, we estimate that genomic-based diagnoses and treatments can extend lives of cancer patients by six months to two years in 2025. We further estimate that 20 to 40 percent of patients would have access to such care in 2025. We note that any estimates of success rates are highly speculative, given the state of development of these therapies.

Longer term, advanced genomics may offer tremendous potential to develop personalized treatments for cardiovascular disease. Every patient responds differently to the mix of medicine they are exposed to, and today high-risk patients are often treated with preventive medications with dosages adjusted on a trial-and-error basis, creating high risks. While the technology is still in early stages, genetic testing could help doctors determine dosages and mixes of substances more precisely. Also, screening can enable customized preventive routines (lifestyle changes, for example), as well as tailored treatments. Based on expected growth rates in cardiovascular disease, 23 million people could be expected to die of cardiovascular disease in 2025. For the purpose of sizing potential impact, we assume that 15 to 40 percent of patients could receive and benefit from genetic-based care and, on average, have one year of extended life.

Another major target for genetic medicine is type 2 diabetes, a growing health problem, especially in advanced economies. Based on current rates of diabetes incidence, some three million deaths could be caused by type 2 diabetes and related complications in 2025. Genome sequencing could enable the creation of treatments that could control the disease more effectively and better reduce the risk of death than the currently imprecise science of daily insulin use. We estimate that 20 to 40 percent of patients could have access to such treatment and might have increased life expectancy of one year. Other areas in which genetic sequencing holds promise, but for which we have not built estimates, include immunology and transplant medicine, central nervous system disorders, pediatric medicine, prenatal care, and infectious diseases.

Next-generation gene sequencing has application in prenatal care. Sequencing a fetus’s DNA would make it possible to predict the health of the baby more accurately than current tests can. Surveys show that parents in advanced economies would be willing to pay $1,000 to have their baby’s genome sequenced. Assuming close to 100 percent adoption in advanced economies and 30 to 50 percent adoption rates in less-developed economies (excluding least-developed nations), this testing could generate value of approximately $30 billion per year in 2025.

Another source of potential economic impact could arise from altering the metabolism of common organisms such as E. coli and yeast to create biofuels; this could be less expensive and require less energy and other inputs than creating biofuels from plants. Production costs could be as much as 15 to 20 percent lower for ethanol produced in this manner. It is possible that the cost of producing diesel using this technology could reach parity with traditional diesel by 2025, and since biodiesel commands a price premium even today (due to factors like government policy and environmental concerns), this new source of biodiesel could see significant demand. We estimate that the price premium over traditional diesel might be as much as 150 to 200 percent, and that micro-organism produced biodiesel could potentially replace 2 to 3 percent of traditional diesel consumption. Producers claim that these fuels derived from microbes could contribute 70 to 90 percent less in CO2 emissions in their production and use than traditional fuels. We estimate that the potential impact could be $100 billion to $200 trillion in 2025, including the savings associated with lower production costs, the value of lower CO2 emissions, and the value of the fuel itself.

In agriculture, next-generation genomics has the potential to both raise productivity in places where food is in short supply and conserve water. Advances in genetic modification of seeds could increase yields by making crops more drought- and pest-resistant. Genomics can also provide information that can be used to optimize crops for specific soils and climates and guide precision farming practices such as “fertigation” (a process in which the exactly necessary amounts of water and fertilizer are delivered to crops). We assume potential increases of 5 to 10 percent from optimized processes and 5 to 10 percent from new genetically modified seeds, leading to a potential economic impact of $100 billion to $200 billion per year in 2025.

BARRIERS AND ENABLERS

There is still much that scientists do not understand about genomics. Deciphering the interrelationships between genes, cellular mechanisms, organism traits, and environment is a complex undertaking that next-generation gene sequencing can speed up. But that work is only just beginning. Fast and cheap sequencing is still a new technology, and much of the initial genome sequencing will likely have unknown or little immediate impact. Understanding and applications will grow once many genomes have been sequenced and sample sizes are big enough to enable advanced analytics. While next-generation genomics technology could speed up this learning process dramatically, it is less clear how quickly this will lead to breakthroughs in understanding biology.

What is more likely to slow progress, however, are the many unresolved regulatory and ethical issues that this technology poses. One issue is the ownership of the data of sequenced genomes, which will be a very valuable resource for performing analyses and testing pharmaceutical treatments, but which might not be available if patients own the data regarding their own genomes and are not willing to share it. In the fall of 2013, the US Supreme Court is scheduled to hand down a key ruling on whether pharmaceutical companies can patent human cells. There are also concerns regarding the confidentiality of patient DNA information: can it be used by health insurers to deny coverage or raise rates, and should patients be given all the information about disease-linked mutations found in their genomes that might someday lead to illness? If these questions are slow in being addressed or not addressed adequately, progress could be delayed, potentially by public resistance.

