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Mon, Nov 12 8:00am · Novel data-driven approach for precision medicine

Thousands of patients’ tumors have been sequenced in the past decade, yielding a rich source of data on the changes associated with the cancer development and treatment response. However, there are no validated methods that are used in the clinic to select the best therapy. Today, Mayo Clinic researchers report an omics-guided (comprehensive) drug prioritization method tailored to an individual cancer patient.

“To date, genomic sequencing data provided to clinicians includes information on a small set of gene alterations. Recommendations for therapy do not account for many other genomic and clinical factors that might dictate tumor response,” says Mayo researcher Krishna Rani Kalari, Ph.D. “Therefore, there is an urgent need for a comprehensive approach to integrate an individual’s clinical, germline and tumor genomic data to identify and select the best treatment for a patient.”

Dr. Rani Kalari, a computational biologist, and lead author of a Mayo Clinic led study, published in JCO Clinical Cancer Informatics showed that combining multiple sources of data to predict the most effective drug choices for patients with cancer is feasible.

“We developed PANOPLY- Precision cancer genomics report: single sample inventory, an open-source computational framework to analyze complex multidimensional data to determine the most appropriate drug to target an individual’s tumor,” says Dr. Kalari. “PANOPLY approach is more comprehensive and efficient than existing single-sample analyses methods,” says Dr. Kalari.

PANOPLY includes existing FDA-approved drugs and prioritizes the drugs for patients with cancer-based on their omics profile and reports the results for oncologists to guide treatment decisions. In this study, PANOPLY was applied to in-house breast cancer datasets, and the findings were confirmed with patient-derived xenograft (PDX) models Tissues or cells from a patient’s tumor are implanted into an immuno-deficient mouse. These mouse models are used to create an environment that resembles the natural growth of cancer, for the study of cancer progression and treatment. In addition, the researchers demonstrated the flexibility of the PANOPLY framework by applying it to colon, breast, ovarian and glioblastoma datasets from The Cancer Genome Atlas.

Dr. Rani Kalari is using high-throughput tumor sequence data and teaming up with basic scientists such as Liewei Wang, Ph.D., M.D. director of the Mayo Clinic Pharmacogenomics Program, to determine whether PANOPLY can identify novel drug targets. After successful testing and benchmarking of the method using PDX repositories, they plan to work towards the ability to merge PANOPLY reports into the electronic medical records so the information is available to oncologists.

“Currently, the vast majority of patients with cancer continue to receive treatments that are minimally informed by omics data. Working with Mayo Clinic surgeon Judy Boughey, M.D. and oncologist Matthew Goetz, M.D., we anticipate that the proposed work will open new research and clinical vistas to allow a more individualized approach for the better treatment of patients,” says Dr. Kalari.

Mayo Clinic authors are:

Krishna R. Kalari, Ph.D.

Jason P. Sinnwell

Kevin J. Thompson, Ph.D.

Xiaojia Tang, Ph.D.

Erin E. Carlson

Jia Yu, Ph.D.

Peter T. Vedell, Ph.D.

James N. Ingle, M.D.

Richard M. Weinshilboum, M.D.

Judy C. Boughey, M.D.

Liewei Wang, Ph.D., M.D.

Matthew P. Goetz, M.D.

Vera Suman, Ph.D.

This study is funded in part by the Mayo Clinic Center for Individualized Medicine; Nadia’s Gift Foundation; John P. Guider; the Eveleigh Family; George M. Eisenberg Foundation for Charities; generous support from Afaf Al-Bahar; and the Pharmacogenomics Research Network (PGRN).  Other contributing groups include the U54 GM114838, Mayo Clinic Cancer Center (P30CA 15083-43) and the Mayo Clinic Breast Specialized Program of Research Excellence (SPORE- P50CA116201).

 

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Mon, Oct 1 8:30am · Mayo Clinic GeneGuide DNA testing application provides genetic testing, insights backed by Mayo Clinic expertise

Today Mayo Clinic launched a new effort to raise awareness for genetic testing and how that may affect health and risk for disease. Mayo Clinic GeneGuide combines genetic testing with a web-based educational application to help consumers understand information about their own genetic background.

Matthew Ferber, Ph.D.

