Sep 28, 2018 | Laboratory Pathology
Even in its early stages the Human Cell Atlas project is impacting the direction of research and development of RNA sequencing and other genetic tests
No one knows exactly how many cell types exist in the human body. Though traditional texts place numbers in the hundreds, recent studies have found ranges from thousands to tens of thousands. Anatomic pathologists and clinical laboratory scientists know that the discovery of new types of human cells could lead to the creation of new medical laboratory tests.
So, it’s an important development that leaders of the Human Cell Atlas Consortium, a project comparable to the Human Genome Project, have set out to determine the exact numbers of cell types. And their findings could open up an entirely new field of diagnostic testing for clinical laboratories and anatomic pathology and lead to advances in precision medicine.
With the ability to identify cell types and sub-types associated with human disease and health conditions, medical labs could have a useful new way to help physicians make diagnoses and select appropriate therapies.
Begun in 2016, the group’s mission according to the Human Cell Atlas website is “To create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human health and diagnosing, monitoring, and treating disease.”
The ambitious project aims to catalog every cell type in the human body and “account for and better understand every cell type and sub-type, and how they interact.”
Striving for Deeper Understanding of the Basics
Cells are the basic building blocks of life, but scientists don’t know exactly how many different types of cells there are.
In an NPR interview, Aviv Regev, PhD, Professor of Biology and a core member at the Broad Institute of MIT and Harvard, investigator at the Howard Hughes Medical Institute, and co-leader of the Human Cell Atlas Consortium, said, “No one really knows how many [cells types] there will be,” adding, “People guess anything from the thousands to the tens of thousands. I’m not guessing. I would rather actually get the measurements done and have a precise answer.”
In an innovative move, Regev and her team improved the method they were already using to sort cells—single-cell RNA sequencing. “All of sudden we moved from something that was very laborious—and we could do maybe a few dozen or a few hundred—to something where we could do many, many thousands in a 15- to 20-minute experiment,” she told NPR.
Dark Daily covered a similar advance in single-cell RNA sequencing in “‘Barcoding’ Cells in Nematodes Could Bring Advances and New Medical Laboratory Tools for Treatment of Cancer and Other Chronic Diseases.”
But the project is massive. A typical human body contains about 37.2 trillion cells. So, the Human Cell Atlas scientists decided to complete preliminary pilot projects to identify the most efficient and effective strategies for sampling and analyzing the various cells to create the full atlas.
“It’s kind of like we’re trying to find out what are all the different colors of Lego building blocks that we have in our bodies,” Sarah Teichmann, PhD, Head of Cellular Genetics and Senior Group Leader at Wellcome Sanger Institute in the UK, and co-leader of the Human Cell Atlas Consortium, told NPR. “We’re trying to find out how those building blocks—how those Lego parts—fit together in three dimensions within each tissue.”
Sarah Teichmann, PhD (left), and Aviv Regev, PhD (right), are co-leaders of the Human Cell Atlas Consortium, an ambitious project of MIT/Harvard Broad Institute that seeks to “create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human health and diagnosing, monitoring, and treating disease.” Such an advance could lead to significant advances in clinical laboratory and pathology testing and move healthcare closer to true precision medicine. (Photo copyrights: University of Cambridge and MIT/Broad Institute.
Some of the early pilot projects include a partnership with the Immunological Genome Project (ImmGen) to study and map the cells in the immune system. According to the Human Cell Atlas website, the partnership “will combine:
- “deep knowledge of immunological lineages;
- “clinical expertise and infrastructure needed to procure and process diverse samples;
- “genomic and computational expertise to resolve the hundreds of finely differentiated cell types that compose all facets of the immune system; and,
- the genomic signatures that define them.”
Other areas the pilot projects will address include:
Progress So Far
In the two short years since the Human Cell Atlas project began much work has already been accomplished, according to a news release. In addition to organizing the consortium and obtaining funding, the collaborators have published a white paper describing their goals and a framework for reaching them, as well as launching the pilot projects.
Such an ambitious project, however, is not without barriers and challenges. Regev and Teichmann, along with other collaborators, outlined some of those challenges in an article published in Nature.