There is also widespread public apprehension about the possible unintended consequences of altering plant and animal DNA. The European Union’s 1998 ban on genetically modified corn remains in effect, and many consumers are concerned about the possible effects of “Frankenfood” on environments, biodiversity, and human health. Advanced recombinant technology and synthetic biology could certainly heighten such concerns. Regulators have imposed limits on research on modified organisms, restricting them to closed environments. The continuation or strengthening of these types of restrictions could limit the potential economic impact of advanced genomics.

IMPLICATIONS

By 2025, continued advancement in gene sequencing speed and cost, along with equally rapid advances in the ability to understand and manipulate biological information, could create tremendous opportunities and risks for technology providers, physicians, health-care payers, biotechnology and pharmaceutical companies, entrepreneurs, and societies.

It is possible that genetic sequencing could become standard practice during medical exams by 2025. If it does, it could create major opportunities for companies and startups to manufacture and sell gene-sequencing equipment, along with the various supporting systems and tools that could be required (including big data analytics tools). The early entrants into this market could have the opportunity to define major industry standards and norms, including sequencing approaches, data standards, and integration with electronic health records. They will also need to win over payers, such as insurance companies and governments, by clearly demonstrating cost-effective efficacy improvements; the technology will also need to become user-friendly for physicians.

Insurers and other health-care payers (for example, state health insurance systems) will have a large interest in shaping how next-generation genomics and the resulting data are used. Improved treatments, reduced side effects, and reduced waste (due to avoiding incorrect diagnoses and treatments) could help reduce payer costs, which could provide the incentive for payers to subsidize routing genome screening. In some countries payers will also need to convince regulators and patients that genomic data will not be used against individual patients.

For biotech and pharmaceutical companies, the ability to sequence more material more quickly and to use the growing body of genetic data to isolate (or engineer) the best candidate substances for drug development has the potential to raise productivity and lower costs for new drugs and therapies. This could significantly impact the economics of drug discovery and testing. Simultaneously, the barriers to entry into biopharmaceuticals could fall when research becomes less capital‑intensive and cycles for development decrease.

Next-generation genomics could drive a major wave of entrepreneurship. Alongside companies that are looking to produce and sell gene-sequencing systems, there are already a growing number of startups and laboratories offering home DNA testing, including results that identify predispositions for known genetic diseases and information on ancestry. Fast, cheap sequencing is making these types of services possible; however, as these technologies become widely available, specialized testing services may have a limited market. Other entrepreneurs are already coming to market with new, unexpected solutions based on next-generation sequencing. For example, a synthetic biology startup that used the peer-to-peer funding site Kickstarter to raise capital has produced a synthetically engineered light-emitting plant, which it says could lead to a new source of lighting.

Policy makers will have many issues to address surrounding the applications of genetic science. Governments have supported the development of genomics through investments in research but have not been as forward-thinking when it comes to crafting policy. Governments can play a critical role in helping next-generation genomics live up to its potential to save lives, feed people, and provide fuels that will be less harmful to the environment.

One possible step could be supporting independent research investigating questions regarding the environmental and health risks and benefits of genomic applications. Governments can also work on regulations and initiatives to enable the success of genome-based advances. For example, the regulatory environment for drugs and diagnostics is likely to have a significant impact on the evolution of personalized medicine. Most experts believe that regulation has not kept pace with the rapid advances in the field of personalized medicine. A more far-sighted regulatory approach could balance many of the objections, including concerns regarding personal privacy, with the potential benefits of these technologies. This would give next-generation genomics researchers the opportunity to continue developing these technologies.

In addition to clarifying rules about ownership of DNA data and confidentiality, governments can facilitate the accumulation of genetic information. Since 2006, the US National Cancer Institute and the National Human Genome Research Institute have been compiling the Cancer Genome Atlas, a project with the goal of collecting all data about what mutations have been linked to cancers. It may soon be possible for governments to sponsor a central database of millions of genome sequences and make the information accessible (with proper precautions) to researchers.

Perhaps the thorniest concern in the near future is prenatal genome sequencing. Prenatal genetic screening raises the specter of eugenics: will parents end pregnancies for reasons other than serious deformities and other congenital medical conditions?

Ever since the creation of Dolly the sheep in 1996 proved that cloning is possible, genetic engineering has inspired both visions of a better world and concerns about the risks of such advances. Recently, scientists revealed that they have successfully inserted mitochondrial DNA into the egg cells of women who have had trouble conceiving. The procedure has been used in 30 successful pregnancies, producing babies with genes from the child’s two biological parents and the mitochondrial DNA donor; in effect, these children have three biological parents. This particular modification was performed to aid in conception, but it could also represent the first step on the path to manipulating human DNA to produce babies with “desirable” traits.

 

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