Whether planning a biological family or worried about familial cancers, patients have questions about genetic testing, and geneticist Robert Wallerstein, MD, MS, has guidance for clinicians trying to give them useful answers. Wallerstein's talk describes the major advances in genetic knowledge and test options, potential benefits as well as limitations, and the array of indications for recommending testing. Reviewing what various tools provide, he explains how advanced techniques – such as next-generation sequencing and cell-free DNA – can lead to better patient care.
I, yeah, I'm a geneticist at UCSF and I'm currently the medical director for pediatric genetics at UCSF Medical Genetics division. So, you know, when they asked me to give a talk to you, you know, I, it's, it's always hard to choose something specific to talk about. So, you know, one of the things that is a specific interest of mine and also I think is very um Useful is to think about the genetic testing because it has changed so much. I've been a geneticist now for close to 30 years and You know, what we have in terms of testing has changed a lot, and it has really changed our practice and it has changed the molecular age has changed medicine. So what I wanted to talk to you about today is I wanted to talk about genetic testing, and this is just an overview. For many of you, this may be a review, but hopefully there's this new information in here and I've, I've kind of looked at genetic testing in various areas of, of medicine, and I think hopefully it's a good primer for everybody. OK. So just so you know, I also work uh for GPA, a subsidiary of Integrated Genetics and LabCorp. And um all the images were either, you know, taken off the internet or with specific permission from patients. OK. So, genetic testing is a type of medical test that Identifies changes in chromosomes, genes, or proteins. OK, that's pretty self-explanatory, right? So, you know, a genetic test confirms or rules out a specific genetic condition. And that's really important because a lot of The way in which we choose testing, you know, and this is kind of a theme. Through this talk Really depends on what is the question that we're asking. There's no test that looks at everything. There's no perfect test. But we have to think about what is the question that we want to ask with that patient, and that really drives what, what testing we consider. OK. So, you know, just a, a brief basis on what we do, you know, genetic testing. is part of overall medical genetics, right? But genetics is in the business of families. And the reason that we, we do this is we want to provide an accurate diagnosis for an individual. And an accurate prediction of risk or future or prognosis. Recurrence risk if a family wants to have more children, but it's about the individual who's in front of us, but it's also about sort of the larger community of a family in which that person resides. And so it's really more than just that one individual. OK. So just to give a little bit of a background about genetics and, and, and the incidence and that sort of thing, you know, we used to think when I started this, that genetic disorders were present in about 5% of the population. OK. And so, you know, given the advances and new understandings, you know, we now think that it's 20% of people have a significant genetic issue, OK. And that's out of the Annals of Internal Medicine um study from 2017. But you know, 30% of pediatric hospital admissions have an underlying genetic diagnosis, 3 to 5% of newborns have a birth defect, and 5 to 10% of all cancers have a genetic predisposition. OK. And, and this again, just a little closer up about, you know, the numbers of babies with birth defects. Um, and this is a march of dime, actually, yes, Center for Disease Control and World Health Organization slide, excuse me. Um, You know, just um letting you know just a little bit about the incidence of this and how prevalent things really are. OK. So Our job is to evaluate people who are suspected to have a genetic condition or a birth defect. And A critical part of this is genetic testing, and a critical part of genetic testing is genetic counseling. Now, why is that important? Because the testing provides information, right? And this, this testing oftentimes has implications like I mentioned for the person who's in front of us, but it can also have implications for multiple family members. I can tell you, um, you know, there's a project that I have just recently worked on. Looking at prenatal testing, so during pregnancy, where there were findings in, in a fetus in a pregnancy that had implications for the mother's health. So, so clearly the mom is coming for testing to evaluate the health of her pregnancy, and we find things that can have incident implications for her health. Um, So it's important for families to just consider a bit that, you know, this may be a little bit more than they were bargaining for, so they just need to be aware. Another thing that's part of this is that, you know, the testing is not good or bad, it's what is, and And it gives us more information. The value judgment ascribed to the information is that from, you know, us as practitioners and the families, right? But, but the, the, um, the information itself is sort of judgment neutral. The other thing is when families really consider genetic testing, maybe they don't want this information, right? So it's important to talk about that ahead of time because as I always say to patients, once you know something, you can't not know it. OK. So here's the basics that you all know, right? Our bodies are made of millions of cells. In the center of each cell there are chromosomes. The typical number is 46. On those chromosomes made of DNA, there are 20,000 genes. So depending on what testing we look at depends on what level of resolution, right? OK. Well, all right, somehow. All right, that went a little slightly