“The Mayo Clinic GeneGuide app puts a wealth of information at a user’s fingertips from experts in genetic medicine. Consumers have access to scientifically-based data that uncover personal genomic insights, backed up with world class educational material. This helps individuals understand their results and learn the language of genetics so they can have informed discussions with their health care providers,” says Matthew Ferber, Ph.D., a Mayo Clinic genomics researcher who led the development of the app.

Mayo Clinic GeneGuide was developed in conjunction with Helix, a partner that handles sample collection, DNA sequencing, and provides secure data storage. Mayo Clinic GeneGuide returns the individual’s personalized genetic test results for select conditions and helps them understand how their genetic makeup, together with their lifestyle and environment, can impact their overall health and wellness.

Keith Stewart, M.B., Ch.B.

“Mayo Clinic is a trusted partner for consumers who wish to learn more about their genetics. With the increase in genetic and genomic testing in the consumer and clinical spaces, we believe it is important for Mayo Clinic experts to provide accurate and reliable education to people to raise genomic literacy and educate consumers/patients about genetics,” says Keith Stewart, M.B., Ch.B., Carlson and Nelson endowed director, Center for Individualized Medicine.

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Mon, Sep 24 6:00am · CIM CON -- What is the impact on health care of genome editing?

Although Mayo Clinic does not use genome editing as part of any treatment in the medical practice, genome editing has promise for treating and even curing previously intractable disorders, such as Duchenne muscular dystrophy.

Genome editing, via methods like CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR-associated protein) can be used to facilitate the targeted modification of specific genes in living cells from the body and germline (inherited) sources. However, there are uncertain and potentially undesirable side effects to genome editing and regulatory oversight of genome editing is also unclear.

Genomic experts discussed the technological basis for genome editing, its current and potential research and clinical applications, and ethical and regulatory concerns at the Individualizing Medicine Conference: Advancing Care through Genomics. The Mayo Clinic Center for Individualized Medicine (CIM) hosted the conference at the Mayo Civic Center in Rochester, Minnesota.

What is gene editing?

Shondra Pruett-Miller, Ph.D.

Shondra Pruett-Miller, Ph.D., Assistant Member of Cell and Molecular Biology, St. Jude Children’s Research Hospital, spoke about the molecular biology behind gene editing and how it works, in addition to its advantages and limitations. Dr. Pruett-Miller explained gene knockout, which is a genetic technique in which one of a cell’s or organism’s genes is “knocked out” of the respective genome for the purpose of understanding the function of the gene.

“Using this technology in agriculture has huge implications from creating heat-resistant cattle to drought-resistant crops,” says Dr. Pruett-Miller.

However, there are still limitations to genome editing.  According to Dr. Pruett-Miller in order for this technology, and specifically CRISPR-Cas9, to reach its full therapeutic potential, every effort must be made to ensure that the genome edits are made with minimal chance of off-target effects on the structure of the gene.

From gene therapy to genome surgery

Stephen Tsang, M.D., Ph.D.

Stephen Tsang, M.D., Ph.D., Laszlo Z. Bito Associate Professor of Ophthalmology and Associate Professor of Pathology and Cell Biology, Ophthalmology, Columbia University, spoke about the current and potential research and clinical applications of genome editing. Dr. Tsang explored the beginnings of gene therapy and the path that led to genome surgery.

“Gene therapy is not the same as gene surgery, also known as gene-editing,” says Dr. Tsang. “CRISPR-Cas9 opened a new chapter in medicine.”

Gene therapy uses genes as a “drug” to treat or prevent disease by modifying, supplying or blocking gene expression or gene products that cause a condition either by their presence or absence.

CRISPR-Cas9 is a method of genome surgery that enables geneticists and medical researchers to edit parts of the genome by removing, adding or altering sections of the DNA sequence. Dr. Tsang used the example of juvenile macular degeneration as a perfect target for CRISPR-Cas9.

“The eye is the ideal system for genome surgery as well as stem cell transplantation: its relative immune privilege and accessibility, and the effects of treatment can be precisely monitored at the resolution of a single cells with non-invasive imaging allowing physicians to monitor what is happening in real time as they put the cell in and interact with eye,” says Dr. Tsang. “The eye is a self-contained area preventing CRISPR off-targeting from going to other parts of the body. As a pair organ, the eye provides the ideal treatment-control conditions and distinguishes itself as the ideal system for Individualized Medicine due to the low risk of off-targeting of genome surgery and stem cell therapies.”

