FDA Guidance to Develop Novel Molecular Diagnostic Tests for SARS-CoV-2

A laboratory advisory from the CDC:

The Food and Drug Administration (FDA) issued new guidance on February 29, 2020, for laboratories to be able to develop novel coronavirus (COVID-19) molecular diagnostics tests and begin use prior to obtaining Emergency Use Authorization (EUA). This permits laboratories that are CLIA certified and meet requirements to perform high complexity testing to start offering severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular diagnostic testing after validation is completed as outlined in the guidance. Laboratories should submit an EUA request to the FDA within fifteen business days after validation. FDA will be hosting a webinar to provide more information on March 2, 2020, at 3 pm ET.

Clinical laboratories should contact their state health departments for guidance if they have a suspected COVID-19 case specimen. Clinical laboratories should NOT attempt viral isolation from specimens collected from COVID-19 persons under investigation (PUIs). For interim guidelines for collecting, handling, and testing clinical specimens from PUIs for COVID-19, please see the CDC Coronavirus Disease 2019 (COVID-19) website.

Microbiology Case Study: A 52 Year Old with a Liver Abscess

Clinical history

A 52 year old patient with a history of recent travel to India presented to interventional radiology from an outside hospital for aspiration of a liver abscess, and was subsequently returned to the outside hospital. The patient had spent 2 months in India before returning to the US, and about 1 month later developed right upper quadrant pain. Abdominal CT showed 2 cystic masses measuring 2-4cm. Aspiration of the cysts yielded 0.5mL of bloody fluid, which was sent for bacterial culture and smear. Infectious disease prescribed antimicrobial treatment consisted of ceftriaxone and metronidazole, followed by paromomycin and levofloxacin.

Laboratory findings

A gram smear of the patient’s liver mass aspirate showed few neutrophils and no bacteria. Culture of the aspirate showed no growth at 5 days. Multiple sets of blood cultures collected at the outside hospital all showed no growth at 5 days.

Image 1. Entamoeba coli trophozoite seen in the patient’s stool ova and parasite exam, demonstrating an eccentric karyosome and coarse, irregular peripheral chromatin.

A single ova and parasite exam of the patient’s stool was sent and showed few Entamoeba coli trophozoites. A sample of the patient’s blood was sent to the Mayo reference lab for serum Entamoeba histolytica antibody testing, which came back positive. Stool was sent for Entamoeba histolytica antigen testing which was negative.


Entamoeba coli is a non-pathogenic protozoan that can exist as a commensal organism in the human gastrointestinal tract. This organism has not been established to have any disease causing effect per se, but its presence may indicate exposure to water sources that could contain parasitic organisms. (3)

Entamoeba histolytica, by contrast, is a parasitic protozoal pathogen. Most infections are asymptomatic, but they can manifest as amebic dysentery or extraintestinal disease. The most common extraintestinal manifestation is amebic liver abscesses.1

Intestinal amebiasis occurs via ingestion of amebic cysts, typically through contaminated food or water, but also through other forms of fecal-oral contact. Infections are seen most commonly in areas with poor sanitation, but can be found in developed countries in patients who have migrated from or traveled to endemic areas.2

Once the amebic cysts pass into the small intestine, they form trophozoites, which are able to penetrate the mucous barrier of the gut and destroy intestinal epithelial cells. This leads to blood and mucus in the stool. (2) Once the amebae penetrate the gut wall, they are able to reach the blood and ascend through the portal system to the liver and form amebic liver abscesses.3

Clinical presentation of these abscesses typically includes right upper quadrant pain and fever in a patient with a history of travel to an endemic area. Serologic testing is used for confirmation if clinical presentation and imaging are suggestive, but this cannot distinguish between current infection and prior exposure, and up to 35 percent of uninfected inhabitants of endemic areas show positive serology.3 Stool microscopy may be the initial, and indeed only test available in some areas, but cannot differentiate E. histolytica from non-pathogenic E. dispar and E. moshkovskii strains.2

Image 2. E. histolytica trophozoite with ingested red blood cell, visible as a dark inclusion, as well as demonstrating a central karysome and fine, uniformly distributed chromatin. (CDC: https://www.cdc.gov/dpdx/amebiasis/index.html) Erythrophagocytosis is suggestive of E. histolytica.

