Biomarker Testing for Cancer Patients: Barriers and Solutions Part 4

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.

Despite being unique hurdles, a few of these barriers can be addressed together.  If you are able to standardize biomarker testing despite the barriers that come with being in siloed disciplines, biomarker testing rates will go up. Sounds easy right! I am a firm believer in the multidisciplinary approach to precision medicine, because I have seen it work in my institution. I have also spoken with organizations where there is no collaboration among the multidisciplinary team (MDT) and observed what happens when the team is not working together. In these cases biomarker testing is often not being performed according to guideline and relationships between the pathology and oncology are strained.

In my organization we have a lot of complexity: 12 hospitals, inhouse and external reference labs, our own private payer, and pathology and oncology groups that are not related to the organization or each other. Everyone wants to do what’s right for the patient, unfortunately if everyone is not working together to help the patient, we tend to get in each other’s way. We found that our oncologists were not getting results back on biomarker tests in reasonable amount of time to make educated treatment decisions. The oncologist chose when to order testing, which biomarker to test, and the performing lab.  This resulted in a great deal of variance in the care provided by each physician. It also added complexity in the pathology laboratory. We had to have shipping containers, portals, collection and specimen requirements that were different for every reference laboratory that the oncologists used. This delayed turnaround time even more as we navigated through the nonstandard process for biomarker testing. As you can imagine tensions were high between pathology and oncology.

Our organization began following the high performance team model some years ago.  With this model we have a “team of teams” that can effect change rapidly despite a complex organizational structure (1). Every stakeholder is represented in the meeting, without every stakeholder having to attend the meeting.  So if you have a team of oncologists that already trust their colleague they are typically comfortable allowing one oncologist to represent their best interest in the committee. We now have a vast structure of committees built on the principle of extending trust from one group into another group with stakeholder representation to build relationships between teams.

One of these committees is a Molecular Steering Committee.  I co-chair this committee along with an oncologist. It is attended by radiologists, pathologists, oncologists, administrators and even the medical director from our payer. Every stakeholder and geographic region is represented. In this committee we discuss how to standardize biomarker testing by tumor type. Although our committee is distinct from a molecular tumor board where you can discuss molecular results for cases, any forum where standardizing the biomarker process can be addressed with a multidisciplinary team is the right forum. We have built relationships between the stakeholders involved in biomarker testing and help keep each other educated on changes to guidelines across tumor types.

This committee has allowed us to develop pathology-driven reflexes for testing in specific scenarios.  Not all biomarker testing can or should be done at the time of diagnosis. However, some tumor types such as NSCLC adenocarcinoma where the tissue is limited and turnaround time is urgent, it makes a lot of sense to perform the testing as soon as we know the patient has this disease.  In these cases the pathologist orders NGS and PD-L1 testing when they determine the diagnosis. This drastically cuts down on the turnaround time (2 weeks vs 6 weeks) and has the added benefit of ensuring all patients with this diagnosis get the standardized biomarker testing that they deserve.

Having a multidisciplinary forum to discuss biomarker testing by tumor type, including which tumor types, what stage, who’s ordering (pathology vs oncology), which test, and where it is performed is necessary to bridge the gap between siloes. In some institutions this can be done without a formal committee, a phone call between oncology and pathology may suffice.  The most important thing you can do to improve your biomarker testing rates and increase standardization is to communicate across silos or disciplines to ensure everyone is in alignment on how to determine patients’ biomarkers status. 

Reference

  1.  McChrystal, T. C. D. S. C. F. S. A. (2015). Team of Teams: New Rules of Engagement for a Complex World.

-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. 

How to Validate a COVID-19 Assay

The FDA is now democratizing the testing of the novel coronavirus: SARS-CoV-2 (the virus which causes the COVID-19 disease syndrome—I will call it COVID-19 from here on as that is the colloquial name most people know) by allowing high complexity testing labs across the United States. This move will permit more labs to test for COVID-19. A previous post by contributor Constantine Kanakis describes the biology of the virus, so I will not repeat that material. Instead, I will focus on some considerations in validating a Lab Developed Test (LDT) COVID-19 molecular assay.

The president of AACC, Carmen Wiley, said there are 11,000 high complexity testing labs in the US, which could qualify for performing this testing. However, not all of these labs have molecular and virology expertise, so others have placed the number of labs with qualified staff and instrumentation at 400.

Published Assays and Targets: As an overview, the figure below (Figure 1) summarizes some published COVID-19 assays. As you can see, the major strategy involves using the TaqMan probe strategy where a short probe is degraded by Taq polymerase releasing a fluorescent molecule (green ball) from a quencher molecule (blue ball). The TaqMan approach allows for quick performance of the assay and easy interpretation. One lab from Japan is using nested PCR amplification and sequencing of the Orf1a and S genes as well.