The science has to advance first

Megan Allyse, Ph.D.

Megan Allyse, Ph.D., Assistant Professor of Biomedical ethics at Mayo Clinic closed the session discussing ethical and regulatory concerns related to genome editing and how they may impact clinical decision-making.

According to Dr. Allyse with the advent of gene therapy and gene surgery the National Academy of Sciences laid out clear guidelines relating to responsible science.  The National Academy of Sciences covers all facets of responsible science from transparency, respect of the person, fairness, to due care (proceeding carefully and deliberately and only when supported by sufficient and robust evidence).

“Although we have a lot of structures in place to monitor gene editing there are many unresolved dilemmas,” says Dr. Allyse.

Dr. Allyse posed several thought provoking questions to the audience concerning the ethical and regulatory issues such as:

  • “Who defines what a serious condition or disease is?”
  • “How do you handle illegitimate stem cell therapies and the exploitation of people who are desperate to solve a health issue?”
  • “Is the human genome sacred?”

The questions set up a hard conversation with those in attendance and the answers were as varied and individual as each person.

“As much as we want to get into humans, the science has to come first,” says Dr. Allyse. “Our goal is to bring people up to health as opposed to pushing them to enhancement.”

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Tue, May 1 2:05pm · Mayo Clinic joins NIH in launching All of Us Research Program

On May 6, the National Institutes of Health (NIH) will open national enrollment for the All of Us Research Program to accelerate health research and medical breakthroughs, enabling individualized prevention, treatment, and care for all of us.

The program will partner with 1 million or more people across the U.S. to build the most diverse biomedical data resource of its kind, to help researchers gain better insights into the biological, environmental, and behavioral factors that influence health.

In 2016, Mayo Clinic was awarded $142 million in funding over five years by the NIH to serve as the nation’s biobank to store the 35 million samples for research.

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Learn more

  • Watch a video about the All of Us Research Program biobank at Mayo Clinic
  • Visit JoinAllofUs.org for more information.

Join us at this year’s Individualizing Medicine Conference

This year’s Individualizing Medicine Conference on Sept. 12-13, will be held in Rochester, Minnesota. Sponsored by the Mayo Clinic Center for Individualized Medicine, the conference brings together precision medicine experts from Mayo Clinic and around the world to share how the latest genomic discoveries are advancing patient care.

 

Tue, Apr 24 6:00am · Discover first-hand how DNA impacts your health — “Genome: Unlocking Life’s Code”

Genomics and Society: photo courtesy of Science North. This interactive program available at the exhibit invites you to consider different opinions about some of the issues surrounding genomic technologies and how they relate to your life.

DNA does more than determine your hair color or eye color — it can provide a roadmap that can help you trace your ancestral past. Understanding more about what is in your entire DNA — the genome — can help you take charge of your health.

This year marks the 15th anniversary of National DNA Day, a national observance to raise awareness about the discovery of DNA’s double helix by James Watson and Francis Crick in 1953 and the successful completion of the Human Genome Project in 2003. Thanks to the pioneering work of the Human Genome Project, we are starting to understand much more about ourselves.

To celebrate these advances “Genome: Unlocking Life’s Code,” produced by the Smithsonian Institute and the National Institutes of Health, is coming to Rochester, Minnesota this summer. The exhibit’s debut was in 2013 at the Smithsonian Institution National Museum of Natural History in Washington D.C., and since then it has been traveling throughout North America. Mayo Clinic is the first academic medical center to sponsor the exhibit with the goal of advancing genomics awareness and education in the community.

Timothy Curry, M.D., Ph.D.

I spoke with Timothy Curry, M.D., Ph.D., education program director at the Mayo Clinic Center for Individualized Medicine about the exhibit and the importance of genomics education.

Q: What impact does genomics have on people’s lives?

A: By learning what genomics is and how it is being applied to wellness and health care, the community will benefit by having a better understanding of the relevance of genomics in their lives and see first-hand how it relates to health and disease. This is an opportunity for visitors to learn how genomics can affect their perspectives about health, identity, and their place in the natural world. They can see themselves in a new way: as an individual, as a member of a family, and as part of the diversity of life on Earth.