Empiric treatment in the setting of consistent epidemiology, clinical picture, and radiology consists of metronidazole or tinidazole for tissue clearance followed by paromomycin, diiodohydroxyquin, or diloxanide furoate for intraluminal clearance.

Infectious diseases was taking care of this patient and decided her clinical syndrome is probably extraintestinal Entamoeba histolytica amoebiasis based on the results of the CT findings and the antibody in the right clinical setting.  Although her stool ova and parasite only showed Entamoeba coli, she clearly has been exposed to contaminated food or water.  In addition, the Entamoeba histolytica stool antigen was negative, but this can be an insensitive test.


  1. Leder, Karin, and Peter F. Weller. “Extraintestinal Entamoeba histolytica amebiasis.” UpToDate, Wolters Kluwer, 27 Jan. 2020, http://www.uptodate.com/contents/extraintestinal-entamoeba-histolytica-amebiasis?search=entamoeba%20histolyticatreatment&topicRef=5727&source=see_link. Accessed 4 Feb. 2020.  
  2. Leder, Karin, and Peter F. Weller. “Intestinal Entamoeba histolytica amebiasis.” UpToDate, Wolters Kluwer, 27 Jan. 2020, http://www.uptodate.com/contents/intestinal-entamoeba-histolytica-amebiasis?search=entamoeba%20histolyticatreatment&source=search_result&selectedTitle=1~46&usage_type=default&display_rank. Accessed 4 Feb. 2020.
  3. Weller, Peter F. “Nonpathogenic enteric protozoa.” UpToDate, Wolters Kluwer, 25 July 2019, http://www.uptodate.com/contents/nonpathogenic-enteric-protozoa?search=entamoeba%20coli%20treatment&source=search_result&selectedTitle=1~6&usage_type=default&display_rank=1. Accessed 4 Feb. 2020.

-Tom Koster, DO is a 1st year Anatomic and Clinical Pathology Resident at the University of Vermont Medical Center.

-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Associate Professor at the University of Vermont.

The Forensic Pathologist as Patient Advocate

Patient advocates are simply people who care about patients as fellow human beings enough to act on that care. Forensic pathology fascinates many people, but hardly anyone realizes how strongly forensic pathologists advocate for patients.

Forensic pathologists have the responsibility of identifying human remains and determining the cause and manner of death for individuals that die suddenly and unexpectedly. Most often, we accomplish this mission by performing an autopsy. Death makes many people uncomfortable, and we’re accustomed to grim jokes about their work when meeting someone. Typically these comments carry an undertone that because decedents cannot talk, we don’t need interpersonal skills. Not only is this untrue, comments such as these provide an educational opportunity.

It is true that our patients have already died, but the relatives of our patients are very much alive. Those relatives have needs that we work to provide and questions we strive to answer. The most common question relatives have is “Why did my loved one die?” which is precisely what the pathologist is working to determine. We regularly talk with relatives of decedents that we’ve examined. We can tell family members why death occurred, including any implications that the death has for remaining members of the family. We can also help families begin to work through the social and bureaucratic requirements that death brings for those still living, such as the need to make arrangements for the disposition of the body and the need for a death certificate. (For example, after a person dies, that person’s financial accounts are frozen until a death certificate becomes available to unlock the accounts.)

Forensic pathologists work to develop a good relationship with the decedent’s relatives. Because anger and bargaining are part of grieving, conversations with relatives sometimes begin as though the relative and the pathologist are adversaries, but with time and compassion, the relationship usually transforms into a more appropriate professional relationship. A particularly important aspect of family interactions is listening to a grieving relative, because listening with care helps someone who is grieving. Attempting to build a good relationship with the decedent’s relatives does not mean that the pathologist is a blind advocate for the family. We won’t change the cause of death so that the family can reap more financial benefit from the death, for example. Lies will not help someone pass through the process of grieving in a healthy way – truth, time, and patient, loving care are the necessary therapeutic measures.

In the case of homicides, forensic pathologists advocate for the decedent by calling the death what it is and then testifying to the medical facts of that death when a suspect is tried in court. The pathologist testifies to the medical aspects of what caused death without trying to ensure that the suspect is either convicted or acquitted. Trying to sway the jury’s verdict is the work of attorneys; presenting the medical facts of why and how the decedent died is the work of the pathologist.

Forensic pathologists advocate for public health by providing an accurate cause of death. Death certificate data provide an essential component for assessing public health, and those data are an important determinant for allocation of medical research funds and for interventions to improve public health.

