Posts (152)

1 day ago · Personalized screening: finding and treating breast cancer sooner

Deborah Rhodes, M.D.

October is Breast Cancer Awareness Month, a time to reflect on new, individualized approaches to detecting and treating a cancer that affects 1 in 8 American women. Deborah Rhodes, M.D. and her Mayo Clinic colleagues are working to identify the best targeted screening tools and guidelines for women with a higher risk of developing breast cancer – those with dense breast tissue and those with an inherited genetic variation linked to the disease.

With support from the Center for Individualized Medicine, Dr. Rhodes and her colleagues have developed research to find the best way to screen for breast cancer in these populations, with the goal of detecting and treating the disease sooner.

“It’s critical to detect breast cancer early because survival is linked to tumor size at the time a patient is diagnosed. If we discover a tumor when it is less than one centimeter, that patient has over a 90 percent chance of surviving. That’s why we are evaluating how to use new imaging techniques and genetic tests to provide the best care for patients who are at higher risk of developing breast cancer.” – Deborah Rhodes, M.D.

“It’s critical to detect breast cancer early because survival is linked to tumor size at the time a patient is diagnosed. If we discover a tumor when it is less than one centimeter, that patient has over a 90 percent chance of surviving,” says Dr. Rhodes, a Mayo Clinic Breast Clinic physician. “That’s why we are evaluating how to use new imaging techniques and genetic tests to provide the best care for patients who are at higher risk of developing breast cancer.”

Evaluating screening tools for women with dense breast tissue

According to Dr. Rhodes, the 27.6 million women in the U.S. who have dense breast tissue may not be effectively screened with mammography alone. Many states have laws that require physicians to notify women if they have high breast density and how this affects breast cancer detection and risk.

As Dr. Rhodes explains, “We want to build awareness so that women understand that high breast density is the primary reason for missed or delayed breast cancer detection. Dense breast tissue can mask cancer tumors on mammography. Since high breast density increases a woman’s risk of developing breast cancer, it’s important that we find effective screening methods to identify the cancer early, when it is most treatable,” says Dr. Rhodes.

Since there are no consensus guidelines on how best to screen these patients, Dr. Rhodes and her colleagues are conducting a comprehensive evaluation of two screening approaches – 3-D mammograms and molecular breast imaging (MBI).

3-D mammograms have replaced 2-D mammograms as the standard screening tool in many centers. Research has shown that the main benefit of a 3-D mammogram is that it reduces the chance that a patient will be recalled for additional testing because of findings that are false positives and not due to cancer.

“MBI has been shown to more clearly distinguish between dense breast tissue and tumors. In a Mayo Clinic study, MBI detected more than three times the number of cancers compared to 2-D mammograms. We’re exploring whether MBI provides this same advantage over 3-D mammograms,” says Dr. Rhodes.

In addition to comparing cancer detection rates, the Mayo MBI research team is also analyzing the costs associated with each screening method.

Carrie Hruska, Ph.D.

“One of the advantages of MBI is that it can be performed at a relatively low cost, comparable to the cost of a mammogram, and many insurance carriers are starting to cover MBI for screening,”says Carrie Hruska, Ph.D., a Mayo Clinic physicist. “In current trials, researchers are tracking the costs of MBI screening as well as costs of downstream testing generated by findings on MBI and 3-D mammograms in order to compare their cost-effectiveness.”

The team is also addressing a common concern about the higher radiation dose used in MBI, compared to 3-D mammograms. Dr. Hruska and physicist Michael O’Connor, Ph.D. have made several modifications to the MBI system to permit the exam to be performed at a low radiation dose that is safe for routine screening.

The researchers are aiming to lower the radiation dose even further to the same level as a mammogram by applying an image processing algorithm to reduce “noise” in the MBI images. In preliminary studies, using this mathematical model allowed radiation dose to be cut in half, yet the ability to detect breast cancers was preserved.

“We’re carefully evaluating both screening tests and hope to have substantial data to support cancer screening recommendations for patients with dense breast tissue – recommendations that are needed to save lives through earlier detection and treatment,” says Dr. Rhodes.

Hereditary breast cancer – guidelines for a lifetime of care

Mayo researchers and physicians are also collaborating to streamline care for patients whose breast cancer is linked to inherited genetic mutations. A finding of hereditary cancer could lead to changes in treatment, and it could alert other family members that they may also be at a higher risk of developing breast cancer.

Along with Myra Wick, M.D., Ph.D., Dr. Rhodes is co-chair of the Mayo Clinic Familial Cancer Cross Disciplinary Disease Group. The group brings together experts from many specialties –radiology, genetics, surgery, gynecology, oncology, endocrinology, laboratory medicine, pathology and primary care. Their goal is to identify the best care guidelines for patients who either have or are suspected to have a genetic variant linked to hereditary cancer.