Figure 1. The COVID-19 genetic structure is abbreviated above with the different genes targeted displayed. The names of institutions that have published their assay procedure along with the TaqMan reagents that were reportedly used with each assay are shown above. Primers are represented by small arrows with a TaqMan probe in the middle represented by a black line with green and blue circles indicative of the fluorescent molecule and its quencher. The double set of arrows for the Japanese assay represents a nested PCR strategy.

In silico Cross-reactivity:

The FDA guidance allows cross-reactivity to be minimally assessed in silico by demonstrating “greater than 80% homology between primer/probes and any sequence present in the targeted microorganism.” The primer locations can be found in the publication of each protocol (except Thermo) and can be confirmed by checking the NCBI Blast site and they actually have a selection for beta-cornavirus (Figure 2) now that allows you to search for your primer’s reactivity across other related viruses- Very helpful!

Figure 2. Select Betacornavirus before entering your primer/probe sequence to confirm cross-reactivity.

Primer/Probe Design:

The N region is the most popular site to probe and is included in most kits once and the CDC kit three times. It was the reagent set for N3 in the CDC kit that was having difficulties, so you may decide to not include that component in your LDT. If you want to see how the different available primer sets align on the N gene sequence you can see below for the primers labeled based on their source. Many are overlapping, perhaps because many people thought the same site was a good target (Figure 3).

Figure 3. N-gene of COVID-19 along with labeled primers from some published assays. The information on the source of the sequence is shown on the bottom right with the link.

Commercially Available Assays:

An important part of validating your COVID-19 assay is to do so quickly. Thus commercially available kits would be helpful, however there are only two commercially available sources at this time: IDT and Thermo. IDT is producing a kit with the CDC design. Thermo produced their kit over the last few months and does not have any published validation information that I could find. Also Thermo when I checked just now for the catalog number, it says this product is unavailable… not sure what that means, but maybe you can try contacting them. Both IDT and Thermo list control plasmid reagents for their assays.

Controls for the Assay:

The wording of the FDA announcement was interesting in that it 1) did not require clinical samples, but allows “contrived clinical specimens.” “Contrived reactive specimens can be created by spiking RNA or inactivated virus into leftover clinical specimens.” A major difficulty is the access to actual COVID-19 RNA or inactivated virus. I noticed that the guidance didn’t say that the assay MUST use RNA. Thus most labs would have access to plasmid DNA, which could potentially be used.

Given the limited availability of RNA for validation use, a lab may consider performing much of the assay optimization with COVID-19 Plasmid DNA while waiting for access to RNA. I would like to be sure my assay could extract, amplify and detect RNA as part of the clinical validation.

Asuragen can produce Armored RNA, with synthetic RNA packaged inside of a viral capsid, which would be a useful control for extraction, amplification and detection. However, we heard this will not be available for another month.

Tom Stenzel (director of the Office of In Vitro Diagnostics and Radiological Health at the FDA’s Center for Devices and Radiological Health (CDRH)) said FDA, BARDA, and the CDC will prioritize and coordinate shipments of viral materials to labs when they are ready to validate tests according to a webinar with labs on Monday. Currently, the FDA is directing inquiries to BEI, which is reportedly prioritizing requests to send out samples in 12-72 hours.

Lastly, one could try to use in vitro synthesized RNA sequences surrounding your primer targets as a control for now and may have better luck in getting the product soon. This is the control that is being shipped with the CDC kits to public labs.

Limit of Detection is an unknown for what is likely to be clinically relevant as we don’t know what the levels look like in people with early vs. late vs. severe vs. mild disease. The FDA just says you should be able to detect 95% of samples (19 of 20) that are x1-x2 the limit of detection.

FDA Notification:

This is the final and important step. Once you go live, you must notify the FDA with an Emergency Use Assay (EUA) form within 15 days. Reviewing the form, there doesn’t appear to have complex explanations or overdue requirements for reporting, which wouldn’t be found in a standard lab validation document.

Final Thoughts/Future commercial solutions:

This information is the best of what I know right now based on current information- this is not a complete guide and the FDA guidance should be read closely for all compliance details. Information is changing quickly and is likely to change more if the number of COVID-19 cases in the United States increases. Cepheid, Luminex, and BioFire are reportedly working on assays that will be out in several months and would be easy to use for many labs that already have one or both of these systems-however it may require a full validation for an LDT, but I’m not sure as it is an EUA-further clarification on this point is needed. Although there are several commercial solutions available, we don’t know how demand could impact supply from each company. Fortunately, some large reference labs like LabCorp and Quest are looking to develop a COVID19 test. Good luck, stay safe, and feel free to contact me with any questions in the comments below so that everyone can benefit from the discussion!

References

In lieu of a list of references, I’ve included web links for the most current and direct sources of information.