Like other pathologists, forensic pathologists typically do their work quietly in the background, advocating for their unique patients in their own special way. People give little thought to professional interactions with a forensic pathologist until forced to do so; in that difficult time we try to serve as best we can.

-Gregory G. Davis, MD, FASCP graduated from Vanderbilt Medical School and trained in pathology at Vanderbilt University Medical Center, Nashville, TN, followed by a fellowship in forensic pathology at the San Diego County Medical Examiner Office in San Diego, CA. Dr. Davis then joined the faculty at the University of Alabama at Birmingham, where he currently serves as a Professor and as Director of the Forensic Division of the Department of Pathology. Dr. Davis also serves as Chief Coroner/Medical Examiner for Jefferson County, Alabama, the county in which Birmingham is located. Dr. Davis has earned a Master of Science in Public Health from the UAB School of Public Health. His research interest is the application of epidemiology to the study and practice of forensic pathology, especially drug abuse. He has published 74 peer-reviewed manuscripts, including serving as lead author on the 2013 opioid position paper of the National Association of Medical Examiners. He is currently working as chair of a panel revising and updating the NAME opioid position paper for expected publication in 2020. He serves on the editorial boards of the Journal of Forensic Sciences and Forensic Science, Medicine, and Pathology. Dr. Davis is a Fellow At-Large Director on the Board of Directors of the American Society for Clinical Pathology.

The Crown

Hello again everyone! Welcome back.

No, I’m not talking about Netflix or HRH Queen Elizabeth II, nor am I making references to tiaras, bars, beer brands, or imminently deliverable babies…I am, of course, talking about Coronavirus as it would certainly have caught most of our collective attention in the media by now.

I really enjoyed writing last month’s list of what I think are important things on the horizon for pathology and laboratory medicine this new year, but this month let’s take a more topical turn. So put your surgical masks on, wash your hands, quarantine the next 10 minutes of your time and get ready as I take a shot at the novel 2019 coronavirus outbreak!

***Let’s talk about you and me, Let’s talk about COVID-19…***

Less-Than-Common Cold

A long time ago, in a galaxy far, far away (aka: last year, about 20 minutes north of my apartment in Manhattan) I was in medical school, on rotations on the floors of a hospital in the Bronx. I experienced the surges of two flu-seasons and had a fantastic little mnemonic to remember the viruses that caused colds in most patients. Depending on age and immune system status, you had to think about the principal three viruses we see all the time—I remembered them as: “c-A-r,” note the capital “A.” Let me explain; the letters correspond to coronavirus, adenovirus, and rhinovirus. The are in a general order of when they appear during the months of the year (as coronavirus and rhinovirus kind of switch off in the spring, while adenovirus is around always thus is capital designation). There are a few hundred viruses which contribute to cold/flu-like symptoms in patients and, unless a patient is compromised in some way, we really worry most about one of them. Hint: it’s the one we give shots for annually, more on that in a minute.

Image 1. Okay this is a little better than my seasonal cold “cAr”…Seasonal variations in frequency of selected upper respiratory tract infection pathogens. Funny that, of all the colors, Influenza gets the good ‘ol fashioned “red alert” from the commanders on the USS Medscape. PIV = parainfluenza virus; RSV = respiratory syncytial virus; MPV = metapneumovirus; Group A Strep = group A streptococcus. (Source: Medscape)

As far as this coronavirus outbreak is concerned, this is a “novel” (i.e. new) variant (read: mutation) of a respiratory viral pathogen that is affecting a disproportionate number of patients in higher severity than expected. Its official entity name has now been filed by the World Health Organization (WHO) as COVID-19—corona virus disease of 2019. The actual virus is a relative of the infamous SARS virus from the early 2000s. That was SARS, this is SARS 2.0—literally. This virus is designated SARS-CoV-2. SARS stands for Severe Acute Respiratory Syndrome and is caused by strains of coronavirus found in the remnants of infected individuals’ coughs and sneezes—please wash your hands—and causes a spectrum of symptoms from mild to severe including pneumonia, respiratory disease, and even renal failure.

Image 2. Heeeerrreee’s COVID, well at least a coronavirus model. Named after the crown-like spikes on its envelope surface which act as receptor anchors in order to attach to cells and infect us. The receptors’ favorite target? ACE2 (angiotensin converting enzyme 2) receptors—am I getting your blood pressure up yet? I said renal failure…full circle, right? (Source: Centers for Disease Control and Prevention)

How Does this Even Happen?