“Whether these patients have already been diagnosed with hereditary breast cancer or have a family history suggesting they may have a hereditary breast and ovarian cancer syndrome, we want to identify the best care pathway for them. We’re mapping each patient scenario to determine how to guide their medical care over a lifetime,” says Dr. Rhodes.

Learn more about individualized medicine

For more information on the Mayo Clinic Center for Individualized Medicine, visit our blogFacebookLinkedIn or Twitter at @MayoClinicCIM.

See highlights from Individualizing Medicine: Advancing Care Through Genomics, which was held Sept. 12-13 in Rochester, Minnesota:

 

 

Thu, Oct 4 6:00am · Meet Lisa Schimmenti: Searching for drug therapies to treat hearing loss

Lisa Schimmenti, M.D.

Lisa Schimmenti, M.D. has always been fascinated with Helen Keller and all she accomplished, in spite of being blind and deaf from a very young age. As the newly appointed chair of Mayo Clinic’s Department of Clinical Genomics and a medical geneticist, Dr. Schimmenti cares for patients with similar conditions.

In her clinical practice, she sees children and adults with Usher syndrome, a rare genetic condition that causes deafness or profound hearing loss at birth and blindness by the time a child turns five. With support from the Center for Individualized Medicine and the Department of Otorhinolaryngology, Dr. Schimmenti is using zebrafish to search for drug therapies that could help restore hearing for these patients.

During her career, she’s seen how genomic discoveries have uncovered the causes of many rare diseases and led to the development of new targeted treatments for many more common diseases like cancer and heart disease. Now in her new role overseeing the Department of Clinical Genomics, Dr. Schimmenti is working to extend genomics medicine across all specialties at Mayo Clinic.

“Our clinical geneticists and genetic counselors are collaborating with all departments to facilitate the use of the latest genomic testing technologies to help improve care for all patients.” – Lisa Schimmenti, M.D.

“Our clinical geneticists and genetic counselors are collaborating with all departments to facilitate the use of the latest genomic testing technologies to help improve care for all patients,” says Dr. Schimmenti.

Here’s a closer look at how she’s using the latest genomics tools in her own research to uncover a treatment for hearing loss.

Restoring hearing to boost language development

For newborns diagnosed with Usher syndrome, the only current treatments available for hearing loss are devices such as hearing aids or cochlear implants. However, cochlear implants cannot be implanted until an infant is 12 months old and many infants do not benefit from a hearing aid alone.

“If we can identify a drug to improve hearing, we can help newborns hear sooner, at a time when language development is so critical. They may then be able to use a hearing aid while awaiting a cochlear implant,” says Dr. Schimmenti.

Zebrafish – the perfect model for drug discovery

Dr. Schimmenti and her team are using zebrafish, a type of freshwater fish, to test drug compounds to improve hearing.

“We are able to use zebrafish to model the conditions that we see in the clinic because they share 70 percent of their genes with humans. The same gene that causes Usher syndrome in humans also causes the syndrome in zebrafish,” says Dr. Schimmenti.

The research team tests different therapies by putting the medication into the water. They then measure changes in the hair cells on the zebrafish, which are an important link in the sensory process for hearing, to identify any changes.

The team’s early research results are promising. The next step is to test therapies that have been shown to improve hearing in mouse models.

“While we are early in the research process, the prospect of finding a drug to bypass some of the genetic defects in the sensory process that are causing deafness is very exciting. It’s possible that these therapies could also be applied to treat hearing loss caused by other conditions. For example, some cancer treatments can cause nerve damage and hearing loss. The implications of these discoveries could eventually be far reaching.” – Dr. Schimmenti

“While we are early in the research process, the prospect of finding a drug to bypass some of the genetic defects in the sensory process that are causing deafness is very exciting. It’s possible that these therapies could also be applied to treat hearing loss caused by other conditions. For example, some cancer treatments can cause nerve damage and hearing loss. The implications of these discoveries could eventually be far reaching,” says Dr. Schimmenti.

A passion for genetics

Dr. Schimmenti became interested in genetics early in her medical training. However, she chose a different path before returning to genetics as the focus of her career.

“During my pediatrics training at Harbor-UCLA Medical Center, I saw many young patients with severe hearing loss and was surrounded by outstanding mentors who were working to uncover the genetic causes of these conditions. But at the time, the Human Genome Project, the first mapping of an entire human genome, had not been completed. Genomic discovery was in the early stages, so I chose to pursue a fellowship in critical care at Yale University rather than continue in genetics,” says Dr. Schimmenti.

As progress in genomic discovery continued and genetic variants linked to hearing loss were identified. Dr. Schimmenti decided to return to her true passion – working in the lab to uncover new therapies for the patients with rare genetic diseases that she cared for in the clinic.