The complexity of the human body combined with rapidly changing technology make simply agreeing on the scope of the project challenging. In order to meet that particular challenge, the collaborators plan to work in phases and drafts, which will allow for some flexibility and increasing focus on specifics as they go.
Other challenges include:
- keeping the entire project open and fair;
- procuring samples with consent and in an appropriate manner; and,
- organizing in an efficient and effective manner.
The collaborators have developed and detailed strategies for meeting each of these challenges.
The Human Cell Atlas could impact treatments for every disease that affects humans and bring healthcare closer to accomplishing precision medicine goals. By knowing what cells exist in what parts of the human body—and how they typically behave at their most basic levels—the MIT/Harvard/Broad Institute scientists hope to understand what’s happening when those cells “misbehave” in expected ways. The knowledge garnered from the Human Cell Atlas is likely to be invaluable to anatomic pathologists and clinical laboratories.
—Dava Stewart
Related Information:
Ambitious ‘Human Cell Atlas’ Aims To Catalog Every Type of Cell in the Body
‘Barcoding’ Cells in Nematodes Could Bring Advances and New Medical Laboratory Tools for Treatment of Cancer and Other Chronic Diseases
International Human Cell Atlas Initiative
The Human Cell Atlas White Paper
A Revised Airway Epithelial Hierarchy Includes CFTR-Expressing Ionocytes
Single-Cell Transcriptomes from Human Kidneys Reveal the Cellular Identity of Renal Tumors
The Human Cell Atlas: from Vision to Reality
‘Barcoding’ Cells in Nematodes Could Bring Advances and New Medical Laboratory Tools for Treatment of Cancer and Other Chronic Diseases
Aug 23, 2018 | Digital Pathology, Laboratory Management and Operations, Laboratory News, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations
Genetic testing, gene sequencing done by clinical laboratories and anatomic pathology groups underpin how first-mover hospitals, health networks are improving patient outcomes
In just a few weeks, an unprecedented gathering will bring together the nation’s most prominent first-mover health networks, hospitals, and companies operating programs that deliver precision medicine daily to patients in clinical care settings.
On Sept. 12-13, 2018, “Breakthroughs with Genetic and Precision Medicine: What All Health Network CEOs Need to Know,” will take place at the Hutton Hotel in Nashville, Tenn. “What differentiates these sessions is the emphasis on each organization’s strategy, how it launched its precision medicine programs, what is improving in patient outcomes, and how payers are reimbursing for these services,” stated Robert L. Michel, Executive Director of the Precision Medicine Institute in Austin, Texas. “This is not about the science of precision medicine. Rather, it is about the practical elements required for any hospital, health system, or physician group to actually set up and deliver a precision medicine service to patients on a daily basis.”
Precision Medicine’s First-Mover Hospitals and Providers to Speak
Health systems and hospitals headlining this special conference are:
Companies scheduled to present include:
- Illumina;
- Humana;
- Sonic Healthcare USA;
- Genome Medical;
- CQuentia, and,
- S. HealthTek.
Exhibitors include the above, plus: Thermo Fisher, Philips, Sunquest, and MyGenetx.
“This meeting will give you the insider’s understanding about delivering precision medicine in real patient care settings that cannot be accessed at other venues,” noted Michel. “The goal is to have first-mover providers share their experiences, thus providing a road map that other hospitals, physician practices, and other providers at this conference can take back and follow with confidence.”
Michel said that sessions will be dedicated to precision medicine strategies, how it is being used in oncology, primary care, the role of pharmacogenomics, and use of healthcare big data. Speakers will describe the clever ways innovative health networks and hospitals are using healthcare big data to inform physicians in ways that improve outcomes, lower the cost of care and, in two real-world case studies, are generating seven-figure reimbursement from shared savings programs with certain health plans.
This year’s keynote address is by Jeffrey R. Balser, MD, PhD (above), President and CEO, Vanderbilt University Medical Center and Dean of the Vanderbilt University School of Medicine, one of the most progressive and innovative health systems in the country. (Photo copyright: Vanderbilt University.)