different direction there. Give me a second. OK, let's try this. There we go. OK. OK, great. So, so this is the chromosomes, again made of genes, all wrapped up, right? Uh the DNA wraps around proteins called nucleosomes, and that's how this long amount of DNA is packaged. If you stretch out the DNA in a single cell, it's about 1 yard long, right? And that's all micro um packaged. And again, these chromosomes. And the different variations. This is the level of resolution that we look at now, OK? And again, just reviewing this with the cell, the nucleus chromosomes DNA. The DNA is then further broken down into exons and introns. Intron is really short for intervening sequencing. It's the intervening sequences. It's the in-between part of the DNA. The exon. Is the coding region, right? So that's the region that codes the protein. Again, as you can see, the exons are what become the messenger RNA that ends up making the protein, which is what the gene codes for. The introns get spliced out along the way. They are the structural DNA that hold the genes together, keep them in the right order, and help the other issues to happen. All right, here's a few terms as we, as we get into this a little deeper. Um, mutations. What's mutation? A mutation is a change in a gene that is linked to a cause for disease. Now, we used to use that all the time and we're really moving away from that. The, the um terminology that we use now is variants. So if there's a difference in a gene, why? It is a variant, and then there's different kinds of variants. There's a pathogenic variant. means it's related to a disease. A likely pathogenic variant means it probably causes a disease. And then there are benign variants, a change in a gene that does not cause a a disease. And we're using the term variants now instead of mutations because people feel like that is sort of a more neutral term to use variant as opposed to maybe some science fiction kind of connotations of mutation. So we typically speak about variants. OK. And syndromes, we talk about that in genetics. So what is a syndrome? A syndrome is a constellation of findings due to a single cause. A syndrome can be due to a chromosome issue. Right, or a single gene, and one of the things I always want people to know is. You know, you can have normal chromosomes. And have a genetic condition because if the genetic changes at the level of the genes, the chromosomes look normal. An example I give people always is sickle cell anemia. Sickle cell anemia is a genetic condition. If you test someone's chromosomes who has sickle cell anemia, their chromosomes are normal. That's a single gene change. OK. So, you know, if you've all have heard of the poet Gertrude Stein, you know, who said a rose is a rose is a rose. Well, what is the benefit of putting a name on a condition or or doing that? Well, There's a number of benefits that I feel really make a huge difference to families. Genetic diagnoses allow families to understand the chance that whatever this condition is can happen again, right? They can also know the prognosis. They can know more about the condition and understand it better. So it really is about empowering families with knowledge about their situation. The other thing is, as we identify more conditions, genetic discoveries drive public health policy in terms of newborn screening, right? We all take care of patients with newborn screening as one example of a public health endeavor, but as we understand conditions better, why that helps with planning for services. From a developmental point of view, the regional centers and developmental services, like as we look at what conditions are there are where and how many of them are in our communities, it can help us in terms of service provision um in other avenues as well. OK. And again, this is just the structure of DNA that we're going to get to with the individual base pairs adenine, thiamine, guanine, cytosine. These are the base pairs in the double helix, and these are where there can be changes on a single gene level and we can get down to the single base pair level. OK. So, a lot of the testing, That we do is at different levels of resolution, and I like to use an analogy to help understand it, and I think about spell check, right? So So if we use this conceit for a minute, when we study someone's chromosomes, like we're looking for a trisomy, like trisomy 21 of Down syndrome as an example, that's like looking for a, a missing chapter in a book, OK? Or an extra chapter. It's, it's looking at that level. Chromosome microarray, which is a way of looking at chromosomes, looks for tiny duplications. And deletions. This is looking for a missing or extra paragraph in that chapter. OK. Gene sequencing looks for mutations within the selected gene at the level of base pairs which I just showed you, but this is like looking for a misspelled word in a selected paragraph. A technology called next generation sequencing looks for mutations in multiple genes simultaneously, so this basically looks for multiple misspelled words in multiple paragraphs all at the same time, and that allows us to look at many genes altogether. Whole exome sequencing, which we're gonna talk a little bit about later, looks through the coding region of all 20,000 genes. So it basically is a technology that finds a misspelled word in the entire book. And whole genome sequencing looks through all the DNA. So this looks for a misspelled word in the entire book, as well as the appendix references, and it also looks to see that the margins are, are formed properly. So, it's looking through the cover to cover. OK, so That's kind of the level of genetic testing and that's the level of what we look at. OK. So, as I mentioned before, my theme is depending on what questions we ask, guides us which technology we're gonna use, chromosomes, chromosome microRA targeted. Genes, mutations or genes, and multi-gene panel, next generation