She returned to University of Minnesota to complete her genetics fellowship and begin her work using zebrafish to better understand the genetic and molecular processes driving hearing loss.

And she’s never looked back.

“It’s exciting to use genomics to search for a drug that could treat hearing loss and make a real difference for patients. At the same time, I am excited to collaborate with all medical specialties across Mayo Clinic to see how we can extend genomics services to all patients and enhance individualized care for many conditions,” says Dr. Schimmenti.

Learn more about individualized medicine

For more information on the Mayo Clinic Center for Individualized Medicine, visit our blogFacebookLinkedIn or Twitter at @MayoClinicCIM.

See highlights from Individualizing Medicine: Advancing Care Through Genomics, which was held Sept. 12-13 in Rochester, Minnesota:

Mon, Sep 17 8:41am · CIMCON18 -- how genomics discovery is transforming individualized care and the path forward

Moderator Cathy Wurzer and Keith Stewart, M.B., Ch. B.

Mining information deeper than genomics, understanding factors linked to disease, analyzing big data, and addressing the challenges of bringing all this information together to advance patient care – these were some of the themes featured at the Individualizing Medicine Conference: Advancing Care through Genomics held in Rochester, Minnesota, Sept. 12-13, and sponsored by the Mayo Clinic Center for Individualized Medicine.

Keith Stewart, M.B., Ch.B., the Carlson and Nelson endowed director, Mayo Clinic Center for Individualized Medicine, opened the conference by explaining genomics discovery is moving rapidly and the conference gives a glimpse of the exciting research taking place along with how it is already improving patient care.

Here are some of the highlights from this year’s plenary speakers, all bringing their expertise to drive precision medicine forward.

The genomics landscape – from the Human Genome Project to next steps for future discovery

Eric Green, M.D., Ph.D.

Eric Green, M.D., Ph.D., director, National Human Genome Research Institute  at the National Institutes of Health (NIH) traced the advances of genomic testing since it was discovered three decades ago. Chief among them is the landmark completion of the Human Genome Project in 2003, which sequenced the first human genome. Since then, Dr. Green says, the cost of genomic sequencing has dropped by 1 million fold, and it can be done in weeks or days in some labs He also spotlighted key advancements:

  • Uncovering genetic links to cancer
  • Understanding drug-gene interactions through pharmacogenomics
  • Using genomic testing to identify more than 4,000 rare genetic diseases
  • Advancing prenatal care so the health of the baby can be assessed through genetic testing from the mother’s blood, rather than with invasive tests like amniocentesis

Now genomic testing is moving from the research setting into clinical practice. Dr. Green and his team forecast that by 2022, more than 80 percent of genetic testing will take place in the health care system. This trend is one of many factors Dr. Green and his team are considering as they develop a 2020 strategic plan for advancing genomics, gathering input from the broad scientific, health care and patient communities.

Dr. Green also highlighted the National Institutes of Health All of Us Research Program, an unprecedented national research  program that kicked off in May.  All of Us  is enrolling a million people into a research cohort to advance an individualized approach to managing health and disease. Mayo Clinic is home of the biobank that will store biospecimens for the All of Us Research Program.  As of August 2018, Mayo had stored nearly 1.7 million samples from more than 57,000 participants.

Moving pharmacogenomics into daily clinical care

Richard Weinshilboum, M.D.

According to Richard Weinshilboum, M.D., pharmacogenomics is the first area of precision medicine that will be integrated into patient care daily, and predicts that it will, eventually touch every patient everywhere.

Dr. Weinshilboum is co-director of the Mayo Clinic Center for Individualized Medicine Pharmacogenomics Program and a pioneer in the field of pharmacogenomics, which explores how a person’s genetic characteristics affect their response to medications.

At the conference, Dr. Weinshilboum shared the promise and challenges of implementing pharmacogenomics into daily clinical practice. He highlighted Mayo’s RIGHT 10K study, which will add preemptive pharmacogenomics test results for 10,000 Mayo Clinic Biobank patients into their electronic health record.

The goal is to understand how  having this genetic information available at the point of care may help improve care.  The idea is that this information will guide health care providers to identify medications and/or make dose adjustments that are compatible with a patient’s genetic makeup, maximizing the therapy benefit and reducing harmful side effects.

Uncovering the mechanisms driving disease

Manolis Kellis, Ph.D.

Manolis Kellis, Ph.D. is going beyond genomics to understand the processes driving disease. Dr. Kellis, a computational biologist at Massachusetts Institute of Technology (MIT) and the Broad Institute, and his team have developed maps to understand how genetic variations and other biological and molecular processes contribute to many diseases, including heart disease, Alzheimer’s, cancer and obesity.

