It’s time to correct some facts on laboratory testing for SARS-CoV-2 (the virus that causes COVID-19)

OK, people, it’s time to correct some facts on laboratory testing for SARS-CoV-2.  The media and our government officials recently seem to think that the reason why SARS-CoV-2 laboratory tests are taking such a long time is because lab staff are twiddling their thumbs, leisurely drinking coffee and occasionally sneaking out of the lab to play golf.  Today, a friend relayed that, if Chick-fil-A were in charge of lab testing, there would be no delays. 

Yeah, that’s like saying that I could drive a lot faster in my car if Honda owned it despite the fact that the gas tank is nearly empty and there’s a million red lights ahead.

For fun, I’ll use a similar theme for an analogy for my non-laboratory friends.

Let’s say that suddenly, there is an incredible new, global and increasing demand for a new kind of fried chicken sandwich that uses the same chicken but which has a new and special coating.  As soon as the fast food chains start developing recipes for the new coating, the federal government says that, even though fast food chains have legally made safe coating for fried chicken in the past, no one can make their own coating for this special fried chicken.  Instead, fast food chains have to use coating that was made by someone else, and then only if that coating was previously approved for emergency use by the FDA.  So, now all the fast food chains have to wait for companies to make the coating and get it approved by the FDA. By the time some companies start to deliver FDA-approved coating to fast food chains, there is a growing national and international shortage of chicken, frying oil and buns.  Some fast food chains start having to import ingredients from outside the country.  In fact, they are having to dedicate multiple full-time employees to do nothing except try to find ingredients from whoever is able to sell it to them while still making sure that the ingredients are safe for human consumption.  Meanwhile, demand has doubled several times over, and fast food chains are being put on allocation by the companies making the FDA-approved coating because they can’t ramp up production fast enough.  Fast food chains try to purchase additional chicken fryers to help meet demand, only to be told that the companies that make them have sold out.  After a few months of this vicious cycle with demand outpacing supply, the beleaguered fast food chains see on the news that journalists and the feds are starting to publicly question the ability of the fast food chains to fry chicken entirely.  

In summary, be kind to your laboratories and their staff.  They are working very hard, and they are breaking through unbelievable and ridiculous barriers (including cuts to staffing in some organizations) to deliver test results.  Because they are not on the front lines, they are sadly more likely to be vilified than to be lauded as the heroes that they are due to their efforts.

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Validation Guideline for Next Generation Sequencing Bioinformatics Pipelines is now available!

The validation guideline for Next Generation Sequencing (NGS) Bioinformatics Pipelines is now available through the Journal of Molecular Diagnostics.  This guideline was constructed by a panel of experts from the Association of Molecular Pathology, the College of American Pathologists, and the American Medical Informatics Association.  It is the third in a series of NGS guidelines published from working groups at the Association of Molecular Pathology. 

Guidelines published by the Journal of Molecular Diagnostics are always freely available.

This latest NGS guideline is a first foundational guideline for the most common types of variants in human DNA detected by NGS technology, specifically single nucleotide variants, insertions/deletions up to 21 base-pairs in length, and multi-nucleotide variants up to 21 bp in length.  Later guidelines are anticipated to address other types of variants which may require special pipeline algorithms (e.g., large deletions, large insertions, duplications, copy number variants, translocations, inversions, epigenetic changes) or which are performed on non-human genomes.

The history of the AMP Informatics subdivision

There is a multi year history behind the evolution of the informatics subdivision at AMP.  The road to subdivision status was started by others who deserve the credit.

Andrea Ferreira-Gonzalez, PhD, was the first to launch an early morning session for the AMP informatics interest group in the early 2000s.  At that time, which was pre-NGS explosion, the interest level in informatics was still maturing.  Through the efforts of Mary Williams (executive director of AMP) and with underlying support from Jeffrey A. Kant, MD, PhD (first president of the Association of Molecular Pathology), several years later, in 2011, AMP organized a working session for several AMP members with dual expertise in informatics and molecular/genomic pathology to determine a path forward for AMP in this area as the rise of NGS and bioinformatics pipelines began to exceed all expectations.  Members of that group included Jill Hagenkord, MD, Federico Monzon, MD, Roy Lee, MD, Rama Gullipalli, MD, PhD and myself.

Still trying to wrap our heads around informatics and next generation sequencing, the strategic plan for informatics continued to brew until 2013, just before the annual meeting, when I was informed that the leadership at AMP believes they had critical mass to form an interest group and hopefully soon a new subdivision. With the seemingly tireless help of Elaine Lyon, PhD (newly elected president of AMP), Nirali Patel, MD (chair of membership affairs committee), Loren Joseph, MD and the AMP Clinical Practice Committee as well as multiple AMP staff including Mel Limson, Robyn Temple-Smolkin, PhD, Catherine Davidge, Mary Williams and Kathleen Carmody, the current iteration of the AMP Informatics Interest Group was born. Messages were sent to the entire AMP community to encourage members to declare their interest in informatics at an informal meeting for informatics phenotypes at the 2013 annual meeting.