Using Healthcare Big Data to Achieve Precision Medicine Success, Shared Savings
“Shared savings successes will be one of the breakthrough achievements reported at the Nashville event,” he explained. “We’ve invited two prominent provider organizations to share how they are using healthcare big data to support physicians in achieving improved patient outcomes while at the same time impressively reducing the overall cost of care. To my knowledge, this is the first time these precision medicine case studies have been presented at a national meeting.”
One such presentation will be delivered by Philip Chen, MD, PhD, Chief Healthcare Informatics Officer at Sonic Healthcare USA Austin, Texas. Their precision medicine goal was to use healthcare big data to help physicians better manage diabetes and other chronic conditions in their practices. This program involved a large primary care practice and a major health insurer. Now in its fourth year, Sonic Healthcare USA is earning six- and seven-figure payments as part of a shared savings arrangement with the insurer.
“Shared savings is definitely a Holy Grail for all large health networks and physician groups as payers drop fee-for-service and switch providers to value-based payments,” said Michel. “The experience of Sonic Healthcare in this innovative three-way collaboration with an insurer and a very large physician group demonstrates that a strong data analytics capability and engagement with physicians can simultaneously bend the cost-of-care-curve downward while improving patient outcomes, as measured year-by-year. This is a presentation every C-Suite executive should attend.
Strategic, Business, Operational, and Financial Aspects of Precision Medicine
“This conference—centered upon the strategic, business, operational, and financial aspects of a precision medicine program—came to be because it is the unmet need of every health network CEO and C-Suite administrator,” observed Michel. “Every healthcare leader tasked with developing an effective clinical and financial strategy for his or her institution knows that the real challenge in launching a precision medicine program for patient care is not the science.
“Rather, the true challenges come from how to support clinical needs with the availability of capital, recruiting experienced clinicians, and putting the right informatics capabilities in place,” he stated. “Most hospital and health network administrators recognize the risk of launching a precision medicine program too early. They know such programs can suck up huge amounts of resources without producing significant improvements in patient care. What adds to the risk is that payers may be slow to reimburse for precision medicine.”
Register today to guarantee your place at “Breakthroughs with Genetic and Precision Medicine: What All Health Network CEOs Need to Know,” (or copy and paste this URL in your browser: https://dark.regfox.com/precision-medicine-institute).
Register by September 1 and save $300 on tuition! Plus, take advantage of our special Team Discount Program, so you and your key team members can get the most out of the conference by attending together.
“Breakthroughs with Genetic and Precision Medicine: What All Health Network CEOs Need to Know” is the gold-standard summit for everyone active or interested in succeeding with precision medicine programs. Don’t miss out—register today!
—Michael McBride
Related Information:
Breakthroughs with Genetic and Precision Medicine: What All Health Network CEOs Need to Know—Full Agenda and Details
Breakthroughs with Genetic and Precision Medicine: What All Health Network CEOs Need to Know—Registration information
Ongoing Growth in Consumer Genetic Testing Pressures Hospitals, Healthcare Networks to Educate and Prepare Physicians
Syapse Creates Precision Medicine Council That Quickly Attracted 200 of the Biggest Hospitals and Health Networks as Members
When Ramping Up Genomic Programs, Health Network/Hospital CEOs and Executives Must Consider Emerging Technologies, Swiftly Rising Consumer Demand
Precision Medicine Success Hinges on Diagnostics’ Clinical Utility
Precision Medicine and Sharing Medical Data in Real Time: Opportunities and Barriers
Ongoing Growth in Volume of Clinical Laboratory Tests That Support Precision Medicine Due to Physician Acceptance; Payers Still Have Concerns
Aug 14, 2018
PRESS RELEASE
PRECISION MEDICINE INSTITUTE, LLC
21806 Briarcliff Dr.
Spicewood, Texas 78669
512-264-7103 o
512-264-0969 f
FOR IMMEDIATE RELEASE
Media Contact: Chris Garcia
Chris@darkreport.com
AUSTIN, Texas (August 14, 2018)—Precision Medicine is happening now at first-mover hospitals and health systems! September 12-13 in Nashville, experts from the nation’s most successful precision medicine clinical programs will gather to share their strategies and lessons learned. The goal of this conference is to provide hospital CEOs with the insights needed to initiate effective precision medicine programs in their own institutions.