Okay, who took a sabbatical to Wuhan, China, and ate a wild fruit-bat salad? No one, that’s not how this works. But, if you’re looking for quick grocery store recommendations at the present moment I’d probably tell you to check out ALDI or a farmer’s market a few spots higher on the list than the Huanan Seafood Wholesale Market in Wuhan which harbored a majority of outbreak case-cause tracings. The bottom line is that COVID-19 and the SARS-CoV-2 have appeared in the world the same way the previous similar outbreaks have—through zoonotic mutations which then spread to humans. This zoonotic transmission is so effective to presenting humans with super infectious entities because it sends us pathogenic material we would have never seen before and our “naïve” immune systems are caught off guard. Now don’t get all panicky; yes, I’ve seen Contagion, Outbreak, and read The Andromeda Strain—in fact, I absolutely love when epidemiological medicine has the media spotlight. It’s a very exciting way to showcase public health, medicine, and—our favorite—laboratory professional work!

Image 3. Okay, no bat salad but this outbreak does involve bats endemic to the regions in question. It also involves, pangolins, kind of like armadillos, which are bought and sold (and trafficked) all around the world for various reasons. The pangolin DNA matches the SARS-CoV-2 genome highly, so scientists assert that its involvement is inherent. The complications in sanitation and animal/food handling are obviously implicated in this and other outbreaks, but dealing with COVID-19 requires a strong public health response. (Source: Osmosis)

Basically, this process of mutation and transmission is the modus operendi of a viral particle. You can’t quite kill them, they’re not quite alive by biological definitions, they’re just packaged proteins on autopilot. They’re kind of like natural robots that want to propagate their species by adapting over time—they’re The Borg or Cybermen, depending on your sci-fi preferences. But both offending automaton predators have a mutual enemy in public health—a doctor (get it? TARDIS pilot and/or Beverly Crusher both work wonders in a pinch…) Anyway, it’s never just physicians, but a whole hard-working team of health advocates that conduct surveillance, field research, epidemiologic studies, and first-hand treatment.

***Side note: if you’re bored, in a hurry, or just don’t like my articles—don’t fret! Go watch that Osmosis video on COVID-19 and you’ll be up to snuff on the current outbreak in no time. Or in 12ish minutes.***

***Hey, you made it this far. Great! Interested to know more about the COVID-19 virus from our very own American Journal of Clinical Pathology? Visit here to learn more about the story of how this pesky coronavirus mutated its way into headlines. Fresh off the AJCP presses this month!***

You Should Update Your Antivirus Software

Image 4. Fake news is the new normal. It’s hard to sift through a sea of garbage. You can’t just ignore it, because sometimes there’s serious situations like war—or viral pandemics! So, you’ve got to update your personal mental anti-spam filter and know how to sniff out suspicious sources. Let’s call it “information hygiene” to be consistent with the zoonotic exposure narrative, yea? (Image source: NPR)
Image 5. Let’s lighten the mood a bit. These situations can drive folks absolutely nuts. People obsess over minutiae and often wrong details when archetypal preventions like hand-washing and isolation are paramount to prevent epidemics. Public health and pandemic situations breed conspiracy thinking—wait, never mind, this is a photo of me explaining the residency match process to my friends and family. Kidding. Kind of. (Source: a popular meme, but originally from It’s Always Sunny in Philadelphia)

No doubt in my mind you’ve probably seen plenty of coverage about SARS-CoV-2 in the media. I’d also be willing to bet a lot of it is either dilute, sensational, or possibly even misleading. Regardless, there are always going to be people that don’t “buy in” to the public health message. If you remember Contagion¸ Jude Law’s character pushes the efficacy of “forsythia,” a homeopathic herb supplement that supposedly mitigates the horrible disease spread from southeastern Asia from improper food handling—if I recall correctly, it was a paramyxovirus that time. In this SARS-CoV-2 epidemic we have no current effective treatments, so prevention is key.