Over 60 people attended that initial informal meeting which took place in a hallway of the convention center on November 13, 2013. Several months later, bi monthly conference calls for the informatics interest group began, and the enthusiasm of the group was clear. The program committee gave the interest group a breakout session at the 2014 annual meeting, and the group submitted a number of excellent abstracts from which four presentations were selected.

In October 2014, a message was sent to the AMP membership asking them to declare an interest in informatics if one existed. Well over 10% of the membership declared an interest, and on Tuesday, November 11, 2014, the AMP governing board overwhelmingly voted to promote the informatics interest group into full subdivision status.

Informatics is the newest subdivision of AMP

I am ecstatic to report that the AMP informatics interest group is now a full subdivision of AMP.  We received over 10% of the membership declaring interest, and the board overwhelmingly voted in favor of moving us to full subdivision status.

This is due to the enthusiasm of the group as well as to the efforts of leadership and staff at AMP in moving this forward.  The board has appointed me as chair during the transition period until elections.  It is my hope that in this position we will ensure the involvement of as many members as possible to achieve a common goal of the success and longevity of this group to the benefit of patients, the practice of informatics and AMP.

We are also looking to collaborate on projects of mutual interest with other organizations.

I've just arrived in Pittsburgh for the Pathology Informatics Summit 2014.  This meeting is my home base.  The place where I can be myself and hang with people who understand what I do for a living.  (No, my family still has no idea...)  I'm really excited to be here, and I know I will be sad when I leave.  There is no other meeting like this one for those of us who practice pathology informatics.  We have a lot of exciting content this year.  Lots of digital imaging and computational pathology for next generation sequencing will be here.  The possibilities for networking and collaboration seem endless and a bit overwhelming. 

We are using Twitter hashtag #PathInfo2014.  I've posted the tweet search on this hashtag here on my blog. 

I'm giving the presidential address this year.  I have a little surprise embedded in it which I hope will be interesting...no, I hope it's just funny.  I may post it here on the blog after all is said and done (and hopefully not in a funereal way...one never knows with humor sometimes).  It will probably all have to be explained later to my parents and to non-informaticists, but one of the joys of this meeting is that I don't have to explain my jokes (and, yes, they really are funny).  I don't even have to finish most of my sentences.  Someone here already knows exactly what I'm talking about.

It has been a year and a half since our last meeting since we changed the venue to the spring.  Way too long.  I'm having withdrawal symptoms. 

And just a small side (and a little sad) note...coming back to the 'Burgh reminds me of a dear mentor that I lost a year and a half ago, Dr. Jeffrey Kant.  I still have a picture of him and his lovely wife in my office at work.  He was like a dad to me in many ways, and I will always miss him.  He was a mentor who managed to get the best out of you without judging or criticizing, and how many mentors always tell you when they are going to be in your neck of the woods so that you can have dinner together with your family? 

I am fortunate to have a lot of other mentors who will be at this meeting.  I cannot enumerate or describe how helpful their attention and guidance has been to me.  It is because I am so grateful to them that I hope to give a lot back to those who are coming behind me.  If you are a trainee or just out in practice in Pathology Informatics, I hope that you will introduce yourselves to me.  I am hatching a plan for mentoring API members who are new into practice.  I would like to run some ideas past you and then bring them to our very dedicated training and education committee chairs, Dr. Mike Riben and Dr. Bruce Levy.

HHS Strategic Plan for 2014-2018 is open for comment

Every four years, HHS updates its strategic plan, which describes its work to address complex, multifaceted, and ever-evolving health and human service issues. Follow this link to the draft and for more information about how to submit comments: http://go.usa.gov/Db4Y

Goal 1: Health Care - http://go.usa.gov/Db2j

This goal focuses on health insurance coverage, healthcare quality and safety, connecting primary and preventive care, healthcare costs, access to care, disparities, and health information technology.

Goal 2: Research and Innovation - http://go.usa.gov/Db25

This goal focuses on health, public health, and human services research, innovation, food and medical product safety, and tobacco regulation.

Goal 3: Public Health and Human Services - http://go.usa.gov/Db2V

This goal focuses on children and youth, economic and social wellbeing, poverty, services for seniors and people with disabilities, prevention, infectious disease, and emergency preparedness and response.

Goal 4: Management - http://go.usa.gov/DbT4

This goal focuses on responsible stewardship and fraud prevention, using data to improve health, the HHS workforce, and environmental stewardship.