This groundbreaking approach has uncovered some surprising results. For example, Dr. Kellis and his team found that the strongest genetic association with obesity acts via a master switch controlling energy storage and expenditure, rather than through the control of appetite in the brain. This finding suggests that there is more to controlling weight than watching your diet and getting regular exercise.

Mining biobank and electronic health record data to uncover genetic links to common diseases

Nancy Cox, Ph.D.

While it is exciting to have additional information about patients – their genomic test results, biological data and health history, how can researchers interpret that information so that it can improve a patient’s care?

Nancy Cox, Ph.D. and her team are addressing this challenge with computer models. Dr. Cox, director, Vanderbilt University Genetics Institute and Division of Genetic Medicine, is using these tools to analyze genetic test results from biobank participants, along with data from their electronic health records to better understand a patient’s risk for disease.

As Cox explained, the advantage of this approach is it allows researchers to look across all of the diagnoses associated with a specific gene at the same time, rather than the traditional approach of focusing on one disease. This uncovers conditions or symptoms that may help predict disease, prompting earlier screening and treatment. They’ve developed a publically available catalog of these associations, which include not only genomic but other biological and environmental factors that can help predict disease.

Imaging biomarkers to predict disease

Gabriel Krestin, M.D., Ph.D.

Gabriel Krestin, M.D., Ph.D. is also developing models to predict disease and has been a leader in combining imaging methods with genomic, biological and environmental data to identify subtle changes linked to disease risk.

Using artificial intelligence to analyze data from large-scale population studies of healthy individuals, he and his team have identified imaging biomarkers to predict complex diseases such as dementia and Alzheimer’s.

Their findings are being used to help detect and treat disease sooner.

Dr. Krestin is chairman, Department of Radiology and Nuclear Medicine at Erasmus MC, University Medical Center Rotterdam, in the Netherlands.

Michael Berger, Ph.D.

MSK-IMPACT – large scale genomic testing to guide cancer care

Michael Berger, Ph.D. has made great strides in expanding the search for genetic links to cancer. Dr. Berger, a geneticist at Memorial Sloan Kettering (MSK), and his team developed MSK-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a genetic test that looks across 468 genes associated with both rare and common cancers.

By using MSK-IMPACT to screen more than 20,000 MSK patients with advanced cancer, Dr. Berger has created the largest gene panel database.

Berger highlighted how this testing has changed the course of treatment for patients. For example, MSK-IMPACT testing revealed that a woman previously thought to have metastatic breast cancer actually had cancer that originated in her lungs. As a result, her treatment was changed from hormone therapy to the appropriate chemotherapy.

Test results are also helping direct patients to clinical trials based on the genetic characteristics of a patient’s tumor, rather than where the tumor originated.

CAR T-cell therapy – reengineering immune cells to fight cancer

Yi Lin, M.D., Ph.D.

Chimeric antigen receptor T-cell therapy (CAR T-cell therapy) is a new immunotherapy that reengineers a patient’s own immune cells to create a  living drug that recognizes and fights a patient’s cancer. The therapy is currently approved to treat patients with B-cell non-Hodgkin’s lymphoma and B-cell acute lymphocytic leukemia (ALL) who have not responded to standard therapy.

Yi Lin, M.D., Ph.D., a hematologist at Mayo Clinic’s campus in Rochester, Minnesota, and chair of the Cellular Therapeutics Cross-Disciplinary Group in the Mayo Clinic Cancer Center, shared promising clinical trial results where the majority of patients responded to this new, individualized treatment. She also explained that it is most appropriate for patients whose disease has stabilized and who can handle the range of side effects that may come with this treatment.

Next steps – expand collaboration, build evidence and boost genomic literacy

Heidi Rehm, Ph.D.

Heidi Rehm, Ph.D., wrapped up the conference  with a presentation on collaboration and data standards that are keys to improving the rate of diagnosing rare, genetic diseases. Dr. Rehm has championed many efforts to discover and share disease-related variants in order to move genomics into clinical care.

Dr. Rehm is a geneticist and genomic medicine researcher at the Broad Institute Chief Genomics Officer at Massachusetts’s General Hospital and Professor of Pathology and Harvard Medical School.

Timothy Curry, M.D., Ph.D. and Cathy Wurzer

So what are the next steps in genomics?

“We need to expand these collaborations to build the critical evidence needed to translate genomics into better prevention, screening and treatment for patients. We’re also working to boost genomic literacy so that physicians and patients understand how genomics,  along with other clinical information, can enhance patient care ,” says Timothy Curry, M.D., Ph.D., director, Mayo Clinic Center for Individualized Medicine Education Program.

