everything possible/Shutterstock.com

How Big Data Can Improve Your Health

NIH helps researchers mine clinical records for genetic links to diseases.

Biomedical researchers and clinicians are generating an enormous, ever-expanding trove of digital data through DNA sequencing, biomedical imaging, and by replacing a patient’s medical chart with a lifelong electronic medical record. What can be done with all of this big data?

Besides being handy for patients and doctors, big data may provide priceless raw material for the next era of biomedical research. Today, I want to share an example of research that is leveraging the power of big data.

NIH-funded researcher Atul Butte of Stanford University recently mined mountains of existing data to find new links among genes, diseases and traits. In this instance, traits are defined as any detectable physical or behavioral characteristic, such as cholesterol levels or other blood chemistries; bone density; or body weight. Butte reasoned that a trait that was closely linked to a disease through specific genes might be useful as a predictive marker of disease risk.

To discover these new links, he tapped into the VARiants Informing MEDicine (VARIMED) database, a resource that he began building in 2008 to interpret the clinical consequences of DNA variation in patients. To create VARIMED, Butte and his colleagues read scientific papers on human genetics—including many genome-wide association studies, which identify common genetic variants that are associated with disease risk—and noted the genes, variations and traits mentioned in each paper, and the connections between them. Over the years, the privately funded database grew; today it contains findings from more than 9,000 studies.

In their most recent study, Butte’s team examined the genetic architecture of each disease—all of the genetic variations that influence disease risk—and made a list of the gene-disease pairs. They found 801 genes that were reliably linked to 69 diseases. Next, the researchers made a list of genes associated with particular traits; 796 genes were reliably linked to 85 traits. Finally, they searched for overlaps between the two lists: Were there any genes that influenced both a disease and a trait?

Butte’s team found 120 diseases and traits that were linked by the activity of just a few genes. Many of these disease-trait associations were already known to the biomedical community, but about 20 percent of these connections were novel.

The next question was whether these traits can be used to predict whether an individual would develop a particular disease. Butte tested his hypothesis by taking five of the new disease-trait connections and examining patient data from Stanford Hospital and Clinics and New York’s Mount Sinai Medical Center and Columbia University Medical Center, all of which had at least a decade’s worth of electronic medical records.

One of the disease-trait pairs was gastric cancer-magnesium, which is a trace mineral found in blood serum. This pair was connected by three genes—MUC1, THBS3, and TRIM46—previously implicated in gastric cancer and also known to influence magnesium levels in blood serum.

However, it wasn’t clear whether serum magnesium levels were actually predictive for gastric cancer. To find out, Butte’s team analyzed the EMRs of 704 patients who had a magnesium measurement one year before they were diagnosed with gastric cancer. For controls, he examined the EMRs of more than 324,000 patients who had magnesium measurements, but no diagnosis of gastric cancer. The comparison revealed that patients with elevated magnesium levels were significantly more likely to be diagnosed with gastric cancer than patients whose levels were normal.

Another surprising connection was made through the CLPTM1L and TERT genes that linked lung cancer with prostate specific antigen, or PSA, a protein that can be detected through blood tests and is a known risk biomarker for prostate cancer. Butte’s team studied 240 men who had their PSA measured one year before their diagnosis of lung cancer and compared them with men who had PSA measurements taken, but did not develop lung cancer. The team found that men with abnormally high PSA levels were more likely to be diagnosed with lung cancer a year later than those with normal PSA levels. One important caveat about this finding is that the study did not control for smoking, which is a known risk factor for lung cancer and has also been implicated in prostate cancer.

Using the same approach, the team also validated links between:

  • The average volume of a red blood cell and the risk of developing acute lymphoblastic leukemia (through shared variants in the IKZF1 gene)
  • Levels of the alkaline phosphatase enzyme and the risk of developing a blood clot in a leg, liver, or lung vein (the ABO and TERT genes)
  • Low platelet counts and likelihood that someone is alcohol dependent (the C12orf51 gene)

The authors emphasize that it is premature to develop predictive blood tests for any of these five diseases because it’s not yet clear whether the trait precedes the disease, or is the result of it. While finding a connection between a disease and trait may someday lead to new blood, genetic, imaging, and other predictive or diagnostic tests, this is not the only clinical implication of the new study. If different diseases are found to be connected by common traits, it’s possible there may be a common biological mechanism underlying those diseases—which could mean that a drug that works for one disease might also be effective for the others. Getting answers to these complicated questions clearly will require much further study in cells, animal models, and humans.

What I find most noteworthy about this work is not the specific findings, but how the researchers demonstrate the feasibility of mining vast troves of existing data—genetic, phenotypic and clinical—to test new hypotheses.

Indeed, we are at a point in history where big data should not intimidate, but inspire us. We are in the midst of a revolution that is transforming the way we do biomedical research. In some cases, rather than posing a question, designing experiments to answer that question, and then gathering data, we already have the needed data in hand—we just have to devise creative ways to sift through this mountain of data and make sense of it.

At NIH, a bold new initiative called Big Data to Knowledge, or BD2K, is providing a focal point for catalyzing this historic research opportunity. I’ve recently recruited the distinguished informatics expert Dr. Philip Bourne from the University of California at San Diego, and he now serves as my associate director for data science (ADDS, isn’t that an appropriate acronym?). If you’d like to learn more about what NIH is doing to enable researchers to capitalize on this wealth of data, check out our BD2K website.