Q: What makes this exhibit stand out from your typical educational exhibit?

A: “Genome: Unlocking Life’s Code,” was a two year collaboration between the Smithsonian Museum and the National Institutes of Health with the goal of creating an interactive and engaging exhibit to educate and inform the public about the revolutionary nature of genomic science. Visitors can explore what a genome is, how it relates to medicine and health, and how it connects humans to all of life on the planet, both past and present. Within the galleries, personalized and interactive experiences offer hands-on and media interactives and videos. In addition, having the Rochester Art Center as the host of the exhibit gives us the opportunity to connect science and art.

First Person Plural, an artistic rendering by Eric Anderson. Attendees interact with a video exhibition inviting them to consider, challenge and share their own perspectives on health and identity.

Q: What can visitors expect to see in the art exhibitions?

A: Several art exhibitions from national and local artists will explore and expand the view of genomics as it relates to human health and disease. The Center for Individualized Medicine and the Rochester Art Center identified artists who explore questions surrounding genomics. Visitors will see a variety of art from a photography display exploring the social and psychological experiences of people of all ages to ethno-cultural heritages living with genetic conditions. Interactive, immersive video displays show how we define identity and hands-on sculptures explore questions or themes visitors may have about the genome.

Q: How do you see genomics impacting health?

A: Today, Mayo Clinic patients can get DNA sequencing tests for numerous disease-causing genes. Physicians may use this information, along with what we have learned from research studies, to help understand symptoms patients may have and even diagnose rare diseases. Mayo Clinic is performing DNA sequencing every day. Our research teams continue to study how genomic testing impacts health, wellness and medical care.

See the exhibit June 23 through Sept. 21

You can discover first-hand how genomics impacts health, disease and treatment.  Mark your calendar this summer to check out “Genome: Unlocking Life’s Code” from June 23-Sept. 21 at the Rochester Art Center.

For more information visit “Genome: Unlocking Life’s Code.”

“Genome: Unlocking Life’s Code” was developed and produced by the Smithsonian’s National Museum of Natural History and the National Institutes for Health’s National Human Genome Research Institute, in association with Science North.

“Genome: Unlocking Life’s Code” is made possible in part by financial support secured by the Foundation for the National Institutes of Health.

The Mayo Clinic Center for Individualized Medicine is sponsoring the exhibit with benefactor support.

Join us at this year’s Individualizing Medicine Conference

See the “Genome: Unlocking Life’s Code” exhibit when you attend this year’s Individualizing Medicine Conference on Sept. 12-13, in Rochester, Minnesota. Sponsored by the Mayo Clinic Center for Individualized Medicine, the conference brings together precision medicine experts from Mayo Clinic and around the world to share how the latest genomic discoveries are advancing patient care.

Tue, Feb 13 2:42pm · New international practice guidelines for using tamoxifen to treat breast cancer

An international group of clinicians and scientists representing the Clinical Pharmacogenetics Implementation Consortium (CPIC) published the first-ever clinical practice guideline for using CYP2D6 genotype to guide tamoxifen therapy in Clinical Pharmacology and Therapeutics.

Tamoxifen is a hormonal agent used for the prevention and treatment of premenopausal and postmenopausal breast cancer that is estrogen receptor positive. CYP2D6 genotype is an inherited factor that alters the metabolism of tamoxifen.

“The goal of the CPIC Guideline for CYP2D6 and tamoxifen therapy is to provide clinicians information that will allow the interpretation of clinical CYP2D6 genotype tests so that the results can be used to guide prescribing of tamoxifen when genotype information is available,” says Matthew Goetz, M.D., a Mayo Clinic medical oncologist, who is the lead author. “The consensus of the consortium tamoxifen group was that there was sufficient evidence to use CYP2D6 genotype to assist with clinical recommendations for women who are being considered for tamoxifen for early stage estrogen receptor positive breast cancer.”

Matthew Goetz, M.D.

Tamoxifen is converted through the process of liver metabolism into forms that result in greater anti-estrogenic potency and anti-tumor activity than the parent drug. Antiestrogens are a class of drugs which prevent estrogens from mediating their biological effects in the body.

