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NIH’s Ambitious Precision Medicine Research Program

Mr. John Wilbanks is the Chief Commons Officer at Sage Bionetworks. Previously, Wilbanks worked as a legislative aide to Congressman Fortney “Pete” Stark, served as the first assistant director at Harvard’s Berkman Center for Internet & Society, founded and led to acquisition the bioinformatics company Incellico, Inc., and was executive director of the Science Commons project at Creative Commons. In February 2013, in response to a We the People petition that was spearheaded by Wilbanks and signed by 65,000 people, the U.S. government announced a plan to open up taxpayer-funded research data and make it available for free.

Prostatepedia spoke with Mr. Wilbanks about Sage Bionetworks role in All of Us, the National Institute of Health’s ambitious precision medicine research program.

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How did you come to work at Sage Bionetworks?

Mr. John Wilbanks: I got involved with Sage when it was first beginning. Sage was an informatics unit of Merck, and in 2009, they began to explore what they could get for the unit. But we convinced them to spin it out into a nonprofit organization instead of selling it off.

I got involved then as a board member because I was able to help negotiate what the IP structure would look like, how we would get rid of some of the patent constraints and other kinds of intellectual property so that we could build a nonprofit. I have been involved ever since, at first as a board member, then as a consultant, and then in 2012, as a full-time employee.

I lead the Governance team at Sage, which means that my group works on things like informed consent, clinical protocol design, data-sharing and access policies. We work on strange and weird structures that enable collaboration in a variety of ways, and we have a pretty broad view across the organization as a result.

What is the All of Us program?

Mr. Wilbanks: All of Us is a longitudinal cohort study. It is fundamentally an attempt to enroll a million people and to characterize them as completely as we can. This means we collect and look at their health records, pharmacy records, their environment, biospecimens, metabolic data, their genomes, data that we collect from their devices and smartphones, surveys over a ten-year period—you name it. Then, we make that data liberally available so that we can run all sorts of interesting queries.

We’re trying to take the Framingham Heart Study model and reimagine it for the 21st Century. Framingham is a breakthrough study, but it studied one town in Massachusetts, and then its diaspora over time. That means that it’s fairly white, and it has all these biases in it. Also, it doesn’t study anything besides heart health.

All of Us aims to take the idea and the impact of a study like Framingham and reimagine it using a completely modern, digital approach to everything. What would happen if you made that data liberally available? What would happen if you made a point of including 700,000 out of 1,000,000 being from populations that are underrepresented in biomedical research?

That’s one of the reasons it’s been hard to talk about; it’s not a study of prostate cancer. It’s a study that will involve hundreds of thousands of people, some of whom may have prostate cancer, some of whom may have survived prostate cancer, and some of whom may develop prostate cancer. But that’s not the focus. The idea is that we’d be able to subdivide that cohort endlessly in ways that let us think about public health and identify populations for sub-studies as easily as possible.

So then, the goal is to pull in as much data about these people as you can and then make inquiries into the data in various ways?

Mr. Wilbanks: That’s right. And we also want to open up who gets access to the data. It’s one thing to say the people at Harvard can run analytics; it’s very different to say that the community being studied can run analytics. That is also part of the design.

A lot of the questions that will be asked will come from advocates who know what questions need to be asked, questions the scientists don’t know need to be asked. We’ve been trying to design the system to maximize the number of people who are allowed to be data analysts and not just data donors. In many cases, we hope that the donors and analysts are the same people. That level of engagement leads people to start asking questions, not just providing information.

Will people be getting their own information back? Obviously, wearables and devices would feed information to their own electronic records, but I know they’re going to be doing some genomic tests. Will people get the results from those kinds of tests?

Mr. Wilbanks: Yes The study is guided by a set of core values and principles, and one is to prioritize the participant’s right to their data. All data provided by the participant will be provided back to the participant—nothing about me without me. We’re still figuring out how to do that because it’s really complicated.

Don’t you de-identify data first? Then, how do you re-identify it?

Mr. Wilbanks: That’s a little easier. You have to de-identify data before you get it to the data user. But, it’s easy to know for a given sample who that sample came from because that’s what allows us to connect it to the demographic data.