More conference highlights

Up next – pharmacogenomics for the modern health care team

Mark your calendar and plan to join us at Drugs and Genes: Pharmacogenomics for the Modern Health Care Team 2018 in Scottsdale, Arizona from Nov. 30 to Dec. 1, 2018.

Keep the conversations going

For more information on the Mayo Clinic Center for Individualized Medicine, visit our blogFacebookLinkedIn or Twitter at @MayoClinicCIM.

 

 

Tue, Sep 4 6:00am · Preemptive genetic testing: could it help you take charge of your health?

Konstantinos Lazaridis, M.D.

A blood pressure check, an immunization and a cholesterol test – these are all parts of your routine medical care. Someday, a genetic test to identify your risk for developing disease may also be added to the list. In fact, researchers believe that day is fast approaching thanks to the rapid advances in genomic medicine.

That’s why Konstantinos Lazaridis, M.D. and his research team are exploring how healthy people may benefit from preemptive genetic testing. The goal of their research is to learn more about how using whole genome sequencing (WGS), a type of genetic test, with healthy individuals may:

  • Affect health outcomes
  • Impact healthcare use
  • Affect behaviors and feelings of those who undergo WGS testing

“There are approximately 60 known genetic mutations linked to an increased risk of developing specific diseases. This number will most likely grow as precision medicine research advances. Yet there is very little research on the benefit that preemptive WGS testing may offer healthy individuals, who have no known signs or symptoms of disease. With a one-time WGS test, patients may learn information that could help them take charge of their health and help physicians guide their medical care over a lifetime,” says Dr. Lazaridis, associate director, Mayo Clinic Center for Individualized Medicine.

Who will benefit most?

Dr. Lazaridis and his team want to study WGS testing results from 500 people, all participants in the Mayo Clinic Biobank. He and his team are hoping to describe the frequency that healthy individuals bear disease causing genetic variants and identify whether certain groups have higher rates of genetic variants linked to disease risk.

“Our research results may help us detect those healthy individuals who would benefit most from preemptive genetic testing. For example, we may find that those participants with a family history of a specific disease have a higher likelihood of having a relevant genetic mutation that puts them at risk for developing the same condition,” says Dr. Lazaridis.

The ripple effect – how will genetic information impact patients, their families?

According to Dr. Lazaridis, his team is also exploring the psychological and social implications that genetic test results may have on patients and their families.

“We may have participants who learn they have a genetic mutation such as BRCA1 or BRCA2, both associated with an increased risk for breast and ovarian cancer. As part of our research, we plan to conduct periodic surveys to assess how this information impacts these individuals’ future decisions about screening and treatment. We also want to learn how this new knowledge affects the decisions of their family members. For example, did other family members choose to have genetic testing?” says Dr. Lazaridis.

Knowledge is the key – for patients and providers 

How can we better understand and act on the preemptive WGS test results as patients and health care providers? That’s a question that Dr. Lazaridis and his team are answering through genomics education for participants and the physicians who care for them.

“We’re working closely with primary care providers to educate them on how to interpret and apply WGS test results, along with other clinical results, to guide patient care,” explains Dr. Lazaridis.

The team has developed educational materials for patients that explain how genomic testing works and how test results may be used to direct their medical care now and in the future.

“The test results of each study participant will become part of their electronic health record and subjects with medically actionable findings will have proper follow up and clinical care. As new genomics discoveries are made in the future, these genetic results may even become more impactful in managing care over their lifetime,” says Dr. Lazaridis.

Join the conversation

For more information on the Mayo Clinic Center for Individualized Medicine, visit our blogFacebookLinkedIn or Twitter at @MayoClinicCIM.

Register to attend this year’s Individualizing Medicine Conference. It will be held in Rochester, Minnesota, on Sept. 12-13, 2018.

Mon, Aug 20 8:32am · Preparing the next generation - interns engaged in precision medicine research

Zachary Stephens

When Zachary Stephens started his summer internship at Mayo Clinic in 2013, he was thrust into a world where solving big data challenges can lead to more individualized care for patients. As a graduate student in electrical and computer engineering at the University of Illinois at Urbana-Champaign, he was used to developing computer models to analyze and

interpret large data sets.

But his information technology (IT) internship in the Center for Individualized Medicine  inspired him to explore a whole new world – managing massive amounts of genomics data from the latest DNA technologies to guide precision medicine research and practice.

“We’re exposing students to careers that didn’t exist 5 or 10 years ago. Our goal is to develop the next generation of physicians and scientists in genomic medicine. In turn, we’re reaping the benefits of having enthusiastic, bright students like Zachary bring their expertise to help us more rapidly translate and apply genomic data into daily clinical care.”– Caer Rohrer Vitek

“We’re exposing students to careers that didn’t exist 5 or 10 years ago. Our goal is to develop the next generation of physicians and scientists in genomic medicine. In turn, we’re reaping the benefits of having enthusiastic, bright students like Zachary bring their expertise to help us more rapidly translate and apply genomic data into daily clinical care,” says Caer Rohrer Vitek, operations manager, Mayo Clinic Center for Individualized Medicine Education Program.

