Getting Results: How Oncologists and Pathologists Can Work Together to Facilitate Molecular Testing

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Pasi A. Jänne, MD, PhD

Dara L. Aisner, MD, PhD

Jan A. Nowak, MD, PhD

Optimal management of lung cancer patients requires tumor genotyping, but understanding the characteristics of the test and potential results are important in choosing the right test.

—Pasi A. Jänne, MD, PhD

Advances in molecular testing mean that highly specific information can be detailed about the molecular characteristics of a patient’s tumor, as well as indications of potential responsiveness to targeted therapy. But getting those detailed results from the pathologists can be a challenge to many oncologists. The wealth of information that next-generation sequencing can provide and how pathologists and oncologists can work together to best access and use that information were elucidated at a lung cancer education session at the 2014 ASCO Annual Meeting in Chicago.

Genetic mutations can be detected by allelotyping, an assay to detect a specific predefined mutation, or sequencing, an assay to analyze DNA changes, including mutations in specific regions of a gene, explained Pasi A. Jänne, MD, PhD, of the Lowe Center for Thoracic Oncology at Dana-Farber Cancer Institute in Boston.1 Allelotyping is fast and sensitive, but not comprehensive, whereas sequencing is comprehensive, but slower and less sensitive.

Next-generation sequencing offers a “souped-up” version of sequencing, “able to do this in a massively enhanced way,” Dr. Jänne said. While traditional sequencing is analog, mixing together all DNA from a sample and analyzing one section of the genome at a time, next-generation sequencing is digital, sequencing all DNA strands in parallel and “can analyze multiple types of mutations at the same time,” Dr. Jänne added. Because next-generation sequencing relies on one test rather than multiple separate assays, it “is ultimately likely to be a cost-effective method,” Dr. Jänne said, adding that most biopsy samples from lung cancer patients “are not amenable” to multiple assays.

He pointed out that there are several different types of next-generation sequencing technologies, including whole-genome, whole-exome, and targeted sequencing, each with its own advantages, disadvantages, and cost issues.

For example, targeted sequencing is highly sensitive and the lowest-cost sequencing method, but it is “not a discovery tool,” Dr. Jänne said. “You are looking for things that you already know about.” Whole-exome sequencing looks at all genes and is a discovery and research tool, but is not as sensitive. Combining the two methods can give the advantages of both, but increase costs.

“Optimal management of lung cancer patients requires tumor genotyping, Dr. Jänne concluded, but “understanding the characteristics of the test and potential results are important in choosing the right test.”

‘Tissue Is the Issue’

Because “molecular testing is relatively new in the world of ‘routine’ medical care,” noted Dara L. Aisner, MD, PhD, Assistant Professor and Co-Director of the Colorado Molecular Correlates Laboratory at the University of Colorado in Denver, logistical processes for molecular testing have not yet been established at many institutions.2 In her talk at the education session, Dr. Aisner maintained that creating processes geared toward accelerating or prioritizing molecular testing is more effective than “one-at-a-time management.” Setting up these processes requires multidisciplinary conversations to implement these approaches and multiple technical steps to preserve material for molecular studies, she added.

There are multiple points where things can go wrong, Dr. Aisner noted. “When you have received a specimen in pathology, it goes through a diagnostic process, and then somewhere along the way it is diverted for this molecular process,” she said. “This can become very complicated because that request for molecular testing can come at any point along the process, including after the slides have been filed and shipped away.” There may be insufficient tissue left for genotyping because the request was received late in the process, or because a pathologist who is unaware that a diagnosis had already been made performed another complete diagnostic workup.

“In my opinion, [lack of] communication is the number 1 obstacle, because the overall process typically involves so many different people along the line. You have the person ordering the biopsy, the person who is procuring the biopsy, and the person who is transporting the biopsy.… As you move along the line, it’s very easy for the message to get lost,” Dr. Aisner said.

“How do you establish specific needs for a specific specimen?” she continued. “Having systems-based approaches is much more effective than culling individual specimens and … saying this one particular specimen needs this [type of testing].”

Specialized Instructions and Handling

The University of Colorado has over 3 years’ experience with a systems-based process to identify cases that are prioritized for molecular analysis, Dr. Aisner reported. Integral to that process are specialized ordering instructions and handling of biopsy material, and increasing awareness among pathologists.

“We have specialized language that goes into our electronic orders,” she explained. “We also have specialized tissue handling. In a typical pathology process, all pieces of a small sample might be put into one block. In order to get a complete cross-section adequate for diagnosis, sometimes you have to dig into that block quite a ways.” For molecular testing–prioritized specimens, “we separate tissue into individual blocks. We do very shallow facing and, by doing that, we are able to preserve a substantial amount of material for molecular testing.”