It’s relatively easy to get it back to the individual, but the question of what to return to them is difficult. If it’s their genome, do we give them their BAM files, which are massive? Or do we give them a VCF, which is the differences between their genome and the reference genome, which is tiny? Do we give them images? How many times do you let people download data because the cloud transfer cost would be high? How do we get consent for that? It’s complicated.

We still have to figure out exactly how we’re going to do all of those things, but it is a core principle of the study that nothing about you happens without you, and by the end of the study, you should have as much of your entire electronic health records in one place as possible, in one form. You should have your genome, all of the survey data you offered, all your wearable data, and you should have all the ancillary information we discovered about you. You should be able to take that with you and do what you want with it.

What is Sage’s role in all this?

Mr. Wilbanks: We are a sub-awardee of what’s called the Participant Center and the Participant Center is led by the Scripps Translational Science Institute in San Diego. We have two different lines of work inside the program, two core jobs. One is governance-based. We work on the clinical protocol, informed consent, and data-sharing systems. The other job is digital health technologies, and that’s a different team than mine. They work on building software modules that sit on smartphones and pull data off as measurements. They design them, figure out how to validate them, and how to feed them into the technology system.

You’re basically trying to figure out how you can pull data from the apps or wearables that participants already use?

Mr. Wilbanks: That’s part of the DHT group, and that’s led more by Scripps. We use the features of devices.

For examples, we think we can get a tremor measure for neurodegeneration with a module that measures the accelerometer in a smartphone. We can measure their gait by having them put their phone in their pocket and taking 20 steps forward and 20 steps back. We can measure phonation through a microphone. We can measure memory and tapping through the touchscreen.

We want to design modules like these that are clinically validated to measure those things so that anyone who wants to measure gait, lung capacity, memory, or what have you can rapidly access that inside the All of Us app or a related app. And they should feel confident that the data is relatively consistent and valid.

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Tech World Helps Prostate Cancer Manage Big Data

Dr. Felix Feng is a physician/scientist at University of California, San Francisco (UCSF) keenly interested in improving outcomes for patients with prostate cancer. His research centers on discovering prognostic/predictive biomarkers in prostate cancer and developing rational approaches to targeted treatment for therapy-resistant prostate cancer. He also sees patients through his prostate cancer clinic at UCSF.

Prostatepedia spoke with him about how technology companies and healthcare organizations are collaborating for prostate cancer research.

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You’re at University of California, San Francisco (UCSF), just north of Silicon Valley, home of the tech revolution. The media talk a lot about how technological advances are changing every aspect of society and healthcare in particular. How will emerging technologies impact prostate cancer research and patients?

Dr. Felix Feng: Certainly, UCSF exposes me to the tech revolution. I also grew up in Silicon Valley and went to Stanford University during the dotcom boom, so I’m pretty familiar with tech. The beauty of technology is that it allows us to think on a much larger scale than before.

Big data refers to analyzing large amounts of data from multiple sources, from clinical data to genomic data and so forth. Big data has impacted our field tremendously. My research team has had a few very productive collaborations with big data industry partners.

We collaborated with GenomeDX Biosciences, the molecular diagnostics company that makes the Decipher assay. To conduct the Decipher assay and look at the 22 genes that make up the Decipher score, they must analyze the expression of the vast majority of genes within the prostate cancer genome. We’ve partnered with GenomeDX to analyze samples from around 40,000 patients to generate predictive biomarkers and to identify genes that are associated with bad outcomes in prostate cancer. This provides direction for what we should study in the lab.

Another exciting collaboration is with a sequencing company called Illumina. We recently sequenced the whole genomes of 100 patients with metastatic prostate cancer. The data from those 100 patients took about 50 terabytes, a very large amount of data. We sequenced these patients, and housed, processed, and analyzed the data using the infrastructure they developed in the Amazon Cloud.

We’ve also partnered with a number of drug companies that run large clinical trials. These companies provided us access to samples from their clinical trials, recognizing that it costs millions of dollars to run a national clinical trial with many patients. The samples from these trials are an invaluable resource. When utilized in the right manner, these industry partnerships help us accelerate discovery to improve prostate cancer therapy.

Would you say that the greatest impact has been in the arena of genomics just because of the massive amount of data that’s generated?