Caer Rohrer Vitek

Now completing his fourth summer as an IT and bioinformatics intern through the Mayo Clinic & Illinois Alliance for Technology-Based Healthcare, Stephens has seen firsthand how computational power can help develop more accurate diagnostic tests and individualized treatments for patients.

Stephens is one of many students who come to Mayo to explore research and careers in individualized medicine through the Mayo Clinic Graduate School of Biomedical Sciences. In addition to IT interns, Mayo has also hosted students from Illinois and other universities through the Summer Undergraduate Research Fellowship (SURF) Program.

Meeting the challenge: computer models that help answer clinical questions

During his first summer at Mayo, Stephens’ computational skills made a big impact. He worked with the IT team in Center for Individualized Medicine to find a more efficient way to check the integrity of genomic data.

“When I started in 2013, DNA sequencing data was being reviewed manually to ensure data quality. Over a two-month period, we developed an interface so that genomic data could be compiled and presented in a summary format that could be reviewed much more quickly, saving time and money. This was important because researchers were able to receive results faster, yet have confidence that genetic variants identified through testing were an accurate picture of a disease or condition,” says Stephens.

Now Stephens is putting his computational skills to work to help Jean Pierre Kocher, Ph.D. , director, Center for Individualized Medicine Bioinformatics Program, and his team develop clinical genetic tests to uncover genetic mutations linked to complex diseases.

“What makes this work so exciting is that we are developing algorithms to analyze data from the latest, cutting edge technologies, known as long-read sequencers. This technology is at the forefront of precision medicine because it can help researchers find differences between very similar DNA variants that conventional methods cannot detect. This work is already helping guide diagnosis and treatment for heart disease, cancer, and rare and undiagnosed diseases.” – Zachary Stephens

“What makes this work so exciting is that we are developing algorithms to analyze data from the latest, cutting edge technologies, known as long-read sequencers. This technology is at the forefront of precision medicine because it can help researchers find differences between very similar DNA variants that conventional methods cannot detect. This work is already helping guide diagnosis and treatment for heart disease, cancer, and rare and undiagnosed diseases,” says Stephens.

With only one year until he completes his Ph.D., Stephens is considering a career that includes precision medicine. “I’m thankful to have already worked with Mayo researchers who are staying ahead of the curve in individualized care.”

Benefactors help educate the next generation

Support from these benefactors has helped many eager students explore the genomics frontier this summer:

  • Brandt Young Scholars Fund
  • Brian P. and Doris G. Monieson Fund for Mayo Clinic Summer Undergraduate Research Fellowships, Center for Individualized Medicine.

“Thanks to our generous benefactors, we are able to bring talented students to Mayo and introduce and engage them in precision medicine research. Each student works with research mentors, many who are leaders in their field. It’s so exciting to see the students share their research projects at the end of the summer. Their eyes have been opened to the promise of precision medicine,” says Rohrer Vitek.

Join the conversation

For more information on the Mayo Clinic Center for Individualized Medicine, visit our blogFacebookLinkedIn or Twitter at @MayoClinicCIM.

Register to attend this year’s Individualizing Medicine Conference. It will be held in Rochester, Minnesota, on Sept. 12-13, 2018.

Mon, Aug 6 12:20pm · Unlocking the power of genomics data: course offers new tools for discovery

The 2018 Computational Genomics Course, sponsored by the Mayo Clinic & Illinois Alliance for Technology-Based Healthcare, was held in June at three locations – Mayo Clinic’s campuses in Rochester, Minnesota; and Jacksonville, Florida; and at the Carl R. Woese Institute for Genomic Biology at the University of Illinois. Pictured above are attendees at Mayo Clinic in Rochester.

Michelle Cox was among the medical students and trainees, research fellows and laboratory staff who recently gathered to attend this year’s Computational Genomics Course, sponsored by the Mayo Clinic and Illinois Alliance for Technology-Based Healthcare. Even before the week-long course ended, Cox, a research technologist in the Mayo Clinic Division of Hematology, was sharing what she had learned with her colleagues.

“In the first days of the course, I learned some new approaches to visualizing and analyzing genomics data. It may help us refine CAR-T cell therapy, which genetically reengineers a patient’s own immune cells to fight their cancer. While this therapy is already helping patients with certain types of leukemia and lymphoma, our team is investigating how it can be used to treat other types of cancer as well,” says Cox, who is also a graduate student in the University of Minnesota Bioinformatics and Computational Biology Program.

