Are Pathologists and Primary Care Physicians Ready for the Genomic Era and Personalized Medicine?

I was reading about the FDA’s recent crackdown on 23andme to stop marketing their saliva based whole genome testing and interpretation service. Rather than resist, 23andme decided to comply and is currently in “talks” with the FDA so that they can complete the process for FDA validation and again begin to market their kits and testing. For now, they can continue to provide their genealogy testing and whole genome sequencing without interpretations.

Currently, in some academic research centers, whole genome or exome sequencing via next generation sequencing (NGS) methods is utilized on a limited basis by researchers and clinicians to identify pathogenic mutations. NGS and bioinformatic analysis methods continue to steadily improve and costs have been decreasing. However, there are limitations and barriers to widespread use at this point. These include but are not limited to: 1) widely used databases such as the Human Gene Mutation Database (HGMD) and the Online Mendelian Inheritance in Man (OMIM) still only contain information that only covers a fraction of the human genome, 2) more research is still needed to identify more variants mutation-disease associations, and 3) most mutations identified fall under the category of “unknown clinical significance”.

Tools such as NGS, despite its improvement over previous technology, still cannot identify large deletions or copy number variations (CNV) and is a technology not accessible, cost-wise and support-wise, to most health care institutions. Despite all of this, primary care physicians, even now, still may be confronted with patients who bring them their genomic screening results, whether obtained from commercial services provided by companies like 23andme or through molecular testing through a health care institution. But today’s physicians, including primary care physicians and pathologists, were not trained in medical school to understand how this testing is performed or the significance of these results. But the time is coming, and maybe sooner than we realize, when we will have to deal with such testing on a daily basis.

So, it is imperative that we train our doctors and doctors-in-training now to be ready for when that time comes. But, my question this week is “How should we go about it?” Additionally, who should compose the health care team to provide guidance and counseling to patients once results are available? And who should regulate how testing should be done and what information should be included in results reporting? Leave me a comment if you have an opinion or any ideas.


Betty Chung, DO, MPH, MA is a second year resident physician at the University of Illinois Hospital and Health Sciences System in Chicago, IL.

Global Health Engagement Month—A Different Perspective

Those of us who work in the international health field are connected in many ways.  We come from a variety of healthcare and public health careers and so approach the needs of global health in different ways. The common thread is strengthening the quality of healthcare and increasing and improving the availability to those in need around the world.

December is designated as Global Health Engagement Month for the US Military communities. All of our branches of service participate in humanitarian assistance and disaster response, and their efforts during times of international need are often the first assistance that some countries receive. In addition to providing care for our military active duty members and their families, our military medical corps from each branch of service provides care, assistance, teaching and disaster response in many different venues. They often work with NGO partners, other countries, and the Ministries of Health and the medical communities of nations in need. It is indeed a “global health engagement” effort that makes a difference. It has been my privilege to work with ASCP laboratory capacity building as a volunteer consultant, and I’ve also had an opportunity to work with the US Navy to build their partnerships with NGOs when they send their hospital ships on humanitarian assistance missions. Seeing global health outreach from several different perspectives keeps me ever mindful of the good work we do, and how much there still is to do in the world!

If you are interested in what our military is doing in providing humanitarian assistance , read about the hospital ships USS Mercy and USS Comfort and see why “Global Health Engagement Month” is so important to our military health colleagues here and here. I’m sure you’ll be amazed and proud of our country and inspired by their stories!



Beverly Sumwalt, MA, DLM, CLS, MT(ASCP) is an ASCP Global Outreach Volunteer Consultant.


Dirty Winds

Over at Body Horrors, Rebecca Kreston writes about public health concerns of infectious disease and parasites. In this thought-provoking post, she discussions musicians (specifically, those who play wind instruments) and lung infections. She cites several small studies that found pathogens (Mycobacterium, Stenotrophomonas, and Cryptococcus) in instruments such as saxophones and trumpets.

The moral of the story: horn musicians, clean your instruments. And don’t ignore a persistent cough.


Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

Personal Genome Testing and You

The recent events with 23andme and the Food and Drug Administration have brought personal genomic testing into the spotlight. In case you haven’t been following the case, the FDA wrote a warning letter to 23andme—a company that will access various points on your genome and give you the results for around $99—that basically states that because the tests diagnose, mitigate, or prevent disease they require regulatory clearance. The FDA also said false positive results for certain breast or ovarian cancer markers could lead to unnecessary preventative surgery.