Dr. Feng: That’s one of the major areas of advances. But there are so many areas of advancement in prostate cancer therapy right now that it’s hard to pick the most exciting. We’re super excited by a technology called CRISPR, a gene editing approach that allows scientists to silence genes, one-by-one in the context of prostate cancer, or in the context of cancer cell line models. These CRISPR approaches allow us to broadly study the function of many different genes and to couple that with what we’re finding from sequencing the tumors.

There are other exciting developments in novel therapeutics that target androgen receptor signaling, which is the major diagnosis of prostate cancer, and also in immunotherapy, targeting DNA repair in prostate cancer, and through drugs likePARP inhibitors.

Partnering with the tech sector has helped us identify the genomic drivers of prostate cancer, and that allows for personalized therapy. Interrogating big data from drug companies has also accelerated the pace of drug development.

Are there any collaborations that are not happening that you would like to see?

Dr. Feng: As a radiation oncologist, I am interested in how radiation can modulate immune response. When radiation kills prostate cancer, it might expose the immune system to proteins found in the tumors, proteins called antigens, which the immune system wouldn’t have otherwise been exposed to. I wish that more companies would focus on combining systemic drugs with radiation as a way to improve patient outcomes. Whatever the reason, I hope that we recognize the potential of radiation to improve patients’ systemic response to immunotherapy.

The field of prostate cancer is advancing rapidly. Academic researchers and industry partners use technological advances, whether big data or improved modeling approaches to identify new therapeutic approaches for patients. Just a decade ago, there was only one FDA-approved drug for patients with metastatic prostate cancer who have become resistant to first time hormone therapy. Now we have six FDA-approved drugs for them. Imagine what the next decade will bring.

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Health/Tech Collaborations For Prostate Cancer

Dr. Paul Nguyen is an internationally recognized expert in prostate cancer clinical care and research. He has published over 250 original research articles, has various national leadership roles and is the Dana-Farber Cancer Center Genitourinary Clinical Center Director for Radiation Oncology, Vice-Chair for Clinical Research in the Department of Radiation Oncology, and Associate Professor at Harvard Medical School.

Prostatepedia spoke with him about collaborations between healthcare and tech industries for prostate cancer.

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Have you had any particular patients or cases that changed how you view your role as a doctor or how you practice medicine?

Dr. Paul Nguyen: Several years after treating him, I heard from a patient who recounted for me what it was like to meet with me when he had first been diagnosed with recurrent disease. He said he’d had a lot of uncertainty and anxiety about his future. He said that the way I spoke with him had changed it entirely for him. He said I had a plan for him, knew exactly what we were going to need to do, and that we were going to do it.

I didn’t do anything particularly different in that encounter than I normally do, but hearing that made me realize how patients really hang on our every word, our every facial expression, our every cadence, and the emotion that we project when we speak. This made me so aware and conscious of making sure that, at all times, in every encounter, I have that combination of being sure about what I need to do and maintaining hope and optimism in every part of our discussions.

That was a good learning cycle for me. I hadn’t thought of it that way when I was with a patient. You just don’t think that every intonation, every gesture has such a huge impact. But it does. That was a very valuable learning experience for me that has really shaped how I think about every patient encounter before I walk into the room.

What are your current research projects? Which are you most excited about?

Dr. Nguyen: I have spent my entire career using information from the medical record about patients’ health status and tumor characteristics to figure out which men should get hormone therapy and for how long. Now, I’m incredibly excited about the opportunity to unleash the power of genetic testing of tumors. This will help us understand, on a genetic and molecular level, which patients should be given hormone therapy and for exactly how long. This will be a lot more precise than the clinical information by itself. I’m working with Dr. Felix Feng and others, which has been a wonderful collaboration.

How do you see evolving technologies impacting prostate cancer research? Dr. Nguyen: Technology gives us opportunities to do the kinds of studies we never dreamed possible, which is amazing.

I’ll give you an example. Dr. Feng and I are about to take prostate cancer samples from biopsy tissues taken 25 years ago from men who had cancer, samples stored without a clear purpose in mind. I give a huge amount of credit to the people who designed these studies in the early 1990s. They had no way to analyze this tissue, but they knew that someday, this tissue would be important to humanity. There wasn’t a specific test that they were storing these samples for, but they knew some kind of technology could decode what was going on in those tumors, to study how the tumors work, and who should get which treatment.