“Precision Medicine for Health Network CEOs: What You Need to Know about Genetic Testing, Precision Medicine, and Population Health Management” is a timely, two-day conference. It takes place at the Hutton Hotel in Nashville. This intimate meeting features nationally-respected, first-mover and early-adopter health networks sharing strategies, patient care successes, and outcomes from their precision medicine programs.
Keynote speaker is Jeffrey Balser, MD, the CEO of Vanderbilt University Medical Center. VUMC is internationally recognized for its pioneering efforts to bring precision medicine into daily clinical care. Attendees will gain essential insights into the early successes of precision medicine at VUMC, and will also learn about how the healthcare big database at Vanderbilt is being used to inform population health initiatives while also guiding the care that clinicians deliver daily to individual patients.
Among the twenty expert speakers sharing their respective experiences at bringing precision medicine, genetic medicine, and genetic testing into the daily care provided to their patients, will be:
- Howard L. McLeod, PharmD, Medical Director, Personalized Medicine Institute, Moffitt Cancer Center, on Precision Medicine in Oncology/Cancer Care
- Mark Van Oene, Chief Commercial Officer, Illumina, Inc., on Genetic Testing and Gene Sequencing’s Role in Precision Medicine
- Julie A Johnson, PharmD, Dean, College of Pharmacy, University of Florida, on Precision Medicine in Pharmacogenomics
- Josh Denny, MD, Vice President of Personalized Medicine at Vanderbilt University Medical Center, on Genetic and Molecular Data in Population Health
For more information and to register to attend “Precision Medicine for Health Network CEOs: What You Need to Know about Genetic Testing, Precision Medicine, and Population Health Management,” click here. You may also contact Chris Garcia at 512-264-7103.
About Precision Medicine Institute, LLC
The Precision Medicine Institute has the unique mission of bringing together the executive leaders and physician leaders of the nation’s leading healthcare organizations, health networks, and corporations to understand the successes of first-movers and early-adopters as they bring precision medicine into clinical settings. The emphasis is on high-level knowledge of business strategies, clinical initiatives, and operational requirements needed to implement and sustain a clinically-effective and financially-sustainable precision medicine service that measurably improves patient care while helping hospitals avoid costs and generating ample reimbursement.
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Mar 26, 2018 | Compliance, Legal, and Malpractice, Laboratory Management and Operations, Laboratory Operations, Laboratory Pathology, Laboratory Testing, Management & Operations, News From Dark Daily
As the public gains awareness of the role clinical laboratories play in modern healthcare, increased engagement and understanding of the technology underlying many of these advances could create risk for labs without transparent reporting protocols to both patients and the public
In recent years, consumers have continually raised the bar in their expectation of quality when they interact with the healthcare system. Not only do patients expect providers—including clinical laboratories and anatomic pathology groups—to improve regularly over time, but the public has even less tolerance for medical errors of any type. Thus, a recent NPR story is one more warning to the medical laboratory profession that it should be devoting resources and effort to improving quality.
Today’s healthcare consumers and patients are more educated about and involved in the care process than ever before. While the exact science and skills may not interest the general public, the technologies underpinning much of the shift toward personalized medicine (AKA, precision medicine) are the same technologies that created the always-connected, digital lifestyles seen around the world.
With this, comes a level of scrutiny and questioning from the public that clinical laboratories or anatomic pathology groups would not have experienced even just a decade ago.
Mounting Scrutiny of Medical Laboratories and Healthcare Professionals
A recent segment on NPR’s “All Things Considered” highlighted this trend and questioned the quality control standards behind many of the procedures powering current testing. The segment also questioned the impact quality control has on the quality of biobanks used to research and create future technologies and tests.
Pathologist Richard Friedberg, PhD, Medical Director of Baystate Reference Laboratories and former president of the College of American Pathologists, told NPR, “We need to be sure that the stuff [doctors and researchers are] looking at is valid, accurate, reliable, and reproducible … If it’s garbage in, it’s garbage out.”
The story highlights improved standards and guidelines surrounding immunohistochemical (IHC) HER2 tests in the early 2000s. In 2007, The New York Times questioned the reliability of the tests, based on studies presented to the American Society of Clinical Oncology the week prior.