Since receiving the letter, 23andme as stopped marketing their genetic testing service. At this writing I’m not aware of the status of ongoing testing or if the company is still accepting new samples. 23andme has 15 working days from the date of the letter—which would be 12/13—to let the FDA know how they’re working to resolve the noted issues.

How does this affect laboratory medicine? On the face of it, not that much. Yes, clinical laboratory scientists and pathologists could lose their jobs of the 23andme labs were forced to close their doors. The field of personal genome testing is a relatively new one—23andme began testing in 2008—but even so, it’s important to realize that this type of testing can positively affect laboratory professionals and pathologists.  More laboratories equal more jobs, after all, and not just for bench techs and pathologists, but for consultants, inspectors, and administrators as well. I know that I’ll be watching to see how this plays out.

-Kelly Swails

Acknowledging and Transforming Pathology Stereotypes

I find that in interactions with other specialties, even attending physicians who far surpass me in age, that many have very little idea of what pathologists do. Those who do not work closely with pathologists are the first to mention CSI, forensics, autopsies, and an office in a windowless basement morgue. In fact, I recently heard the story that when a group of attendings and residents from another specialty along with their medical students were told to meet a pathologist for a teaching session in the anatomic pathology department…that they waited outside the locked morgue door before realizing that no one was there and that the morgue was not probably not the intended meeting location.

And for those who work more closely with pathologists, there exists a spectrum of attitudes and perceptions about our profession. We have surgeons who were trained “old school” style with six months of surgical pathology during residency who will sit at the multi-headed scope during intra-operative consultations and who know more than beginning junior residents. Hematology/oncology physicians often stop by hematopathology to look over slides together or to discuss a case. And then there are those who think that pathologists exist to provide them only with diagnoses and who do not look at us as equal members of the patient care team. I’ve heard some even question a diagnosis without ever seeing the slide and others grumble or joke that pathologists take too long to render diagnoses.

I’ve more than a few times had to call attendings, residents, or fellows to recommend canceling an inappropriately ordered test or less commonly, to suggest ordering an indicated one. I found that this more often occurs when there is not a strong differential of diagnoses. Even so, I still have the person on the other end of the line bellowing at me that they just MUST have this expensive molecular test ASAP.

Recently, a medical student who is interested in pathology told me that some residents from a non-pathology rotation harassed and made fun of this student for choosing pathology as their future career. I could continue with more examples but instead I ask this question, “Why is pathology as a field not valued?” especially with respect to specialties like surgery where there is a heavy reliance on pathologists to provide them with diagnoses?

I believe part of the reason lies in lack of exposure to the practical and daily aspects of pathology as a legitimate medical field during medical school. Furthermore, those who chose pathology as a career are often not personality types who proactively engage in promoting or advocating on behalf of the profession, especially at the state and federal levels. We also subconsciously contribute to this issue. For example, we often refer to all non-pathologists as “clinicians” as if there is a difference between these types of doctors and pathologists even though we all completed four years of medical school.

So, what are other reasons do you think contribute to the undervaluing of pathology as a profession, and more importantly, what can we do to change these stereotypes and misconceptions? Let me know by leaving a comment.

-Betty Chung

Is Sample Quality in the Eye of the Beholder?

Here’s a simple experiment to try in your lab: Find a hemolysed sample and separately ask five different medical laboratory scientists to judge the amount of hemolysis present. What you’ll probably find is that “grossly hemolyzed” is most definitely in the eye of the beholder.

Along with hemolysis, lipemia and icterus are determined by judgment calls made by laboratory scientists. Considering that these three interferences make up the bulk of interferences found in patient samples, “eye of the beholder” may not be good enough. Luckily, with most modern chemistry analyzers, it does not have to be.

Most major chemistry analyzers now perform what we like to call “indices”. The HIL (hemolysis, icterus, lipemia) indices are directly measured by the instrument for a given sample. If any of these three interfering substances are present, the instrument will determine both its presence and its concentration. This last point is important also, because some analytes are only affected by a significantly large amount of the interfering substance. Being able to directly measure these interfering substances, allows the instrument to be set to deal with the affected sample in the most appropriate way. It can be set to not analyze those tests affected, or to not report the results on affected tests, or to simply flag the result for footnoting. Computer systems across the interface can likewise be automatically programmed to accept the HIL numbers and respond appropriately.