I feel so fortunate to come along 25 years later, when we do have the technology to analyze this tissue, and research it. This is the research I’m about to do now, which would never have been possible without new technologies.

Do you see technology impacting how we design clinical trials from the get-go?

Dr. Nguyen: Absolutely, because now people are designing trials with technology. There’s a trial being led by Dr. Feng from UCSF and Dr. Dan Spratt at the University of Michigan that incorporates genetic technology.

All the patients are tested upfront with this new technology to help decide which arm the patient goes into, which is really cool. This new scientific technology is being worked into clinical trial design.

Which innovations or technologies have the biggest impact?

Dr. Nguyen: There are two kinds of impacts. One is the ability to do large-scale genomic studies for a relatively low price. That has been a game-changer because it used to be so expensive to sequence the DNA of patients, but now you can approximate that rather cheaply and then do studies on thousands of patients. This way, we can pick up very small signals, which are very valuable.

The other invaluable impact is the ability to detect very minute amounts of tumor in the blood, very tiny traces that can tell us a lot.

In the circulating tumor cell?

Dr. Nguyen: Exactly.

Do you think artificial intelligence will play a role?

Dr. Nguyen: For sure. I’ve spent most of my career working on simple, clinical data. You can see the patterns of simple data yourself by doing simple statistical analyses. But now, the patterns are much more complex. Instead of five datapoints, you might have two million datapoints per patient. So we need AI. We need sophisticated machine learning to help us discern some kind of pattern out of that huge amount of data, to help us make sense of it.

Are there any specific collaborations, other than the ones we’ve already discussed, that you think look promising?

Dr. Nguyen: We’re seeing a lot more collaborations across specialties and disciplines to get research done. So much of what we’re seeing now is team science whereas people used to do studies with their own group.

Now, if you look at a paper, it’s not just one group or one discipline. At each institution, it’s five disciplines, and then you might have ten institutions on a paper, each contributing something different because that’s just what it takes now.

Every group has its own, little special expertise that gets put together to get a big paper or a big trial done. That’s what has really exploded. We’ve all recognized that, in order to get good science done, we have to team up.

Is just it easier to collaborate with people now via email and sharing of data? Or is there something about the way cancer research has been funded that has fostered that collaboration?

Dr. Nguyen: Yes. Those factors definitely contribute. It is definitely easier to share data now with the internet. Efforts to fund team science have definitely led teams to be created that might not have been created organically before.

There’s something fundamental about the increasing use of technology in studies and trials where only certain groups have this kind of technology expertise. You might have one group that knows a lot about the technology and another group that has a large number of patients and ideas. And you have to reach outside of your little sphere in order to get these kinds of exciting studies done.

It seems like before everything was pretty much siloed: you had tech, you had healthcare, and then, within healthcare, you had prostate cancer versus pancreatic cancer versus breast cancer. But now, the walls are coming down between those silos, with things like increased genetic testing. Would you say that’s true?

Dr. Nguyen: Absolutely. For example, some of the cool studies done in prostate cancer genetics were modeled on similar research done in breast cancer genetics several years before. Breast cancer had the Oncotype study, and then prostate cancer developed the Oncotype test many years later. We’ve seen molecular subtypes of breast cancer (luminal A, luminal B, and basal), and now there’s a study led by Dr. Feng suggesting that you’ve got similar kinds of subtypes in prostate cancer. We have to be knowledgeable about other fields. You can’t just be in your own silo now.

Last week, I spoke with engineers at University of Pennsylvania who are working with microchip-based technologies and machine learning to increase liquid biopsy’s usefulness in pancreatic cancer. They said this allows them to process much more data than they could before. They hope this has potential in other cancers. I know that’s more along the lines of diagnostics than what you’re doing, but do you have any thoughts about that?

Dr. Nguyen: We are all trying to take those same kinds of approaches with the folks who do machine learning. We need them desperately now because we’ve got so much data, and we just can’t figure it out on our own.

That’s exactly where we’re all headed.

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Genomics, Predicting Side Effects, + Clinical Trial Design

Dr. Felix Feng is a physician-scientist at University of California, San Francisco (UCSF) keenly interested in improving outcomes for patients with prostate cancer.

