Next-Generation Sequencing: Will It Really Replace Single-Gene Tests in Pathology Labs?

“Like many in the field of cancer diagnostics, we’re starting to substitute next-generation sequencing for a lot of our traditional tests,” says Matt Hiemenz, Assistant Director of the Clinical Genomics Laboratory at Children’s Hospital of Los Angeles (CHLA). It’s a shift well worth making, he continues. “With NGS, you can multiplex hundreds of different fusions in a single test. That’s incredibly helpful in terms of diagnosing challenging lesions and maximizing your chances of finding a useful prognostic indicator or treatment target.”

Hiemenz is not the only laboratory medical professional making the move. Tabetha Sundin, Molecular Diagnostics and Serology Scientific Director at Sentara Healthcare, says, “We moved to NGS for non-small cell lung carcinoma testing, which allowed us to bring many of the single-gene tests together. Now, we can look at DNA mutations and structural variance, such as copy number variance and fusions, all in one assay. That saves us time, tissue, and cost.”

With that latter observation, Sundin is highlighting some of the most significant benefits NGS has to offer. A more comprehensive approach like NGS can offer a shorter turnaround time, consume less of a precious sample, and open up new opportunities for collaborative care.

Giulio Settanni, Pathology Department, Negrar Hospital, Calabria, Italy, says, “A single NGS platform provides multiple answers to multiple clinical requests, leading to deep and accurate results in a very short time. The heterogeneity of the diseases treated in a molecular pathology lab makes NGS the best way to approach each molecular analysis. The cost per analysis has also dropped in recent years and nowadays, in my opinion, NGS represents the most cost-effective technology for DNA sequencing in pathology.”

It’s about saving time

Hiemenz says that moving to internal NGS testing has yielded significant time savings in his laboratory. “The average time to result with our reference labs is around two weeks. With our in-house testing, it’s closer to one week.” And the effect on patient care is huge, especially in cases where clinicians need urgent results. “We had a young patient in intensive care with a large head and neck tumor. It was inoperable, so we needed to know what to do as soon as possible. Because our testing was in-house, we were able to expedite it – and, in less than a week, the child was enrolled in a promising clinical trial. Rapid NGS testing made a big difference to that patient’s care, so it’s valuable to have that flexibility.”

Scott Cross, Hematologist/Oncologist at Virginia Oncology Associates, has seen patients’ frustration at long wait times firsthand. “Typically, I would inform my patients that we had diagnosed their cancer, but needed further testing to be sure that we were providing them the best possible therapy. We would often tell people that it would take two weeks or more to get results – which was always difficult.” No patient who has already waited for a chest X-ray, a chest CT, a PET CT, and a biopsy wants to add yet another delay before beginning treatment for a life-threatening disease.

Sentara now conducts NGS in-house, and Cross says that one of its biggest benefits is in reducing time to results. “It removes a layer of trying to track down the specimen, which improves the turnaround time. Additionally, if the patient has any questions or issues, it’s very easy for them to pick up the phone, speak with the professionals who have ordered and conducted the tests, and get answers immediately.”

Settanni agrees. In his opinion, time savings is one of the clearest advantages of NGS. Why? Because it allows users to determine multiple different molecular markers at the same time, moving patients swiftly toward diagnosis and treatment.

It’s about saving tissue

“Tissue conservation is a major point of focus for our laboratory and every laboratory out there,” says Sundin. “There’s never enough. We’re doing more and more biomarker tests for these patients, and every test means another section of tissue removed from the block. We want to go into that block as few times as possible so that we can conserve tissue for when it’s really needed.”

Cross’ experience is similar. “Prior to having NGS available locally, it was not uncommon for us to need to send a tumor specimen to two or three separate locations to obtain molecular diagnostics. So we needed to obtain a large amount of sample up front – but it’s not always easy to obtain a larger specimen without putting the patient at risk for other complications,” says Cross. “Having the opportunity to do multiple tests on a small amount of sample under our own roof has certainly cut down on the number of occasions on which there’s not enough tissue.”

Hiemenz adds, “We ask for as much tumor sample as we can get, but in-house NGS allows us to test samples on the low end of tumor percentage. We input 20 ng samples, but we’re able to process amounts lower than that as well.” And for patients with difficult-to-access tumors, in-house NGS testing can mean the difference between missing an important mutation and discovering it.

“A good NGS analysis is strictly related to the quality of the preanalytical phase,” says Settanni. “We set the histology quality standard to permit subsequent high-quality NGS. In this way, our failure rate has dropped to less than 3 percent, even with samples containing low numbers of cells.”

Encouraging collaborative care

As diagnostic technology advances, so too does the knowledge required to corral the available information to make the best decisions for each person. Hiemenz explains, “We discuss every single patient in a multidisciplinary conference. By having this bidirectional communication about each case, we’re able to help the oncologists understand the prognosis for a given cancer type or even enroll a patient in a clinical trial.” Previously, such a back-and-forth could be expected to introduce potentially dangerous lag time – but not now, says Hiemenz. “Because we’re in constant contact with the clinicians, they help us prioritize the cases that are really important. As soon as those results come off the sequencer, we get the variance, write and issue the report, and talk to the clinicians by phone.”

The increased information yield of NGS testing also prompts more dialogue between specialists. “I think it has enabled us to build a stronger relationship with the oncologists,” says Hiemenz. And Cross agrees: “Local NGS has made it very easy to pick up the phone, and it also helps you to know that the people performing the tests are doing a good job and that the results can be trusted. We’re able to obtain information much more rapidly and reliably by having NGS available in-house.”

Sundin and her colleagues use in-house NGS for reflex testing on lung cancer. “That has vastly improved our relationship with oncology,” she says. “They no longer consider us a barrier – instead, we’re a partner in patient care.” It’s a phenomenon that Tim Triche, Co-Director of the Center for Personalized Medicine at Children’s Hospital Los Angeles, echoes. “Pathologists and oncologists have forever had to learn how to speak to one another,” he says. “I need to know what’s important to the oncologist, and the oncologist needs to know what information I have that could help them manage the patient.”

With the introduction of NGS, oncologists must now learn aspects of genomics that they may never have expected to need. That’s why Triche and his colleagues established special tumor boards that run every other week. “We have three different classes – brain tumors, liquid tumors, and solid tumors – in which we share information.” The groups have been highly effective because, instead of just sharing a written report, each specialty has the opportunity to ask questions of the other. “Everybody walks out of the conference far better informed than they were when they walked in, and it translates immediately into practice. I think that has been one of the most surprising and rewarding aspects of introducing in-house NGS. The utility of molecular testing for both clinicians and patients is profoundly enhanced when the oncologists can literally walk into the laboratory and say, ‘Can we go over this together?’”

For Hiemenz and his colleagues, the benefits of NGS cannot be overstated. “I remember the first time I saw actual reads from NGS,” he says. “I knew looking at my computer screen that this was going to have a huge impact, and we’re still at the very beginning of what we can do. There is so much left that we can imagine – and, one day, NGS will help us achieve it.”