-Jeff SoRelle, MD is a Chief Resident of Pathology at the University of Texas Southwestern Medical Center in Dallas, TX. His clinical research interests include understanding how the lab intersects with transgender healthcare and improving genetic variant interpretation.

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.

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).

Procurement:

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.

Fixation:

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.

Processing:

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.

References

  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. 

Forget DNA Sequencing, Protein Sequencing is Here!

Every so often I have the distinct pleasure of hearing of a new technology that I’d never imagined before. This last week, a study in Nature Biotechnology described using nanopore to perform protein sequencing. Thinking of the difficulty and complexity of sequencing just 4 nucleotides, it’s hard to conceive of the exponential difficulty to sequence 20 amino acids.

The technology is still in a nascent period working on the ability to differentiate 20 amino acids- some with very similar sizes and charges. However, as has been the case with many technologies, the speed of advancement can increase rapidly. The possibilities of this technology are very exciting.

Figure 1. Aerolysin structure from CyroEM. This pore comes from Aeromonas hydrophila, a Gram-negative bacterium associated with diarrheal diseases and deep wound infections.

Nanopores have been used mostly for sequencing DNA. Pacific Biosciences have created a platform that reads long sequences of DNA by synthesizing DNA from a single strand moving through a pore. Another company, Oxford Nanopore has made several devices that use nanopore technology to perform sequencing in portable devices. The key to most of these technologies involve functionalizing the pores to have properties desirable for specific purposes.

For protein sequencing, amino acids need to move through the pores slowly enough to have their charges accurately measured. To accomplish this goal, the French start-up, DreamPore, used a bacterial derived cytolytic pore called aerolysin. Aerolysin was found to slow down the passage of amino acids as it has a single molecule trap, which binds to single amino acids with carrier cations. This method detects 13 of the20 amino acids. Additional chemical modifications, instrumentation advances, and nanopore imaging allowed two additional amino acids to be detected. The last few were too similar in charge to be differentiated. However, this study provides a path forward where it is conceivable to sequence each of the 20 amino acids.

In the future, detecting post-translational modifications such as glycosylation and phosphorylation will be an important advance. It will be fun to follow the progress of this technology to see how it might be applied clinically.

References

  1. Iacovache I, De Carlo S, Diaz Nuria et al. Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process. Nature Communications 2016. 7:12062.
  2. Ouldali H, Sarthak K, Ensslen T et al. Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore. Nature Biotechnology 2020; 38: 176-181

-Jeff SoRelle, MD is a Chief Resident of Pathology at the University of Texas Southwestern Medical Center in Dallas, TX. His clinical research interests include understanding how the lab intersects with transgender healthcare and improving genetic variant interpretation.

Biomarker Testing for Cancer Patients: Barriers and Solutions, Part 2

As you may recall last month I shared common barriers to biomarker testing for cancer patients in the community. I also began to dive-in to a few solutions that I have seen implemented to overcome the barriers. Last month I shared solutions that may help with high cost and long turnaround times for biomarker testing. This month I would like to discuss issues with tissue including quantity.

Here 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.

Sample quantity and quality are both important when considering biomarker testing. If we don’t have enough material we cannot perform the test (quantity not sufficient or QNS). If we have poor quality we cannot trust the results. The old adage of garbage in garbage out holds true for biomarker testing just as it does for all other lab tests.  

I’ll start with sample quantity this month and cover quality issues next month. The issue here is that a variety of biopsy types are performed on patients depending on the location and size of a suspicious mass. Historically we only needed enough material for the pathologist to make a diagnosis. Now we often need enough material for diagnosis and biomarker testing. Some tumor types such as breast and ovarian cancers produce enough material in locations that are easily accessible that tissue quantity is rarely an issue, however other tumor types such as lung and pancreatic cancers there is often an issue with tissue quantity. These tumor types must be handled with care to ensure no tissue recovered is lost.

The first step in addressing tissue insufficiency is knowing where you are starting. Do you have an issue with quantity not sufficient (QNS) rate? If you don’t know how many of your cases are insufficient for biomarker testing, then you can’t determine if you have an issue. If your testing is performed at a reference laboratory, you can request your QNS rate from the lab. They may also be able to provide you with the national QNS rate and then you could benchmark yourself against your peers. It is important to have an accurate QNS rate, so if there are blocks that are not sent to the reference lab because the pathologist has determined the block to be exhausted (no tissue is left) then the QNS rate provided by the reference lab may be artificially low.

It is important to agree upon what is QNS. We consider a specimen to be QNS if we cannot perform biomarker testing on the block. Others may consider the block QNS only if there wasn’t sufficient material for diagnosis. We have to ensure there is enough tumor content in the tissue to proceed with biomarker testing, in our case 10% of the nucleated cells (not volume) must be tumor (determined by pathology review of an H&E slide). If we have enough tumor, we can still end up with a QNS block due to low DNA and RNA yield. So we need sufficient tumor and sufficient tissue. 

