Defining Germline Sequencing and Incidental Germline Findings

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EP: 1.Defining Germline Sequencing and Incidental Germline Findings

EP: 2.Tumor-Normal Matched Sequencing and Platforms Utilized for Tumor Profiling

EP: 3.Experience with Interpreting Somatic Reports

EP: 4.Identification of Patients for Germline Testing

EP: 5.Role of ctDNA in Germline Testing

EP: 6.Operational Processes and Challenges

Mark Robson, MD: Good evening everybody. Welcome to this OncLive production, “The Evolving Role of Next Generation Sequencing and Germline Sequencing in Patients with Advanced and Metastatic Cancer.” I'm joined tonight by an excellent group of individuals. Professor John Henson, who is the director of the Hereditary Cancer Clinic at the Georgia Cancer Center in Augusta University. Dr Ashley Ross, who is associate professor of urology at Northwestern School of Medicine, the Feinberg School of Medicine in Chicago. And Dana Farengo Clark, who is a senior genetic counselor at the Abramson Cancer Center, University of Pennsylvania in Philadelphia. We're going to have an interesting conversation today about a relatively complicated area reviewing some information about germline testing and so called, incidental germline findings. And we'll come back to that in a second. We will provide you with some recent data on germline variation that's detected in the course of tumor profiling. And then wrap up with some pragmatic conversations about operational challenges and approaches to this difficulty. But what I want to start by doing is getting us on the same sheet of music when it comes to terminology because this is a complex area. We're working with DNA but we're working with DNA from 2 different sources. A lot of what we're going to focus on today is tumor sequencing, which is also known as somatic sequencing, which is the analysis of DNA from a biopsy of the malignant tissue. And of course, most of the DNA sequence that's in a tumor will be the same as the DNA sequence that the individual was born with. So called, constitutional DNA or germline DNA. The changes that occur as the tumor evolves are the kinds of alterations that we're looking for to identify therapeutic targets in particular. Also, sometimes assistance with diagnoses and the like. But most of the tumor DNA is the same as the inherited DNA. And the way you actually look directly at that inherited DNA, also called normal DNA or constitutional DNA is through germline sequencing. And this, of course, is the analysis of DNA from the normal tissue, which is usually white blood cells but increasingly now, we're doing testing on cells in saliva, which are also frequently white blood cells or epithelial cells. And sometimes you actually do direct testing of normal DNA that's dissected out from the tumor in a biopsy specimen. But most of this is either blood or saliva. A new and evolving area is sequencing of circulating free DNA. In other words, DNA that is actually in the plasma that shed from a couple of different sources. One is it's actually shed from dying tumor cells themselves into the circulation. And the other is that some proportion of circulating free DNA is normal. It's either derived from lysed white cells that shed their DNA into plasma or it occurs from normal tissue as you're doing the processing. So, ctDNA sequencing is an attempt to circulating tumor DNA but what you're actually doing is sequencing circulating free DNA, most of which is going to be tumor in a cancer setting. Other things that we're perhaps going to touch on but not in the same detail is RNA sequencing, which is the analysis of the sequence, of course, from the RNA that is transcribed from the DNA template. This is important because sometimes by doing RNA sequencing you can identify or characterize genetic alterations that have led to a particular form of damaged called nonsense-mediated decay which just means that the RNA is not working or not being transcribed which means the change that was in the DNA is meaningful. So, some laboratories are using RNA sequencing to help cure a, if you will, DNA variation as to its significance. And lastly, an important area in somatic sequencing which is not so important from the standpoint of what we're going to talk about tonight is fusion testing, where you're analyzing either DNA or RNA for particular genomic rearrangements that have created fusions between 2 genes that are driving the cancer. And this is particular issue in lung cancer, or a particular observation in lung cancer. But that's really not going to be much of what we're going to talk about. The other thing I want to touch on is 2 terms which get very, very confused. And we're going to launch into a little bit of a conversation about this because we talk about incidental findings and secondary findings. And incidental findings just technically are things that you find that are unexpected or unanticipated. And this term was first came into consciousness in radiology. You're doing a CT scan for, I don't know, lung discomfort and you find an abdominal mass or something like that. But it applies in genetics as well. When we're doing sequencing for one purpose and sometimes, we find things for another. Secondary findings are a different concept which is, when you are deliberately looking for abnormalities that were not part of the original reason for the test. And in genetics this really came up in the context of whole exome sequencing where people were doing exome sequencing for rare disease diagnosis or the like. And then certain professional societies felt that it was incumbent upon the laboratory to explicitly look for changes in particular genes that could be clinically meaningful. Secondary findings really aren’t important in the tumor space because we don't do a whole lot of exome sequencing right now. But incidental findings is a term that comes up all the time. And Dr Henson, I just would like to start the conversation because when you and I met a day or two ago, you had particular views about this idea and this term of incidental findings. And I was wondering if you could explain where you were coming from on that.

John Henson, MD: Thanks Mark. So, the thing that worries about, or bothers me about the term incidental is it often means present but not a major part of. That's the thing that doesn't quite match up to my understanding or interest, particularly in germline findings. I think if by incidental we mean that it was unexpected, that's one thing. But often times incidental also means that it's a minor issue. And I think by the time we finish this evening, hopefully the participants will have, the audience will have a better understanding of just how significant germline actually is.

Transcript Edited for Clarity