Analyzers measure the HIL indices in different ways and until recent years, pediatric labs have often been unable to take advantage of analyzer-measured indices. In pediatrics, especially in infant patients, sample volume is often an issue, and so this feature has traditionally been turned off in pediatric labs. However, there are instruments on the market that measure the indices through the pipet tip without using up any sample volume including most of the Ortho Diagnostics analyzers, like the Fusion 5,1 and the 5600. This feature is one of the reasons these instruments are so often found in pediatric labs. In addition, those instruments that use sample volume are now capable of using microliter quantities, like the Siemens Vista or the Roche Cobas 6000.  Utilizing minimal sample volume for this measurement allows the HIL features to be used on these instruments in almost all situations.

Thus the good news is that the sample quality and appropriateness for any given test no longer needs to be in the eye of the beholder.

-Patti Jones

World AIDS Day

This past Sunday (December 1) was World AIDS Day, a day when the international community recognizes the millions of lives that have been taken by AIDS and the additional millions that are living with the disease. As all lab people know, the lab is a crucial part of the diagnosis and care and treatment of HIV/AIDS. From the initial diagnostic tests to the CD4 monitoring tests, the lab plays a crucial role in individual treatment.  Thus, I’d like to take a moment to recognize World AIDS Day on this blog and highlight important statistics about HIV/AIDS.

In the United States, perception of AIDS has progressed greatly from the initial fear of the unknown, to the AIDS quilt and Red Ribbon awareness raising campaigns, to the understanding and knowledge that many people have today.

There is so much that has been done and there have been huge advances in medicine making it possible for people to enjoy a high quality of life while living with the disease. And yet, as the facts and figures below illustrate, there is still so much more to learn and do.

Following are some Facts and figures obtained from the WHO website:

35.3 million people were living with HIV in 2012. An estimated 2.3 million people were newly infected in 2012. An estimated 1.6 million people died of HIV/AIDS in 2012.

2.1 million adolescents (age 10-24) were living with HIV in 2012. A large portion of those are young people in sub-Saharan Africa where girls are more susceptible than boys.

9.7 million people in low- and middle-income countries were receiving ART (anti-retroviral therapy) at the end of 2012. Over 16 million others living with HIV do not have access to ART.

In 2011 56% of pregnant women received the most effective drug regimens to prevent MTCT (mother-to-child transmission). MTCT is almost entirely avoidable with access to the right care.

People living with HIV have the strongest risk for developing active TB. Over 79% of TB cases worldwide are people living in sub-Saharan Africa.  In 2011 it was estimated that a quarter of all HIV related deaths were due to TB.

For an additional summary of facts and figures you can check out the UNAIDS 2013 Global Fact Sheet.

As a quick, related aside, in my information gathering for this post I came across information on the Red Ribbon campaign that I hadn’t known before and thought I’d share. Most of us know the ubiquitous red ribbon which is a universal symbol of awareness and support for those living with HIV. The red ribbon was the first ever ribbon symbol, now commonly used for awareness of many other causes in a rainbow of colors. The idea came from a gathering of artists in 1991 who were trying to come up with a visual to support a NY arts organization that raised awareness for AIDS. Clearly, they were successful in coming up with a powerful visual that is easily replicated and understood around the world. Cheers to those artists!

-Marie Levy

A Special Thanks

I am watching the sky turn brilliant shades of rose, gold, lavender and light blue as the sun rises over Fargo, North Dakota—(speaking of remote places) and I am reminded of so many sunrises I have enjoyed around the world.  When working in another country I often rise very early, make myself a cup of tea and watch the world wake up.  It is such a special time of day, a time of personal reflection and awe of the beauty in the world around us.  It never fails to remind me that no matter who you are, or where you are, “sunrises and sunsets” are universal and give us the promise of a new day, and the rest and peace of day’s end.

The American holiday of Thanksgiving is my favorite day of the year.  It celebrates friends, family, life’s blessings, and the chance to take time to be thankful for what’s been given, and to give in return.  And this year I am again thankful for the unique and exciting places, challenges, and experiences I have had working around the world, and seeing so many of the world’s most beautiful sunrises!

Pictures of course don’t do them justice…but they often find their way to my desktop as the wallpaper, so if you want to see a few, let me know at , I’d be happy to share! In the meantime, I hope you had a Happy Thanksgiving, and perhaps I can encourage you to take a moment to enjoy a sunrise!

Beverly Sumwalt


On the Lab Medicine Website

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