Here is a brief overview of solutions I have seen work to address limited tissue that can lead to high QNS rates:

  • Education. The person collecting the biopsy needs to understand how much material is needed. Remember we have moved the goal post. Sufficient material for diagnosis was enough in the past, now we need more material to perform biomarker testing. Educating the team on why we need more material is valuable in ensuring sufficient material is collected.
  • ROSE. Rapid onsite evaluation (ROSE) by a pathologist in the procedure room to determine sufficiency has been shown to decrease the repeat biopsy rate [1]. The pathologist can ensure the biopsy is being collected in a tumor rich region and help ensure areas of necrosis are avoided.  
  • Embedding cores separately. We often get core needle biopsies on lung cancer specimens. We prefer 3-5 cores. It is best practice to independently embed the cores in separate blocks. I have also seen labs that embed no more than 2 cores in one block. This would allow one block to be conserved for diagnosis and the other to be used for biomarker testing.
  • Visual cue for limited tissue. Someone far more creative than me developed a process in histology where in cases of limited tissue the tissue was embedded in a red cassette. This cassette color was a visual cue for everyone handling the block that the tissue was limited and care should be taken when facing into the block. This has evolved over time to a red bead being embedded beside the tissue. Any visual cue and an associated procedure to ensure tissue conservation can help ensure we are conserving tissue in cases where it matters.
  • Limited IHC Stains. The primary reason a biopsy is performed is for diagnosis. It is recommended that as few IHC stains as possible be used to make the diagnosis. This will conserve tissue for biomarker testing.
  • Unstained Slides. Cutting 15-20 unstained slides is considered best practices in tumor types such as lung where biomarker testing will be performed within 30 days. Long term storage of unstained slides is not recommended.
  • Reduce the number of times the block goes on the microtome, because every time the block is put back on the microtome it must be refaced. This results in wasted tissue. This can be prevented by thinking ahead and cutting everything you know will be needed while the block is on the microtome.

References

  1. Collins BT, Murad FM, Wang JF, Bernadt CT. Rapid on-site evaluation for endoscopic ultrasound-guided fine-needle biopsy of the pancreas decreases the incidence of repeat biopsy procedures. Cancer Cytopathol. 2013;121:518-24.

-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. 

Association for Molecular Pathology (AMP) – Another Valuable Membership for Technologists

This past November, I was lucky to attend the Association for Molecular Pathology (AMP) annual meeting held in Baltimore, MD. It was the 25th Anniversary of the association and it was interesting to see how it had grown over time. I went to a session moderated by members that had seen AMP in its infancy and it was remarkable to hear how the first meeting was a group of people that could fit in one of the small conference rooms, and how it had grown to offering this meeting for hundreds of people from all around the world. They have been on the forefront of the field of Molecular Diagnostics and have worked hard for many causes affecting those in the field. They discussed important events in the history of the association, such as when AMP, along with other groups, sued Myriad Genetics, Inc, on the practice of gene patenting. Myriad had filed patents for the BRCA1 and BRCA2 genes, and thus they were the only ones who could test those genes for patients. The Supreme Court ultimately ruled that genes are products of nature, which cannot be patented, and this has led to an increase in choice for patients. This, among many other activities, is the way AMP continues to impact the field. They even had a Day of Advocacy the day before the annual meeting began when a group traveled to nearby Washington D.C. to visit with lawmakers about current issues.

If you are a technologist working in a Molecular lab, this meeting is, I believe, the most relevant one for any technologist to attend. If you are not a member of AMP, consider this a shameless plug for membership. The great thing about it is that the association really does its best to be for every one of its members. At the annual meeting, there are sidebars for each type of member, from technologist to trainees, to pathologists. I attended a lunch for trainees and technologists that included two speakers that described their journey through their different careers in the field. They were available to speak with after the session as well. I also attended an informal talk on the exhibit floor that explained the tools available for technologists through AMP, such as the technologist list serve, where I can email every technologist on the membership list for AMP if I have any questions or issues. They also described the website that guides techs to different types of certification tests and links to study guides. These were both great places to network with other technologists as well. The best thing about a technologist membership? It’s discounted compared to the pathologist membership – it’s only $75 a year and provides access to an account that has continuing education opportunities, as well as a digital subscription to the Journal of Molecular Diagnostics. Besides my membership to ASCP, I believe being an AMP member is key to staying up to date in this amazing field.

rapp_small

-Sharleen Rapp, BS, MB (ASCP)CM is a Molecular Diagnostics Coordinator in the Molecular Diagnostics Laboratory at Nebraska Medicine.