“The work of the consortium is an example of Mayo’s commitment to taking a comprehensive, collaborative team science approach to deliver advanced genomic medicine to our patients. We work with other academic medical centers, hospitals, and clinics to bring the latest discoveries to improve the practice of medicine.” – Matthew Goetz, M.D.

“The work of the consortium is an example of Mayo’s commitment to taking a comprehensive, collaborative team science approach to deliver advanced genomic medicine to our patients. We work with other academic medical centers, hospitals, and clinics to bring the latest discoveries to improve the practice of medicine,” says Dr. Goetz.

Read more.

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Save the date for this year’s Individualizing Medicine Conference. It will be held Sept. 12-13, 2018 in Rochester, Minnesota.

 

Mon, Jan 29 7:04pm · Direct-to-consumer genetic testing—a rapidly shifting landscape

Direct-to-consumer genetic or over the counter testing emerged in the early 2000s as a means of allowing consumers to access information about their genetics without the involvement of a physician. While early models were popular with consumers, they were controversial in medical and regulatory circles.

In the January 2018 issue of Mayo Clinic Proceedings authors Megan Allyse Ph.D., David Robinson, Matthew Ferber Ph.D. and Richard Sharp Ph.D. trace the history of direct-to-consumer genetic testing, discuss its regulatory implications, and describe the emergence of a new hybrid model.

Direct-to-consumer testing — the early days

Megan Allyse, Ph.D.

In 2007 the journal Science named human genetic variation the “breakthrough of the year” and direct-to-consumer companies were offering microarray panels for $1,000. Fast forward five years and the curious consumer could get a microarray panel for $99. Microarray refers to a microchip-based testing platform that allows high-volume, automated analysis of many pieces of DNA at once.

“Consumers liked the convenience of direct-to-consumer testing, the appeal of gaining access to their personal genetic information, and its promotion of preventive and individualized medicine,” says Dr. Allyse, a Mayo Clinic bioethicist, and lead-author of the paper.

However, critics quickly raised concerns about direct-to-consumer testing.

  • Risk of misinterpreting genetic test results
  • Making health decisions on inaccurate or incomplete information
  • Lack of consideration for ethnic and racial differences across human populations
  • Potential for unnecessary, expensive, or time-consuming downstream medical testing
  • No clear regulatory mechanisms in place to assess the analytical and clinical validity, and clinical utility
  • Poor procedures in place to ensure informed consent for the testing process
  • Consumers may not understand the health implications of the information they received
  • Companies could sell aggregate data to third parties or use consumer’s data for research without their awareness

By 2011 the government began cracking down on the practices of direct-to-consumer testing companies. In 2013, the U.S. Food and Drug Administration (FDA) ordered 23andMe to immediately discontinue marketing and sales of its health-related testing services until they received FDA authorization for these devices.

A new model emerges — direct-to-consumer 2.0

In 2015, 23andMe received FDA device approval for its carrier screen for hereditary Bloom syndrome. The FDA confirmed that 23andMe had submitted evidence demonstrating that members of the public were capable of correctly interpreting the test report at a 90 percent comprehension level.

“At the same time the FDA announced that it would classify direct-to-consumer genetic carrier screens as lower risk devices. This opened the way to testing for additional autosomal recessive conditions and signaled the FDA’s willingness to consider at least some forms of direct-to-consumer medical testing under the regulations,” says Dr. Allyse.

That same year Illumina one of the largest providers of genomic sequencing in the U.S. launched Helix, a personal genomics platform that utilizes a “sequence-once-query-often” model. Helix stores genomic information in a central database and allows its partners to develop various testing strategies that interrogate portions of genomic datasets for its customers. In 2017, the FDA approved the marketing of the first direct-to-consumer test for genetic health risk, 23andMe’s Personal Genome Service, which tests for 10 diseases or conditions, including Alzheimer’s risk, Parkinson’s disease, and hereditary thrombophilia.

“These emerging models of direct-to-consumer genetic testing attempt to strike a balance between the need to ensure consumer safety and the knowledge that personal genomic information is both highly desirable and potentially beneficial to some consumers,” says Dr. Allyse.