sequencing, whole exome or whole genome. Are we screening for a diagnosis or are we testing for a specific diagnosis? So this is, you can't leave a talk on genetics without looking at chromosomes, right? This is what they look like in the in the microscope in the in the laboratory under the microscope. We take photographs and then with the computer we line them up. Like this, there's 23 pairs. The last pair is the sex chromosomes. This is an X and a Y, but these are the, the chromosomes. And again, if we're looking for a trisomy, we see a whole another chromosome. OK. And this is trisomy 21, and we speak about this in genetics because it is one of the more common um genetic issues. Um, it happens about 1 in 600 births. So if you think about how many babies are born at your hospital or how many people are in your community, you can kind of do the math yourselves to think about how many people this is. But it's very, um, it's common. Individuals with Down syndrome have intellectual disability, congenital heart defects. Those are the two most common things. 50% have a congenital heart defect, duodenatresia or low muscle tone. And as you can see, there's 3 chromosome 21s. So again, when we see a baby in the nursery and we're thinking about Down syndrome, we do a chromosome study. And a couple of other more common chromosome studies are trisomy 1318, and Turner syndrome, and this is an artist's rendition. Um, the first here, this is Down syndrome, trisomy 21 with a sort of a schematic representation. This is trisomy 18. Again, these babies tend to be more severely affected than individuals with trisomy 21. Um, multiple birth defects with heart, kidneys, um, and severe developmental Um, difficulties, many babies with trisomy 18 die in the newborn period. Another one is trisomy 13, again, severe, um, Abnormalities with clefting of the face, heart defects, kidney abnormalities, and many, many do not survive the newborn period. But again, when we see babies that fit into this category of constellations, a chromosome study is the fastest and most efficient way to get to that result. To that diagnosis. OK. Now, chromosome microarray that I mentioned looks at tiny pieces of chromosomes that are missing or extra. It's done like this on slides, OK, where chromosomes, the DNA is hybridized across a slide and then there's a microarray scanner. Um, and again, it's not as visually appealing, I think, as a chromosome study, but it is uh an outstanding tool that we use all the time. And when we have a deletion syndrome, OK? Why, this means there's a tiny piece of the chromosome where the chromosome itself might look normal, but a piece of it is missing or extra. And here's a few um chromosome deletion syndromes, 22Q. Deletion syndrome, which is also called yellow cardiofacial syndrome. And this picture here was a cover of the American Journal of Medical Genetics, and these are, um, I, I always think this is an interesting picture to look at because these are individuals who all have tri uh uh 22Q deletion syndrome. They all have 22Q. They're all from different families and all from different backgrounds, so that they look different. From each other to a degree, but yet they have the same underlying genetic issue. And so, um, there are definitely similarities between them, but one of the things in genetics is sometimes People from different ethnicities have different appearances, and so sometimes we find that some syndromes are underdiagnosed in some ethnicities because the classic presentation is different. But Williams syndrome is another um microdeletion syndrome on 7Q. People have intellectual disability, heart defects, and the 1P36 deletion syndrome, another 11 of the common features for most of the deletion syndromes is intellectual disability to a certain degree. intellectual disability to a certain degree and also um And also, um, We, uh, congenital heart defects are also quite common. OK. So, and these are pictures of of different people with Williams syndrome. Um Here and the 1P36 deletion syndrome again. They do look like each other. Um And yet they're different too. All right, so next generation sequencing. This is next generation sequencing here. This, uh, well, hang on. This is sort of a schematic, um, This is, well, the schematic. I'm sorry, I'm just messing with my um Cord cause I just had uh I plugged in a second and all of a sudden it's not. OK, I wanna make sure I don't run out of juice and we we just disappear. OK. So, this is a schematic of next-generation sequencing, and this is how, this is something that really changed genetics quite dramatically because we have um Here we go. We have multiple um Genes we can look at at the same time by looking at genomic DNA and with all these fragments that we look at it, it lets us look at multiple genes together and this has really changed genetics dramatically. We use multi-gene panels through next-generation sequencing in a variety of regions, epilepsy gene panels, looking at the cause of epilepsy, um, which is really very helpful for in the neurology area. Um, it's done by next-generation sequencing, and there's different panels that look at between 75 and 500 genes. Um, and, well, again, why do we care? Well, we care because if we find a specific gene that causes the epilepsy, there are some medications that respond. That are used because there's a better response, so it helps to guide medication therapy. It also helps families understand if, what's the chance that this can happen again if they have other children. We also, if we find this in a child, we may go back and test parents and they may be at risk for seizures themselves and have not known that. OK. We also use a lot of different testing in the evaluation of a child with autism, and that's something I'm particularly interested in and uh we have a genetics and autism program here at UCSF, um. And that we're we're evolving in the division of genetics, but basically