In an effort to address this type of health misinformation the WHO and CDC are actively disseminating as much educational information and graphics as they can write. Trying to dispense advice for the public including proper mask wearing, education videos, and myth-busting (i.e. hand dryers do NOT kill the COVID-19 virus, UV lamps do NOT kill the virus, thermal readers are effective in screening populations for symptoms within limitations, alcohol and chlorine do NOT kill the virus, receiving packages from China is still safe, pets don’t harbor the virus at this time, other vaccines do not affect this virus, saline nose sprays do not affect this virus, garlic/oils/other supplements have no effect on this virus, and all age groups are affected)—good stuff there. The most trusted sources of information regarding epidemics should be the representatives of functional medicine and health outcomes, doing work every day to make people healthier. Often times, politics, misinformation, or complex situations make information delivery harder than you’d think and the risks are increasingly high.

Image 6. BONUS MATERIAL UNLOCKED: Glad you made it this far. I mentioned Netflix’s The Crown above, but if you’re looking for a fantastic series that breaks down public health epidemiology, influenza burden, research and surveillance on emerging pathogens as updated as 2019, check out Pandemic. 5/5 surgical masks would binge again. (Source: Netflix)

A Crown of Thorns: Don’t Forget About the FLU!

Flu vaccine deniers: turn away now or be healed! —or at least exposed to another point of view rooted in evidence-only concepts in medicine and population health. Consider the following: as of this month, COVID-19 has infected 43,000 people and killed 1,000 (approximately 2-3%). Remember SARS? That infected 8,000 and killed 700 (approximately 10%). MERS? 2,500 infected, 860 deaths (approximately 34%). And what about Ebola? 29,000 infectious cases with 11,000 deaths (approximately 40%). That was sourced from the Osmosis video with data from the WHO. Pretty impressive right? Well, not if you look at this: according to the CDC, the 2019-2020 influenza burden statistics include 36,000,000 infectious cases, with 17,000,000 clinical visits, 440,000 hospitalizations, and 36,000 deaths. One might say “hey, Dr. Kanakis, slow down there you’re spitting out all these numbers and the facts won’t lie. Looks like influenza only killed 0.1% of cases.” And you know what, you’re right. 0.1% is lower than the other viral epidemics. But check this out, because of the sheer number of cases, that means more people died of influenza than COVID-19, SARS, MERS, and Ebola COMBINED and those happened in other years. That‘s just this year’s flu season alone. I’ve talked before about recognizing and detecting the common cold vs. influenza before, check it out if you’d like a refresher!

Image 7. What’s a statistical percentage data point if it’s a relative, a loved one, or yourself? Protect yourself, protect others, and let’s find ways to make proper health knowledge available and acceptable to the masses while promoting excellent healthy behaviors, together! (Image source: New York Post)

We have influenza every single year, and it kills so many more people than we realize. If you want to talk about a terrifying, global viral epidemic, we’ve already got one. And it’s closer than you think. So wash your hands, reduce exposures if you’re sick or immunocompromised, get proper rest, eat well, exercise, read my articles every month, but most importantly—and I cannot stress this enough—get your FLU SHOT!

Thank you so much, see you next time!

Constantine E. Kanakis MD, MSc, MLS (ASCP)CM completed his BS at Loyola University Chicago and his MS at Rush University. He writes about experiences through medical school through the lens of a medical lab scientist with interests in hematopathology, molecular, bioethics, transfusion medicine, and graphic medicine. He is currently a 2020 AP/CP Residency Applicant and actively involved in public health and education, advocating for visibility and advancement of pathology and lab medicine. Follow him on Twitter @CEKanakisMD

Microbiology Case Study: A Teenager with an Infected Wound

Case History

A male teenager presented to the emergency department following a 4 wheeler accident. He sustained extensive trauma to his right lower leg with a large, dirty laceration and grossly exposed muscle. His pulses were intact and motor & sensory nerve function were preserved. The wound was irrigated at the bedside and the patient was admitted with a plastic surgery consult for wound coverage. Cefepime was empirically started. After 10 days in the hospital and multiple surgeries to care for the wound, the patient developed a fever and increased pain, erythema, and swelling at surrounding the wound. The trauma service ordered blood and wound cultures.

Laboratory Identification

Image 1. The wound culture grew lavender-green colonies on blood agar (48 hours of incubation in CO2).
Image 2. Clear, lactose-negative colonies on MacConkey agar (48 hours of incubation in CO2).
Image 3. Gram stain from the blood agar plate showed gram negative rods (100x, oil immersion).

The oxidase reaction was negative. MALDI-TOF mass spectrometry identified the isolate as Stenotrophomonas maltophilia from the wound culture. Blood cultures were negative.