The intensive course, a collaboration between Mayo Clinic and the University of Illinois at Urbana Champaign (Illinois), provides an overview of the latest tools available to rapidly analyze and interpret the vast amounts of data generated by DNA testing.

Integrated curriculum helps put the pieces together

Michelle Cox

For Cox, the course format and curriculum helped her see how all the complex pieces of genomic analysis come together.

“The course curriculum is a great integration of biology, computation and genetics. I came to the course as a biologist without a lot of programming background. Now I am starting to put all the pieces together and seeing how these tools can improve our understanding of the treatment of disease,” explains Cox.

University of Illinois faculty taught lectures and led hands-on lab exercises in a variety of subject areas.

Krishna Rani Kalari, Ph.D.

Mayo Clinic researcher Krishna Rani Kalari, Ph.D., also shared how she is applying novel computational approaches to analyze and visualize publically available large-scale cancer genomics data sets. She provided examples of how a researcher or a biologist with limited programming skills could mine multi-omics data with existing bioinformatics tools. She also presented novel omics-guided drug prioritization methods developed by her team. The goal of these algorithms is to identify mutations and dysregulated pathways that are associated with the tumor of an individual patient for personalized treatment.

A springboard for discovery, collaboration

Michael Kalmbach

According to Michael Kalmbach, a lead analyst and programmer in Bioinformatics Systems at Mayo Clinic and teaching assistant for the course, many participants become inspired like Cox – ready to look at genomics data in their own research in a new way.

“Every year, the Computational Genomics Course serves as a springboard for discovery and future collaborations. Each participant leaves with new tools, helping them ask the next set of questions to move discovery forward and improve patient care. We stay in touch with many participants over the years, helping to answer questions and collaborate on research solutions. Participants also network and collaborate with each other,” says Kalmbach.

The sixth annual Computational Genomics Course was held June 18-22 in three locations: Mayo Clinic’s campuses in Rochester, Minnesota; and Jacksonville, Florida; and at the Carl R. Woese Institute for Genomic Biology at the University of Illinois

Genomics data challenges, CAR-T cell therapy highlighted at 2018 Individualizing Medicine Conference

Sponsored by the Mayo Clinic Center for Individualized Medicine, the conference will be held on Sept. 12-13 at the Mayo Civic Center in Rochester.  See the full schedule and register to attend here.

Join the conversation

For more information on the Mayo Clinic Center for Individualized Medicine, visit our blogFacebookLinkedIn or Twitter at @MayoClinicCIM.

 

Mon, Jul 30 8:41am · Tool of the trade: researcher applies artificial intelligence to uncover causes, risks for disease

Manolis Kellis, Ph.D.

Some diseases, such as certain breast and colon cancers, are linked to genetic mutations passed down in families. But for many other diseases there are no direct genetic links that explain why the disease develops. That’s why Manolis Kellis, Ph.D. and his team are using artificial intelligence to uncover the hidden cause of disease.

Dr. Kellis will discuss his team’s landmark research in combining computational models and experimental techniques to help analyze genomic, epigenomic and health care data at this year’s Individualizing Medicine Conference: Advancing Care through Genomics. His plenary presentation will highlight how his approach can identify epigenomic factors, which are elements in the human genome and associated proteins involved in regulating gene activity, and how these elements respond to environmental factors to control genes. He’ll also highlight how these environmental influences can be revealed by analyzing patients’ electronic medical record.

Dr. Kellis, a computational biologist at Massachusetts Institute of Technology (MIT) and the Broad Institute, and his team have developed computer models to sift through large amounts of genomic, biological and health care data to identify mechanisms driving disease. They’ve already made great strides, identifying underlying factors leading to obesity, heart disease, cancer, psychological disorders and Alzheimer’s disease. Dr. Kellis’ computational model that enables the systematic discovery of functional elements of the genome and the functions of noncoding genetic variants is now a tool of the trade, used widely to define disease processes and predict disease risk.

Defining the “dark matter” of the genome to uncover disease risk

Tamas Ordog, M.D.

Dr. Kellis and his team have helped define what is often called the “dark matter” of the genome — large regions between genes, which contain 93 percent of disease-associated genetic variants. Investigators have been puzzled for a long time about what underlying mechanisms mediate the effects of genetic variations on disease risk.  Thanks to the work of Dr. Kellis and his colleagues, we now have a better understanding of how these variants modify the regulation of gene expression by biological and environmental signals and affect the development and course of human disease.

“Dr. Kellis’ landmark research has helped define what was previously unknown — the function of the vast amount of DNA material that exists outside of known genes. His work has helped reveal mechanisms that cause disease and predict where in the body disease may develop. This information will be invaluable to researchers working to develop tests to identify which patients are at risk for specific diseases, allowing earlier diagnose and treatment,” says Tamas Ordog, M.D., director, Mayo Clinic Center for Individualized Medicine Epigenomics Program.