(Image via everything possible/Shutterstock.com)

X
This website uses cookies to enhance user experience and to analyze performance and traffic on our website. We also share information about your use of our site with our social media, advertising and analytics partners. Learn More / Do Not Sell My Personal Information
Accept Cookies
X
Cookie Preferences Cookie List

Do Not Sell My Personal Information

When you visit our website, we store cookies on your browser to collect information. The information collected might relate to you, your preferences or your device, and is mostly used to make the site work as you expect it to and to provide a more personalized web experience. However, you can choose not to allow certain types of cookies, which may impact your experience of the site and the services we are able to offer. Click on the different category headings to find out more and change our default settings according to your preference. You cannot opt-out of our First Party Strictly Necessary Cookies as they are deployed in order to ensure the proper functioning of our website (such as prompting the cookie banner and remembering your settings, to log into your account, to redirect you when you log out, etc.). For more information about the First and Third Party Cookies used please follow this link.

Allow All Cookies

Manage Consent Preferences

Strictly Necessary Cookies - Always Active

We do not allow you to opt-out of our certain cookies, as they are necessary to ensure the proper functioning of our website (such as prompting our cookie banner and remembering your privacy choices) and/or to monitor site performance. These cookies are not used in a way that constitutes a “sale” of your data under the CCPA. You can set your browser to block or alert you about these cookies, but some parts of the site will not work as intended if you do so. You can usually find these settings in the Options or Preferences menu of your browser. Visit www.allaboutcookies.org to learn more.

Sale of Personal Data, Targeting & Social Media Cookies

Under the California Consumer Privacy Act, you have the right to opt-out of the sale of your personal information to third parties. These cookies collect information for analytics and to personalize your experience with targeted ads. You may exercise your right to opt out of the sale of personal information by using this toggle switch. If you opt out we will not be able to offer you personalised ads and will not hand over your personal information to any third parties. Additionally, you may contact our legal department for further clarification about your rights as a California consumer by using this Exercise My Rights link

If you have enabled privacy controls on your browser (such as a plugin), we have to take that as a valid request to opt-out. Therefore we would not be able to track your activity through the web. This may affect our ability to personalize ads according to your preferences.

Targeting cookies may be set through our site by our advertising partners. They may be used by those companies to build a profile of your interests and show you relevant adverts on other sites. They do not store directly personal information, but are based on uniquely identifying your browser and internet device. If you do not allow these cookies, you will experience less targeted advertising.

Social media cookies are set by a range of social media services that we have added to the site to enable you to share our content with your friends and networks. They are capable of tracking your browser across other sites and building up a profile of your interests. This may impact the content and messages you see on other websites you visit. If you do not allow these cookies you may not be able to use or see these sharing tools.

If you want to opt out of all of our lead reports and lists, please submit a privacy request at our Do Not Sell page.

Save Settings
Cookie Preferences Cookie List

Cookie List

A cookie is a small piece of data (text file) that a website – when visited by a user – asks your browser to store on your device in order to remember information about you, such as your language preference or login information. Those cookies are set by us and called first-party cookies. We also use third-party cookies – which are cookies from a domain different than the domain of the website you are visiting – for our advertising and marketing efforts. More specifically, we use cookies and other tracking technologies for the following purposes:

Strictly Necessary Cookies

We do not allow you to opt-out of our certain cookies, as they are necessary to ensure the proper functioning of our website (such as prompting our cookie banner and remembering your privacy choices) and/or to monitor site performance. These cookies are not used in a way that constitutes a “sale” of your data under the CCPA. You can set your browser to block or alert you about these cookies, but some parts of the site will not work as intended if you do so. You can usually find these settings in the Options or Preferences menu of your browser. Visit www.allaboutcookies.org to learn more.

Functional Cookies

We do not allow you to opt-out of our certain cookies, as they are necessary to ensure the proper functioning of our website (such as prompting our cookie banner and remembering your privacy choices) and/or to monitor site performance. These cookies are not used in a way that constitutes a “sale” of your data under the CCPA. You can set your browser to block or alert you about these cookies, but some parts of the site will not work as intended if you do so. You can usually find these settings in the Options or Preferences menu of your browser. Visit www.allaboutcookies.org to learn more.

Performance Cookies

We do not allow you to opt-out of our certain cookies, as they are necessary to ensure the proper functioning of our website (such as prompting our cookie banner and remembering your privacy choices) and/or to monitor site performance. These cookies are not used in a way that constitutes a “sale” of your data under the CCPA. You can set your browser to block or alert you about these cookies, but some parts of the site will not work as intended if you do so. You can usually find these settings in the Options or Preferences menu of your browser. Visit www.allaboutcookies.org to learn more.

Sale of Personal Data

We also use cookies to personalize your experience on our websites, including by determining the most relevant content and advertisements to show you, and to monitor site traffic and performance, so that we may improve our websites and your experience. You may opt out of our use of such cookies (and the associated “sale” of your Personal Information) by using this toggle switch. You will still see some advertising, regardless of your selection. Because we do not track you across different devices, browsers and GEMG properties, your selection will take effect only on this browser, this device and this website.

Social Media Cookies

We also use cookies to personalize your experience on our websites, including by determining the most relevant content and advertisements to show you, and to monitor site traffic and performance, so that we may improve our websites and your experience. You may opt out of our use of such cookies (and the associated “sale” of your Personal Information) by using this toggle switch. You will still see some advertising, regardless of your selection. Because we do not track you across different devices, browsers and GEMG properties, your selection will take effect only on this browser, this device and this website.

Targeting Cookies

We also use cookies to personalize your experience on our websites, including by determining the most relevant content and advertisements to show you, and to monitor site traffic and performance, so that we may improve our websites and your experience. You may opt out of our use of such cookies (and the associated “sale” of your Personal Information) by using this toggle switch. You will still see some advertising, regardless of your selection. Because we do not track you across different devices, browsers and GEMG properties, your selection will take effect only on this browser, this device and this website.