Stenotrophomonas maltophilia is a common non-fermenting gram negative rod that is ubiquitous in moist environments but is not commonly a member of human flora. S. maltophilia can readily be isolated from hospital surfaces and those with traumatic injuries, prolonged hospitalizations, on mechanical ventilation, and with in-dwelling devices are more susceptible to nosocomial infections by this organism. Those who are immunocompromised or have cystic fibrosis are also at an increased risk.  

In the laboratory, S. maltophilia is characterized as an aerobic, Gram-negative rod that grows as lavender-green colonies on blood agar (Image 1) and has an ammonia-like odor. This organism is catalase and oxidase negative and DNase positive. S. maltophilia is motile and is able to utilize glucose and maltose by oxidative fermentation. Current automated identification systems and MALDI-TOF mass spectrometry are able to accurately identify S. maltophilia.  

S. maltophilia is intrinsically resistant to many broad-spectrum antibiotics, including carbapenems and aminoglycosides. Beta-lactam resistance is due to two beta-lactamases and renders beta-lactam inhibitors ineffective. Trimethoprim-sulfamethoxazole (TMP-SMX) is the antibiotic of choice to treat S. maltophilia infections; however, resistance can develop. In the case TMP-SMX resistance, ceftazidime, minocycline, ticarcillin-clavulanate, ciprofloxacin, and levofloxacin can be tested. 

In the case of our patient, susceptibility testing was performed on the Vitek2 instrument and the isolate was susceptible to TMP-SMX. He was switched to TMP-SMX and underwent additional surgical procedures to wash out the infected area.

-Karla Perrizo, MD, is a Clinical Pathology resident at the University of Mississippi Medical Center.

-Lisa Stempak, MD is the System Director of Clinical Pathology at University Hospitals Cleveland Medical Center in Cleveland, Ohio. She is certified by the American Board of Pathology in Anatomic and Clinical Pathology as well as Medical Microbiology. Her interests include infectious disease histology, process and quality improvement, and resident education.

Biomarker Testing for Cancer Patients: Barriers and Solutions Part 3

This month we will continue discussing the common barriers to biomarker testing for cancer patients in the community.

As you may recall, these are the top 10 barriers that I’ve seen to biomarker testing in the community:

  1. High cost of testing.
  2. Long turnaround time for results.
  3. Limited tissue quantity.
  4. Preanalytical issues with tissue.
  5. Low biomarker testing rates.
  6. Lack of standardization in biomarker testing.
  7. Siloed disciplines.
  8. Low reimbursement.
  9. Lengthy complex reports.
  10. Lack of education on guidelines.

As I mentioned last month sample quantity and quality are both important when considering biomarker testing. We covered tissue quantity issue last month; let’s move on to tissue quality issues. I will focus on what happens to the tissue prior to testing being performed, called the preanalytical phase of testing. We now know that preanalytical variables can alter protein structure, DNA, and RNA (1). This can alter the results that are used to diagnose and treat patients. Despite the impact to downstream assays, this area is typically poorly controlled. Some of the sources of variance due to preanalytical processes include procurement, fixation, processing, and specimen storage (1).


ROSE: I covered rapid onsite evaluation (ROSE) during procurement last month with regards to tissue quantity. Having a pathologist evaluate both tissue quality and sufficiency during the biopsy is invaluable. For molecular analysis, areas of necrosis should be avoided.


Time to get specimen into fixation (cold ischemic time): Tissue begins to degrade as soon as it is removed from the body. The amount of time between removing tissue from the body and fixing it is referred to as the cold ischemic time. This time should be as short as possible. Less than 1 hour is recommended if molecular studies are going to be performed on the specimen (1). Tissue begins degrading immediately and this degradation can affect the results of biomarker test such as IHC & FISH (1). I’ve seen cases where the biopsy was collected, but due to a busy day in the OR, it was not sent to pathology immediately. This can cause the tissue to be so degraded that testing cannot be performed. Unfortunately, sometimes we don’t know there was a fixation issue until the molecular assay fails repeatedly. This is an expensive way to determine something went wrong in the preanalytical phase.