His research centers on discovering prognostic/predictive biomarkers in prostate cancer and developing rational approaches to targeted treatment for therapy-resistant prostate cancer. He also sees patients through his prostate cancer clinic at UCSF.

Prostatepedia spoke with him about genomics, predicting side effects and the future of prostate cancer clinical trials

Can genomics predict who will have certain side effects?

Dr. Feng: There have been a number of studies that have used single nucleotide changes within DNA sequences, called single nucleotide polymorphisms (SNPS), to predict who will be most likely to experience side effects from radiation therapy for cancer.

In general, the signal from these toxicity studies has been weaker than the signals from biomarkers that predict responses to particular therapies, like the ones that I mentioned earlier. This may be reflective of the fact that radiation acts through a variety of mechanisms, so any single biomarker may not work well. Even when you cluster biomarkers, it may not account for the heterogeneous manner in which radiation causes a biological effect.

What should patients know about how genomics is impacting treatment?

Dr. Feng: Many of the clinical trials being developed nowadays incorporate genomics. We have clinical grade assays to look at genomics. We have strong biological rationale for why certain genomic biomarkers may identify subsets of patients who can respond to specific therapies. Because genomics is routinely used to personalize treatment in the context of diseases like breast cancer, colon cancer, and melanoma, it’s only expected that genomics will have a major role in prostate cancer going forward.

Will incorporating genomics into clinical trial design accelerate the speed of innovation?

Dr. Feng: I think it will. If you look at metastatic castration-resistant prostate cancer, for example, a number of therapies have been approved by the FDA over the last decade for those patients, including agents like Zytiga (abiraterone) and Xtandi (enzalutamide), next generation taxanes, Provenge (sipuleucel-T), and Xofigo (radium-223). All of these agents extend survival by just a few months.

This is invariably what happens when you treat prostate cancer as one disease entity rather than a variety of different entities that are governed by different genomic events. As we become better at selecting therapies based on a patient’s genomic events, we should see longer response times to available therapies and those currently being developed.

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Patients Speak: I Had Genomic Testing

Steve S. talks to Prostatepedia about how genomic testing gave him confidence that active surveillance was a safe choice for him.

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How did you find out that you had prostate cancer?

Steve: I don’t remember exactly, but I think I went to the urologist on the recommendation of a doctor who said I should have some PSA tests. I went to the urologist. The urologist ran some PSA tests and said, “They’re a little elevated. Maybe we need to run a biopsy,” which they did. That was about ten years ago. The biopsy came back with three or four cores indicating cancer with a Gleason score of 6 (3+3), which has remained the same over the last ten years. I think that’s what happened.

What kinds of genomic tests did you have and when?

Steve: That happened about five years later. I went to a support group and I heard about genomic testing. My doctor at the time hadn’t mentioned anything about genomic testing to me. I said to him that I didn’t see any downside in having genomic testing. Why couldn’t I have it? He said that he didn’t think it would be covered by my insurance and it’s not something they had done. I felt like a little bit of a pioneer.

I actually got on the phone with the people at Genomic Health in California and asked how much the test would cost. They mentioned a figure of about $500. I asked, “So that’s what I’m going to be charged?” They said, “Probably.” They weren’t really clear about it. In the end I was never charged.

They sent three results to my physician after a few weeks. Because my physician had never given them instructions as to what risk category he felt that I was in, they sent back three results based on different risk profiles. To this moment, I still don’t know exactly which risk profile I fit into.

All three results looked somewhat encouraging to my layperson’s eyes. I discussed the results with the doctor at the time and he said, “I think this confirms what we’re doing at the moment is right. You can continue on active surveillance, but of course it’s your choice.” They will always say that….

The results definitely changed your treatment path?

Steve: I was already on active surveillance, although in the first two or three years, I was thinking about some form of radiation therapy.

We talked about seeds. We talked about beams. I even talked to a friend a few years older than me who had gone through proton beam therapy and he was very encouraged by his results. My insurance at the time did not cover that, so proton beam therapy came off the table. I was not thinking about surgery. I was turned off by the idea of surgery, even though they had a DaVinci robot.

Then I got the OncoTypeDX test. I looked at the results with my physician and decided to proceed. It confirmed what I was already inclined towards.

Do you feel like it gave you more confidence in your decision?