Personalizing the search – adding clinical data to identify individualized treatments

Dr. Kellis and his team are now refining their model by adding clinical information from electronic health records to advance personalized care for patients.

“We’re excited to be collaborating with Dr. Kellis and his team as they refine their model to identify individualized treatments for patients. To date, Dr. Kellis’ approach has successfully integrated multiple layers of epigenomic data and genetic information to better understand disease. By adding patients’ clinical information, he and his team are accelerating the search for more personalized approaches to treating many diseases,” says Dr. Ordog.

Dr. Kellis directs the MIT Computational Biology Group. He has helped lead several large-scale genomics projects, including the National Institutes of Health Roadmap Epigenomics project, the comparative analysis of 29 mammals, the Encyclopedia of DNA Elements (ENCODE) project, and the Genotype Tissue-Expression (GTEx) project. Dr. Kellis has also received several awards for his work, including the US Presidential Early Career Award in Science and Engineering (PECASE), the NSF CAREER award, and the Alfred P. Sloan Fellowship.

Join us at the conference

Mayo Clinic Center for Individualized Medicine is hosting the Individualizing Medicine Conference on Sept. 12-13, 2018.  The conference brings together experts from Mayo Clinic and around the world to discuss how the latest discoveries in precision medicine can be applied to improve patient care.

 

Mon, Jul 16 9:46am · Bioethics in the Cinema Program celebrates our WONDERful differences

Megan Allyse, Ph.D.

For many young children, the first day of the school year is filled with excitement. But for August (Auggie) Pullman and his parents, the first day of fifth grade at a public school is an anxious time. That’s because Auggie has facial differences from a genetic condition called Treacher Collins syndrome and has always been taught at home.

Auggie’s story is featured in the film Wonder that will be shown as part of the “Bioethics at the Cinema” series on Sunday, July 22, from 4 to 7 p.m., at the Rochester Civic Theater Company, in Rochester, Minnesota. Mayo Clinic Biomedical Ethics Research Program and Rochester Public Library are sponsoring the series, which seeks to create dialogue with the community around appreciation for difference. The event is free and open to all ages.

Wonder explores the challenges and triumphs Auggie and his parents face as the school year unfolds. After the movie, a panel of community members will lead a discussion about bioethical issues raised in the movie. With the rapid advances in genetic testing technology, more patients like Auggie are being diagnosed with genetic disorders that often cause multiple medical complications. As these patients and their families navigate daily life, they encounter many bioethical issues, such as access to appropriate medical care, education and support resources.

“A group of community members from a variety of backgrounds chose the film to highlight the challenges as well as the joy that children with genetic conditions and disabilities and their families experience. We encourage families to attend this event because, as the film illustrates, it’s never too early to learn about our differences. We hope our discussion will shed light on the biases and misconceptions that these patients and their families encounter. I see these issues arise as we work with young patients with genetic conditions and their families. Often times, parents tell us that while their families face challenges, they are also living a full and wonderful life,” says Megan Allyse, Ph.D., a Mayo Clinic bioethicist and chair of the Bioethics in Cinema Committee.

The disABILITY Mayo Employee Resource Group (MERG) and Minnesota Children’s Museum in Rochester are also collaborating in this event.

The program will feature:

4 p.m. Movie screening of Wonder

Based on the New York Times bestseller, Wonder tells Auggie’ s inspiring story as he makes friends and shows his peers that he is a “wonder” not because of his physical differences, but because of his perseverance, intelligence and sense of humor.

The film also sheds light on his parent’s journey, highlighting the ups and downs as they strive to give their son opportunities to reach his full potential.

6 p.m.: A community conversation  

Cassandra Runke

Following the movie, stay for a community conversation about bioethical issues faced by patients with genetic disorders and their families. Hear a panel of local community members – teachers, students and those who work with individuals with disabilities – share their perspectives.

In addition, Cassandra Runke, a Mayo Clinic genetic counselor who works with patients with craniofacial conditions, will answer questions about genetic disorders and explain how genetic counselors help patients and their families access services and resources for support.

Bioethics at the Cinema community conversation series

Mayo Clinic Bioethics Research Program staff and the Rochester Public Library are collaborating to pair screenings of classic and contemporary films with lively presentations by notable science and technology experts. Each film is used as a jumping-off point for a speaker to create dialogue with the community around complex and timely topics.

Join the conversation

For more information on the Mayo Clinic Center for Individualized Medicine, visit our blogFacebookLinkedIn or Twitter at @MayoClinicCIM.

Register to attend this year’s Individualizing Medicine Conference. It will be held in Rochester, Minnesota, on Sept. 12-13, 2018.

 

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