The future of direct-to-consumer testing 

Dr. Allyse and colleagues speculate on several promising strategies to align the interests of the direct-to-consumer market and the practice of medicine:

  • Improve pre-test education to facilitate the kind of informed consent expected in a medical setting
  • Separate consent to receive testing by purchasing a product from agreeing to the storage, use or sale of samples for research
  • Create clearer pathways into the medical system in the event of high-risk results by partnering with licensed medical providers to ensure information integrity
  • Provide a supportive environment for consumers acknowledging the entertaining nature of genetic information and provide for counseling and follow-up

The Mayo Clinic Center for Individualized Medicine continues to seek ways to apply the latest genomic, molecular and clinical science to personalized care for every individual, so patients receive the exact care they need — when they need it — and to address unmet needs of the patient.

Disclosure: The authors have no personal financial relationships to disclose. Mayo Clinic holds a commercial interest in Helix. There was no relationship between Helix and the contents of this paper.

Mayo Clinic Proceedings Symposium on Precision Medicine 

This paper is part of the Mayo Clinic Proceedings Symposium on Precision Medicine, a series of articles that cover a wide range of topics in personalized medicine. Watch for an upcoming article in the symposium focusing on how personalized medicine and genomics are impacting patient care in the area of heritable cancers.

Read more about the ethical issues of home DNA kits

Learn more about biomedical ethics

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Save the date for this year’s Individualizing Medicine Conference on Sept. 12-13.

Dec 7, 2017 · Microbiome emerges at the frontier of precision medicine

Our genes help determine what makes us unique, such as our eye color, height and whether we are left- or right-handed. But did you know that you also have a unique community of bacteria that live in and on your body, known as your microbiome?

Research has shown that a person’s microbiome affects their health and susceptibility to disease. Your microbiome can be influenced by medications or diet. That’s why microbiome research holds promise for developing individualized approaches to treating a wide range of diseases.

In the latest issue of Mayo Clinic Proceedings, Mayo Clinic researchers reviewed the importance of the microbiome as a key component of personalized medicine to improve diagnosis, reduce disease risk and optimize early detection and treatment. The microbiome is the combined genetic material of the microorganisms in a particular environment.

Purna Kashyap, M.B.B.S.

“The ability to characterize the microbiome, which includes microbes that reside within and upon us and all their genetic elements, using next-generation sequencing allows us to now incorporate this important contributor to human disease in developing new preventive and therapeutic strategies,” says Purna Kashyap, M.B.B.S., a Mayo Clinic gastroenterologist, associate director, Mayo Clinic Center for Individualized Medicine Microbiome Program and lead author of the review.

Potential role of the microbiome in human disease

Here are some applications which highlight the role of the microbiome at the frontier of personalized medicine:

  • Microbial fingerprints could serve as precise, noninvasive, accessible and economical tools that could be used for personalized disease diagnosis, including phenotypes (observable physical characteristics of an individual) severity and prognosis.
  • The role of the microbiome in the metabolism of many chemical compounds makes it a key player in determining drug availability, effectiveness and harmfulness. This could be indispensable for developing personalized drug therapies.
  • The ability to change the microbiome makes it appealing in developing personalized treatment approaches targeting specific microbial pathways tailored to an individual’s microbiota. This may help development of treatments for disorders such as inflammatory bowel disease, obesity and diabetes.
  • Other possibilities include altering the microbiome by using genetic engineering approaches, next-generation prebiotics selectively fermented by gut microbes that confer a health benefit, personalized dietary therapies such as microbiome markers to optimize dietary interventions, and changing the diet based on the microbiome.

Watch: Mayo Clinic offers insights on the microbiome at the frontier of personalized medicine.

Dr. Kashyap expands on the promise and challenges of microbiome research here. 

Mayo Clinic Proceedings Symposium on Precision Medicine 

This paper is the eighth in the Mayo Clinic Proceedings Symposium on Precision Medicine, a series of articles that cover a wide range of topics in personalized medicine. Watch for upcoming articles in the symposium, which will focus on how personalized medicine and genomics are impacting patient care. Learn more about the series.

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See highlights from our recent Individualizing Medicine Conference 2017: Advancing Care Through Genomics:

Save the date for next year’s Individualizing Medicine Conference. It will be held September 12-13, 2018 in Rochester, Minnesota.

 

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