Steve: Yes. I think so. I think that’s fair to say.

Would you recommend that other men take these tests?

Steve: Everybody has a very different psychological makeup. For example, I’ve got a brother-in-law who doesn’t have prostate cancer, but is very educated on medical matters. He’s a smart guy, and so I talked to him about it. He said, “God, if it was me, I would take care of it right away. I’d have that prostate out of there and have peace of mind.” I responded with: “I’ve lost very little sleep over the years about it.” That’s just my makeup. It doesn’t bother me. I’ve got other things to think about, other things I care about. Health is very, very important.

I’m not a complete passenger in this process. That’s why it’s called active surveillance. I’m very careful about going to my doctor’s appointments, following up, trying to keep myself educated, and so forth. Would I recommend it to somebody else? Somebody else who has the same psychological makeup that I do? Absolutely. Somebody who is a nervous person, a Type A person, somebody who is likely to lose sleep? Perhaps not. I don’t see any possible downside to the testing, though. It’s another tool for you and your doctor to use to help you make your decisions.

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Genomics + Prostate Cancer Care

Dr. David J. VanderWeele is an Assistant Clinical Investigator in the Laboratory of Genitourinary Cancer Pathogenesis at the National Cancer Institute. He is particularly interested in investigating the progression of clinically significant prostate cancer.

Prostatepedia spoke with him about how genomics impacts patient care.

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What is genomics, and how does it differ from genetics?

Dr. VanderWeele: Typically if you’re talking about genetics, you’re talking about an individual gene or a small set of genes. When you refer to genomics, you’re referring to all the genes or a very large set of genes. Genomics usually refers to the genes–the DNA sequence. But sometimes genomics is also used to refer to when those genes get expressed (as RNA), or to other changes to the DNA that don’t change the DNA sequence (also called epigenetics).

What do and don’t we know about why some men develop curable or indolent prostate cancers while some develop widely lethal diseases?

Dr. VanderWeele: A lot of effort has been put into trying to learn more about the genes you inherit from your parents and how that influences the likelihood that you’re diagnosed with cancer. Most of that effort has been unable to identify which alterations in your genes make it more likely that you will get an aggressive versus an indolent cancer.

As many of your readers probably know, many people get indolent prostate cancers. In fact, many autopsy studies have looked at patients who have died of other reasons and have never been diagnosed with prostate cancer. Once men reach their 70s or 80s, it looks like more than half of men develop prostate cancer. Of course, those are relatively slow-growing cancers.

The most information that we have now is that men who come from families with breast and ovarian cancer syndrome appear to be more likely to get cancer and more likely to get aggressive cancer. These involve BRCA1, BRCA2, and other DNA repair genes in a similar pathway. Though there aren’t FDA-approved therapies yet, there are trials suggesting that these patients are also more likely to respond to certain therapies approved for breast and ovarian cancer.

This is a pretty small subset of all the men with prostate cancer, but the percentages increase with any kind of measurement of aggressiveness. If you look at people with localized cancer, that percentage increases if you have high-grade cancer versus low-grade cancer. The percentage increases if you compare people with advanced castrate-resistant prostate cancer to those with localized cancer.

If you look at the length of time between a man’s diagnosis and when he dies, that rate increases significantly the shorter that time is. That is just looking at three of these genes, BRCA1, BRCA2, and ATM. If you look at a broader number of these DNA repair related genes, it looks like ten to twelve percent of all patients with castrate-resistant prostate cancer harbor a mutation that they inherited from their parents. It seems likely that for most of those patients, that inherited gene contributed to their prostate cancer.

That has led to some debate about how often we should test for mutations in these genes. Is that a high enough number that we should test everyone with castrate-resistant prostate cancer? Should we still rely on family history to provide guidance for which people should be tested?

Is it really expensive to test those men? Why wouldn’t you just go ahead and test?

Dr. VanderWeele: Depending on how you do it, testing costs have come down quite a bit.

But when you’re testing for genes that could potentially be passed on to your offspring, or that siblings or other family members may have inherited, there are implications for your other family members, not just for you.

Some members of your family may definitely want to know that information and think that more information is better. Others may feel that if they find out that they harbor that gene mutation, they will just feel like they’re waiting for the other shoe to drop. It’s not information that they’d want to know.