In response, the American Society of Clinical Oncology and the College of American Pathologists released guideline recommendations outlining the exact standards required to reduce assay variation and ensure that data produced is accurate and reproducible. NPR’s coverage claims this is the only test with such strict guidelines.
“I don’t think physicians think this way about their entire medical system,” Carolyn Compton, PhD, CMO of the National Biomarker Development Alliance, CMO of the Complex Adaptive Systems Initiative, and professor of Life Sciences at Arizona State University, told NPR. “I don’t see how we’re going to get precision medicine at the end of the day when everything under the hood is so imprecise.”
When data and previous research powers much of the innovation taking place across the modern healthcare landscape, the accuracy of said data would seem critical. Yet, without standards in place, there’s not always safeties by which to verify sample integrity and other critical concerns.
Late last year, Dark Daily reported on a study published in PLOS ONE from Radboud University in the Netherlands questioning the accuracy of more than 30,000 published scientific studies that contained misidentified or contaminated cell lines. Guidelines, such as those created for IHR and FISH HER2 testing, provide standards intended to prevent such issues from occurring or detecting them when they do occur.
Quality versus Quantity: A Gamble Worth Taking?
Apart from challenges with healthcare reform and the regulatory landscape surrounding precision medicine, medical laboratories also must struggle with the challenges of gleaning and maintaining useful, accurate information from an ever-growing trove of data produced by analyzers and assays.
Yet, these mediocre datasets include the results of tests that carried a potentially significant impact on patient lives. In the first two weeks of February alone, both the St. Louis Post-Dispatch and The Telegraph published stories related to erroneous testing related to cancer and the potential impact on the clinical laboratories involved and the patients tested.
Increased coverage shows that the world is watching what goes on in medical laboratories, hospitals, and data centers as healthcare continues to evolve. Clinical laboratories must move forward with this in mind or risk pushback and questioning from the public. Transparency regarding standards, and reporting information to patients surrounding testing or concerns, might effectively address this rising trend.
“We are moving faster and faster and faster as this whole precision medicine train is moving down the track,” Tim Allen, MD, Laboratory Director at the University of Texas Medical Branch Department of Laboratory Services, told NPR. “I suspect standardization of these things is going to become a reality much quicker than I would have expected even a few years ago.”
That quality control issues in anatomic pathology are considered newsworthy by no less than NPR is a sign of increased public attention to the quality of lab testing. The story was written to educate the public about the gap that exists in the quality control of anatomic pathology testing. All of this is consistent with the trend for providers to be transparent and report their quality metrics to the public, including patients.
—Jon Stone
Related Information:
Hormone Receptor Testing Volume 1: Investigation and Findings Commission of Inquiry on Hormone Receptor Testing
Precision Medical Treatments Have a Quality Control Problem
HER2 TESTS: How Do We Choose?
Cancer Drug May Elude Many Women Who Need It
American Society of Clinical Oncology/College of American Pathologists Guideline Recommendations for Immunohistochemical Testing of Estrogen and Progesterone Receptors in Breast Cancer
Impact of Electronic Health Record Systems on Information Integrity: Quality and Safety Implications
His Doctor Said It Was Cancer. It Wasn’t. But the Lab Mix-Up News Came Too Late.
Up to 60,000 Cancer Test Results May Have to Be Reviewed After Women Wrongly Given the All-Clear
Over 30,000 Published Studies Could Be Wrong Due to Contaminated Cells
Netherlands University Researchers Question Validity of More Than 30,000 Published Scientific Studies; Findings Have Implications for Medical Laboratories
Feb 15, 2018
More and more physicians are now including elements of precision medicine in their clinical practice, thus requiring them to use molecular and genetic tests. Physician demand for these tests will continue to increase for a powerful reason: patients want the benefits from a diagnostic test that delivers a more accurate diagnosis, while pointing the doctor to the right therapy that minimizes side effects. Because tests in support of precision medicine will be the fastest-growing sector of laboratory medicine for years to come, every clinical laboratory and pathology group needs a strategy for how it will serve precision medicine lab testing. Learn more about this important webinar now!
