MayoComplete Next-Generation Sequencing: Oncology Subpanels

Presentation

Originally posted: November 7, 2022

Presenter

Kevin Halling, M.D., Ph.D.

Professor of Laboratory Medicine and Pathology
Division of Laboratory Genetics and Genomics
Mayo Clinic, Rochester, Minnesota

Transcript

Introduction

Hello everybody. My name is Kevin Halling. I am a professor in laboratory medicine and pathology in the Division of Laboratory Genetics and Genomics at the Mayo Clinic. I'm a molecular pathologist and my specialization is cancer/molecular oncology. 

Disclosures

None.

Learning Objectives

Today I'm going to speak on the new NextGen sequencing testing we have available for various tumor types. We call this our MayoComplete disease-specific oncology panels. During my talk, I'm going to discuss the current testing that we have and the rationale for the enhancements we've made. I'll explain the gene additions that we've made, the fact that we provide full exon sequencing for all of the exons, and in each of the genes that are in the panels, I’ll explain that we offer microsatellite instability (MSI) testing for all of our subpanels. I'll talk a little bit about the work we've done to validate cytology specimens for use with this test, and finally, I'll finish with a brief discussion of some of the disease-specific standalone tests that we offer out of this panel, too.

MayoComplete Oncology NGS

As I said, the name of our tests are the MayoComplete Oncology NGS Panels. We have actually created 16 different test orderables based on tumor type. 

Disease-specific panels

This test uses a master panel which consists of 55 genes, which are shown on this slide, and out of that, we have created five cancer-specific panels. For instance, we have one for lung cancer, one for gastrointestinal stromal tumor, one for colorectal cancer, one for melanoma, and one for sarcoma. In addition, as I mentioned, we have several standalone tests, which I'll talk a little bit more about towards the end of this presentation. 

MayoComplete orderables

These are the 16 orderables that we have created. In the first column, you can see what they were created for. For instance, for lung cancer patients, sarcoma patients, et cetera. The actual test name, the test code, whether an MSI, or a microsatellite stability result, is provided with that particular test, the types of variants that we assess for. So when we say mutations, we mean single nucleotide variants or indels, and then by rearrangements for the most part we mean gene fusions, and then also the MET exon skipping mutation. These are the test orderables if we just go through one of them, here is the MayoComplete lung cancer panel, so the test code is MCLNG. We provide an MSI result with that orderable and this test actually tests for both mutations in the DNA and RNA. Each of these are explained on this slide. 

Test performance characteristics established during verification

Of course, before we went live with the test, we validated it to determine the performance characteristics. And from this side, you can see that the accuracy of the test for single nucleotide variance and indels was 99.7% and 96.6%, respectively. For microsatellite instability, it was 98%. The limited detection of the test was 5% for SNVs and indels, and we can go down to 20% tumor for microsatellite instability. The test has high reproducibility, and it requires at least 20% tumor cells.

Additional genes and full exon sequencing

Some of the enhancements we have made is we have added a number of additional genes to expand the clinical utility of the tests. We have gone from hotspot testing to testing full exon sequencing for all the exons in all the genes in the panels, with the exception of TERT, which we just sequenced the promoter region, and BCOR, where we just sequence exon 15. By doing this, by adding these extra genes and doing full exon sequencing, we are providing a more comprehensive coverage and higher diagnostic sensitivity.

Microsatellite instability (MSI)

As I said, we also offer microsatellite instability results with all of our subpanels. There are five subpanels that I mentioned. As you all know, microsatellite instability is a hallmark of defective DNA mismatch repair (MMR) in tumors, and testing for it has several clinical utilities, which are shown here. Probably first and foremost is by testing for microsatellite instability, you can predict which patients may respond to immunotherapy; and that's important because in 2017, the FDA approved the use of an immunotherapy known as pembrolizumab for the treatment of adult and pediatric tumors or pediatric patients with unresectable or metastatic solid tumors with microsatellite instability. In addition, microsatellite instability testing is helpful for screening colorectal cancer and endometrial cancer patients for Lynch syndrome. And finally, it can help identify colorectal cancer patients that may have a more favorable prognosis.