Generally, we advise people to get counseling to help them think through some of these issues before getting tested for genes they’ve inherited from their parents.

Do we know why some men respond to certain drugs and therapies and others don’t?

Dr. VanderWeele: There’s a lot of interest in that. There has been some progress made in terms of identifying the biomarkers that might suggest which patients are more likely to respond to which types of therapies. At this point, however, most patients still get treated with most therapies.

There are some genetic biomarker-driven therapies that look like they’re on the horizon. Patients with mutations in BRCA2, ATM, and related genes are more likely to respond to a type of therapy called PARP inhibitors, which are currently approved for patients with ovarian or breast cancer, but not yet for prostate cancer.

There was a single Phase II study that showed that patients who had loss of a specific tumor-suppressor gene called

PTEN are more likely to respond to a certain type of targeted therapy. There are larger ongoing trials to demonstrate that these are indeed predictive biomarkers for response to these therapies.

There are companies like FoundationOne and GenomeDX that look at the molecular features of a man’s cancer. Are those tests useful? What do they tell a patient?

Dr. VanderWeele: The FoundationOne test looks for mutations, deletions, or amplifications of specific genes that are relevant for a wide array of cancers. There are a lot of companies offering this type of sequencing.

Many hospitals offer their own version of it. A FoundationOne type of test can tell you if you have a mutation in BRCA2 or ATM. They should also be able to tell you if you have a deletion in PTEN. When they detect a mutation is present, however, generally they are not looking to determine if you inherited those changes from your parents versus the mutation being present only in the tumor cells.

These genetic tests are more popular in other types of cancers, because for prostate cancer there aren’t yet any FDA-approved therapies that would be given based on the results of these tests. These tests will become more popular as we make progress in demonstrating the benefit of these specific therapies and in our ability to predict which patients are most likely to respond.

If a patient reading this gets one of those tests, is it likely that his doctor is going to know what to do with the results? Will the results actually impact his treatment?

Dr. VanderWeele: There are probably a small number of patients who will have a result that will directly impact their therapy. At this point, the way that it would impact therapy is that it might suggest that they should find a clinical trial testing a specific type of drug.

I see.

Dr. VanderWeele: There are also other commercially available prostate specific genetic tests, like the one performed by GenomeDX, that are mostly aimed at men with localized prostate cancer who are trying to decide how aggressive their therapy should be. Typically, this means whether they should pursue active surveillance or get surgery or radiation.

Sometimes these tests are also used to determine if a patient should get radiation after undergoing a prostatectomy or if he should just continue to follow PSA numbers. The prostate specific gene expression tests are RNA-based tests, which are a little different.

They measure the levels of expression of a few specific genes. Tests like FoundationOne look for mutations, amplifications, or deletions of genes—which means they are DNA-based tests.

Tests like Decipher are more widely used now, right?

Dr. VanderWeele: Yes. They’re probably used mostly by urologists. My sense is that how often urologists order those tests and how heavily they rely on them versus other ways to predict the risk level of the prostate cancer varies quite a bit from urology practice to urology practice.

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Dr. David VanderWeele: Why Prostate Cancer?

Dr. David J. VanderWeele is an Assistant Clinical Investigator in the Laboratory of Genitourinary Cancer Pathogenesis at the National Cancer Institute. He is particularly interested in investigating the progression of clinically significant prostate cancer.

Prostatepedia spoke with him about why he became a doctor.

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Why did you become a doctor?

Dr. VanderWeele: Physicians come to the job through a number of ways. For me, it was both an interest in biology in general and in cancer biology specifically. I really enjoyed learning in undergraduate school, and later on in training, how cancer represents a normal biological process gone awry.

Of course, many people also have a family member who helped inspire their choice, either directly or subconsciously. My mother had breast cancer; I’m sure that was part of my internal motivation and interest in oncology.

How did you end up specializing in prostate cancer?

Dr. VanderWeele: I was interested in genitourinary oncology—prostate cancer, bladder cancer, kidney cancer, and testicular cancer—because there is a wide range in the natural history of those diseases and how we treat them. I became especially interested in prostate cancer in part because some prostate cancers are very aggressive and others are more indolent. The first step of managing prostate cancer is assessing the risk of the disease and not just treating all cancers the same way.

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