Other special instructions involve molecular testing for bone metastases. “In a pathology gross lab setting where we are operating on volume and mass movement of tissue, if a sample comes in and the requisition says ‘bone,’ it can be a knee-jerk reflex to put that sample into decalcification solution,” Dr. Aisner said. “However, tumor metastatic to bone often does not require decalcification. That lytic lesion may have consumed the very hard portion of the bone that would normally render decalcification a requirement. Again, this comes down to communication—letting the laboratory know in advance that this is a sample for molecular testing, that it’s a bone sample, and that you would like them to see if it’s possible to do this without decalcification,” she continued.

Suitable Specimens

“Resection specimens are nearly always acceptable for molecular analyses, but you need to recognize that some specialized tests require that fresh tissue be submitted and not formalin tissue. That’s something that requires specialized procurement approaches be employed,” Dr. Aisner advised.

“One rapid-growth area is the post-treatment biopsy,” she noted. “Biopsy at the time of progression is certainly becoming more common, but it is important to recognize that treatment-related changes often impact the ability to use that specimen.”

There are also “substantial challenges” to getting a post-treatment biopsy, she added. “As we increase our use of post-treatment biopsies to explore molecular mechanisms of resistance and new therapeutic options, we may have to be more aggressive about tissue acquisition.”

How to Talk to Your Pathologist

“The focus I’d like to take on this is the more nebulous issue of not what it is you’re talking to your pathologists about, but how you talk to them,” noted Jan A. Nowak, MD, PhD, Director of the Molecular Diagnostics Laboratory at North Shore University Health System, Evanston, Illinois.3

“We are a relatively small four-hospital health-care system. In all of our hospitals, we probably see 50,000 to 60,000 surgical specimens per year. We have 13 or 14 full-time surgical pathologists, and we have a molecular diagnostic laboratory,” he said.

“Our volume has grown from fewer than 200 molecular tests in 2008 to more than 1,000 in 2013. Most of this increase has come from non–small cell lung cancer. We added ALK FISH [fluorescence in situ hybridization] a few years ago, as well as EGFR and KRAS testing. It just continues to grow,” Dr. Nowak reported.

“Our results typically are available in under 2 days. If a patient has a procedure during the week, by noon the following Tuesday, when we have our chest conference where treatment planning is made, we have those results available,” Dr. Nowak said. “It is rare that we say that there’s insufficient material.

Pathologist-Oncologist Interaction

One of the major reasons Dr. Nowak cited for why molecular testing is working well at the North Shore University Health System is the interaction between oncologists and pathologists. As an example, he cited e-mails he and other pathologists received from an oncologist—the first e-mail requesting that a specimen from a patient with lung cancer not be delcalcified, so that molecular testing could be done, and the second updating the patient’s status and reiterating his requests concerning decalcification and EGFR testing.

“What’s important here? First, this oncologist was wise enough to give us a heads-up. He sent us an e-mail saying look out for this specimen; I need something important here…. Second, he knows multiple pathologists by name; he can contact us. Third, he is wise enough to know that you can’t decalcify these specimens and expect to get molecular testing done. He is telling us exactly what he needs,” Dr. Nowak reported. “I get these e-mails all the time.”

Dr. Nowak predicted that biomarker testing in a large community hospital setting, with “clinically relevant turnaround times” and even with very small specimens is “going to be the standard in the next few years. To do all of this, however, you need to have an engaged pathologist, someone who can look at the cytology and say, yes, there’s enough here for molecular testing. Whether the testing is done in house or sent outside to a reference laboratory, you still need that interface,” Dr. Nowak said.

Summing up, Dr. Nowak stated, “You need to engage your pathologist in the care of your patients. They are his patients, too. Whatever new technologies come into play, the tissue specimen will always be critical because that’s variable. The pathologist is the key interface between the specimen and the test; between your patient and the choices you will have to treat him. Don’t call the laboratory. Call the pathologist. That’s your colleague.” ■

Disclosure:  Dr. Jänne is a consultant or advisor for AstraZeneca, Boehringer Ingelheim, Chugai Pharma, Clovis Oncology, Genentech, Pfizer, Roche, and Sanofi, owns stock in Gatekeeper Pharmaceuticals, and has received other remuneration from LabCorp. Dr. Aisner is a consultant or advisor for Boehringer Ingelheim and has received honoraria from Abbott Molecular. Dr. Nowak reported no potential conflicts of interest.


1. Jänne PA: What are we talking about: Next-generation sequencing, Sanger sequencing, etc. ASCO Annual Meeting. Education Session. Presented June 1, 2014.

2. Aisner D: Tissue is the issue: The pathologist’s role in facilitating molecular analysis. ASCO Annual Meeting. Education Session. Presented June 1, 2014.

3. Nowak JA: The practitioner’s guide to using molecular testing. ASCO Annual Meeting. Education Session. Presented June 1, 2014.