Cytology specimens for MayoComplete testing

I also mentioned that we have done a lot of work to validate our tests for use on cytology specimens. FFPE (formerly fixed paraffin-embedded) specimens are the most commonly used specimen for NGS testing, but they're not always available. Our lab, unlike many other labs, has validated our tests, our NGS oncology tests, on cytology specimens. By cytology specimens, I mean cytologic smears and thin prep samples.

Advantages of cytology specimens

The reason this is valuable is there are a number of advantages of cytology specimens, and those advantages are shown here. From a procedure perspective for the patient, it’s nice because it’s less invasive, it’s less uncomfortable, it’s less likely to cause complications, and it’s less expensive. From a laboratory perspective, cytology specimens are nice because they generally result in a higher quality DNA and RNA because of the gentler fixation. In addition, cytologic sampling of a lesion frequently produces a higher tumor percentage, which will enable easier detection of mutations that have low variant out low frequencies. And finally, a very important thing is that by using these cytology specimens, you can save FFPE tissue for other tests, such as immunostains.

There are a few disadvantages of cytology specimens, such as you may not get as much tissue as you would get from resection or a biopsy specimen. In addition, some of our molecular tests and some of our IHC assays are not validated for use with cytology specimens.

MCLNG (DNA+RNA)

All right. Now I'm going to go through each of the subpanels. I’ll talk about the lung cancer panel. This is replacing a panel that had fewer genes on it. The genes on the previous panel are shown in light blue. We had all those in the previous panels. This is the DNA panel and this is the RNA panel. So, you can see that we have added three additional genes on the DNA side: RET, ROS1, and STK11. And on the RNA side, we've added MET exon skipping mutations, and we have added NTRK2/3 fusions. 

MCCRC

This is our colorectal cancer panel. You can see the previous panel again in blue. Four genes. We have added five additional genes so these four DNA mismatch repair genes for MLH1, PMS2, MSH2, and MSH6, and then also the familial adenomatous polyposis gene (APC gene). And I will say for each and every one of these, as I said, we are sequencing the entire exon and we're including MSI testing.

MCMLN

This is our melanoma panel. It had just five genes, which we have shown here, and we have added an additional 12 genes, which are shown here. This panel is useful for patients that have cutaneous melanoma or uveal melanoma. And additionally, these rare tumors, which are referred to as melanostoma. The ones that are useful for cutaneous melanoma are shown with a superscript C after them, and the ones that are useful for uveal melanoma are shown with a U after the gene name. And there are a few that are useful for both, such as BAP1 and SF3B1. 

MCGST

This is our gastrointestinal stromal tumor panel. It had just two genes. It had KIT and PDGFRA. Those two genes actually pick up about 95% of the mutations you see in GST, but there are some mutations, rare mutations, in other genes and we have added those to our panel, too, to get more complete coverage.

MCSRC

This slide talks about our sarcoma testing. So, we have for approximately three years now been offering a gene fusion detection panel for sarcomas, which consists of testing for gene fusions in 138 genes, but we have not had a DNA panel to accompany that. We're adding that now and you can see the genes on that panel. And while I expect that this will be ordered a little bit less frequently because mutations in these are a little bit less common than in the gene fusions, there are still occasions where these are important. For instance, mutations in MYOD1 can be useful for diagnosing spindle cell rhabdomyosarcoma. And I won't go through the whole list, but that's basically the rationale for adding these, because they have additional diagnostic utility beyond the gene fusion panel.

Stand-alone offerings

And finally, I'm going to end with a discussion of our stand-alone offerings. So, we have a number of orderables that just consist of one or two genes that can be helpful for various tumor types. So we offer TURT promoter testing, IDH1/2 testing, and H3-3A/H3-3B testing for gliomas. We have a stand-alone test for BRAF and KIT for cutaneous melanoma; stand-alone tests for ESR1 for predicting resistance to aromatase inhibitors and breast cancer patients; FOXL2 testing for making a diagnosis of granulosis cell tumor; BRCA1/BRCA2 testing for predicting whether breast cancer patients will respond to PARP inhibitors. And finally, CTNNB1 testing for desmoid fibromatosis. So those are our new and improved MayoComplete oncology subpanels, and they represent an improvement over our previous testing. 

Thank You

Thank you very much.

Questions?

Contact us: mcleducation@mayo.edu

Image credit: Getty / Yuichiro Chino