For small biopsies such as core needle biopsies or even fine needle aspirates, one way to decrease time to get the specimen into fixative is by having the fixative in the suite where the biopsy is collected so that it is put into fixative immediately. This won’t work for large pieces of tissue that may need to be dissected for optimal fixation penetration. For these biopsies, diligence needs to be taken to get the biopsy to the laboratory as soon as possible. Multidisciplinary communication will help ensure the hand-off occurs in a timely manner. Specimens may need to be dissected for optimal fixation penetration.  Other specimens may need to be decalcified prior to fixation.  

Decalcification: Most decalcification processes with formic acid have negative downstream effects on molecular testing. We have about a 50% success rate of PCR actually being able to amplify DNA after standard decal due to degradation. The solution to this is to use EDTA-based decalcification; however this could lengthen the fixation time drastically. Some new gentle decals are on the market that could be used without increasing the turnaround time.

Proper Fixative: We also need to ensure specimens are fixed in the appropriate fixative. The most common and widely accepted fixative is 10% neutral buffered formalin (NBF).  DNA yield and some downstream biomarker tests are negatively impacted if unbuffered formalin is used (1). Tissue fixation in alcohol such as 70% ethanol may be even better than NBF if the downstream assay involves DNA extraction; however ethanol fixation may negatively impact IHC or FISH assays (2).

Time in Fixative: Studies show that the appropriate amount of time a biopsy needs to be in fixative is about 6-72 hours (1). The wide range of times is due to the range of specimen sizes, it is generally accepted that formalin penetrates tissue at the rate of 1 mm/hour (3). Tissue may need to be dissected to ensure complete fixation within a reasonable time. If the tissue is not fixed appropriately, the tissue will degrade. However, too much time in fixative can lead to degraded DNA.

Downstream biomarker assays such as FISH, PCR, and ISH can be affected if the fixative time is greater than 72 hours (1). Small community sites that do not have someone processing specimens over the weekend may need to adjust their biopsy schedules on Fridays to ensure specimens do not sit in fixative for more than 72 hours. Unfortunately, unless the specimen is a breast biopsy, in which CAP requires fixation times to be documented and controlled, fixation times are rarely documented and controlled. This is an area we could all improve on. It would be nice to know how long a specimen was stored when we are troubleshooting a downstream assay.


The impact of processing variables on biomarker testing has not been well published. One variable that has been called out as having a negative effect on PCR is mixing beeswax with paraffin wax. Only pure paraffin wax should be used. Other changes to the processing schedules should be performed with coordination between departments. If the anatomic pathology laboratory makes changes to their process, a verification study on the impact to the downstream assays should be performed. How extensive that study is should be determined by the medical director.

Specimen Storage:

As long as the specimen was properly fixed, FFPE block storage is normally fairly hearty. The literature recommends blocks that are used for molecular analyses be less than 10 years old (1). Although I wouldn’t recommend using blocks older than 10 years, cases positive for some biomarkers are rare, so during our validations some blocks used were over 10 years old, and the downstream PCR-based assays still worked. However, I have no way to know if the DNA yield was compromised.

Unlike FFPE blocks, long-term storage of FFPE slides does affect downstream testing (4). Room-temperature storage seems to be worse than refrigerated storage of slides. Slides should be used for IHC and biomarker testing relatively quickly (< 30 days).

Unfortunately I cannot cover all sources of preanalytical error thoroughly in a 1,000 word blog post, but hopefully this sparks your interest enough to check out the references where the authors give a more detailed explanation of preanalytical issues.


  1. Bass BP, Engel KB, Greytak SR, Moore HM. A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen? Arch Pathol Lab Med. 2014;138:1520-30.
  2. Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, et al. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med. 2018;142:321-46.
  3. Howat WJ, Wilson BA. Tissue fixation and the effect of molecular fixatives on downstream staining procedures. Methods. 2014;70:12-9.
  4. Economou M, Schoni L, Hammer C, Galvan JA, Mueller DE, Zlobec I. Proper paraffin slide storage is crucial for translational research projects involving immunohistochemistry stains. Clin Transl Med. 2014;3:4.   

-Tabetha Sundin, PhD, HCLD (ABB), MB (ASCP)CM,  has over 10 years of laboratory experience in clinical molecular diagnostics including oncology, genetics, and infectious diseases. She is the Scientific Director of Molecular Diagnostics and Serology at Sentara Healthcare. Dr. Sundin holds appointments as Adjunct Associate Professor at Old Dominion University and Assistant Professor at Eastern Virginia Medical School and is involved with numerous efforts to support the molecular diagnostics field.