Imagine taking a simple, low-cost test that could predict with 100 percent accuracy whether, absent preventative measures, you will contract one or another type of cancer by a certain age. That would indeed be a powerful test, one that could transform medicine, quality of life and those with a financial interest in health outcomes. Not least among them: life insurers.

An ability to accurately predict the onset of disease — and ultimately to extend and enhance healthy lifespans — is also a primary objective of Dr. Craig Venter and his team at Human Longevity Inc. Founded in 2013, the San Diego-based firm is creating a comprehensive database of whole genome, phenotype and clinical data using large-scale computing and machine-learning.

Following his main stage presentation at the AALU 2016 annual meeting, held May 1-3 in Washington, D.C., Dr. Venter met with LifeHealthPro Senior Editor Warren S. Hersch. The Q&A exclusive explored HLI’s advances in genomics research, and what discoveries resulting from gene sequencing may portend for human health and society. The following are excerpts.

Hersch: When you got into this space, did you anticipate the discoveries you’ve made to date? Were any findings unexpected or surprising?

Venter: Back in 2001, I would have suggested you get your genome sequenced once — maybe at birth — and perhaps again if you get cancer or another life-threatening disease. I never predicted that we would be able to tell your age very precisely just by looking at your genetic code. That means genetic code changes over time, and that the changes are quantifiable. This discovery was the single biggest surprise for us.

Hersch: To what extent have advances in genomics research at HLI rested on gains in information technology?

Venter: In 1999, we paid $50 million for the third largest computer in the world — a machine operating at the speed of teraflop, or a trillion floating point operations per second. Today, you can buy a teraflop card for your PC for a few hundred dollars.

As computing power has increased, the time and cost and of DNA sequencing has declined dramatically. We’re still pushing the very limits of computing. People never thought genomics would evolve to become a big data problem; they never did the math on it.

HLI is among the top one percent of Amazon cloud users, right up there with big providers of video streaming services. If computing technology were 5 years behind where it is now, we would not be able to do this work.

Hersch: How large is the genomics field now? Do you compete with other players in certain domains?

Venter: Today, the competition is about getting the right solutions and the right quality of data. There are a lot of gene-sequencing machines, but not a lot of data has accumulated in public databases.

One reason for this is the need to protect people’s anonymity. Today we can accurately predict someone’s face using fingerprints he or she leaves on a water bottle. You can’t de-identify this data — prevent a person’s identify from being connected with the genetic information — if that material is held in a public database that can’t guarantee anonymity.

Our HLI database is highly secure. That allows us to protect people’s identities and the results of tests we run on them. Genomics information needs to be kept confidential; this is a very important aspect of the research today.

Hersch: Regarding the public sphere, do you believe that greater involvement by the government is needed, either in respect to genomics research or in addressing privacy and ethical issues?

Venter: I think it’s critical that the government be involved in some aspects of the research. Privacy guidelines, for example, need to be developed for using genomics data in different spheres.

Hersch: I imagine this need is increasing in tandem with the accuracy with which genetic testing can forecast health outcomes … Yes?

Venter: The accuracy levels are getting extremely interesting. We have some hints that we can predict when you’re likely to die — information you may not want to share with many others. Accuracy in such predictions will be key to being able to plan your life appropriately.

Hersch: In respect to average life expectancy, do you have certain expectations as to how much it might increase over the next 3 years, 5 years or 10 years?

Venter: I don’t. That’s not a focus of HLI’s research, which is more about insuring healthy lifespans. Also, there are social issues to be solved before we can contemplate extending lifespans, such as how to ensure a lifetime of retirement income for people who are living longer.

Hersch: Tell me about HLI’s Health Nucleus subsidiary. What’s its focus?

Venter: Health Nucleus uses whole genome sequence analysis, advanced clinical imaging and innovative machine learning — combined with a comprehensive curation of personal health history — to deliver a complete picture of individual health. The unit thus provides a novel approach to exploring, quantifying and understanding an individual’s health and disease risk. 

This has implications for medical testing. If, say, a gene sequencing test indicates you have an increased risk for cancer but not for heart disease, then there’s no need to undergo comprehensive tests for both when getting a whole body MRI for cancer will do. So we can use genomics data to triage medical testing and, ultimately, treatment.

Hersch: How do you anticipate research at HLI evolving going forward? What new initiatives do you hope to pursue?

Venter: We’re constantly finding new associations as a result of our research. The more predictive our genomics data gets, the more valuable it will be.

Mutations identified in tests of BRCA1 and BRCA2 — these are genes that produce tumor-suppressor proteins — increase the risk of female breast and ovarian cancers, or prostate cancer in men.

But these tests only have a predictive value of 50-50: Without knowing an individual’s family medical history, you can only say with a 50 percent confidence level that someone will contract one of these cancers.

That means that BRCA1 and BRCA2 aren’t directly involved in breast, ovarian or prostate cancer. They’re surrogate markers for these diseases; there are other genetic factors we’re not measuring.

Our goal at HLI is to find the actual genetic factors associated with a cancer — factors that will either increase the risk of disease onset to 100 percent or reduce it to zero — and to do so at low cost. Today, we can sequence a whole genome for far less than what most people pay for a BRCA1 test.

So the future of the field lies in transitioning from broad, general markers of disease risk to specific and precise information that allows for accurate predictions. Based on this data, we’ll know whether you’re going to get cancer or not.

 

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