we use chromosome microarray and fragile X. So the American Academy of Pediatrics recommends chromosome microarray and fragile X for all children with a diagnosis of autism spectrum disorder. We find significant variance in 5 to 10% of individuals with autism by microarray. We find up to 5% of fragile X. Um, in my personal practice, I think it's much lower. Uh, I don't know if there's a selection bias there, but I find less of that. But anyway, um, we also can use an autism gene panel looking at a selected number of genes that are related to developmental issues. We find about 5% of individuals with that. We also use exome that scans through all of the genes, and studies have shown that we find approximately 25% of individuals with autism. Have a specific single gene finding. Um, so it really can be quite useful with a significant percentage of individuals. OK. So what do you do, right? So there's all this testing. So what do we do? Well, it depends, right? It all depends. So, you know, clearly, you know, a neonate with multiple anomalies needs genetic testing. If there's a pregnancy with multiple anomalies, if there's a family history of cancer, um, you know, genetic testing is appropriate. Um You know, prenatal genetic carrier screening is another area where genetic testing is involved. Um, their society recommended screening, the American College of OBGYN recommends that pregnant women are offered cystic fibrosis carrier screening, spinal muscular atrophy carrier screening, and screening for hemoglobinopathy like sickle cell and thalassemia. And that's to determine a pregnant woman's risk. Typically how it works is if a pregnant woman is identified to be a carrier, testing is offered to her partner to assess risk. If only one is a carrier. The, the pregnancy is not at risk to be affected. If both are, then the pregnancy would be at 25% risk to be affected and prenatal diagnosis is an option. We also know that Ashkenazi Jewish carrier screening for people of Ashkenazi Jewish, which is Eastern Europe, Russia, Ukraine, Germany, Romania, those that part of the world, um. Hay-Sachs disease was the first, but there's many others. Gaucher, Canavan, uh, a long list, um, that screening is offered to people of Ashkenazi Jewish ancestry. And then there's also a thing called expanded carrier screening, which is between 2 and 500 genes, which is panethnic and includes everything, and we used to identify people by their self-reported ethnicity. We know that that's not always correct, but we decided You know, the community decided that we would go by how people self-identify, but now we have sort of these pan-ethnic panels because people often have ancestry that they are not aware of for a variety of family and historical and social reasons. So carrier screening when people want to determine risk to have a baby with a recessive condition is appropriate. OK. And just to give you a, you know, you may know about cystic fibrosis already. This is one of the most common single gene disorders. Um, it's a recessive, it affects the lungs and digestive system. There's more than 20, excuse me, 2000 mutations identified in this gene. Um, the American College of OBGYN specifies that a minimum of 23 mutations are done with all CF screen because even though there's 2000 mutations, 23. Um, does encompass a large percentage because the Other over 1000 mutations are really very quite rare. Um, commercially, between 23 and 97 mutations are available. Or full gene sequencing, but these, a gene panel like this detects between 80 and 95%. Of the CF variants in Caucasians, 70 to 90% in Latinx Hispanic people, between 40 and 80% of the cystic fibrosis changes in African Americans, and 30 to 70% in Asian Americans. So we often use full gene sequencing to increase the detection. OK. So, the American College of OBGYN recommendations, which were updated in 2011, say that CF screening should be offered to all women of reproductive age, um, although it is most efficacious in the non-Hispanic, white, and Ashkenazi Jewish populations because that's where cystic fibrosis is most common. Um, but this is the basic statement, um. And again, all of these things are changing, but as I mentioned, when both parents are carriers, they undergo genetic counseling to determine if they wish to have prenatal testing and consider their reproductive options. Prenatal diagnosis is another, oh. is another arena in which um genetics has a, has genetic testing has had a big impact. Maternal serum screening with alpha fetoprotein and other markers. Um was has been used for a long time, but now we have cell-free DNA which is also called non-invasive prenatal testing or NIPT. Looks for the common trisomies 1318, 21, and depending on which test you use, sometimes X and Y for abnormalities of sex chromosome abnormalities. Um, all these technologies can be um Utilized. In conjunction with amniocentesis or CVS, um, To provide increased diagnosis. Cell-free field DNA looks at fetal chromosomes that are in the maternal circulation. Again, 1318, 21, and sex chromosome abnormalities, but this is expanding too, and this is just a, a sort of a mockup, right, of, of the DNA from the fetus because what happens is cells from the placenta cross and are in the mother's circulation, but those cells are lyced and so the DNA is just free floating, OK? The future will be looking at all chromosomes and single genes and um The American College of OBGYN recommends discussing with all prenatal patients as part of prenatal diagnosis education about whether all moms are interested in this testing because this is different from an amniocentesis or CVS and that this is from maternal blood. OK. Cancer genetics, which I mentioned here a minute ago. Um, and what I wanna say, you know, 5-10% of all cancers are related to a genetic factor. So most of the hereditary cancer. Um, issues are single genes, and these single genes. are inherited typically in a dominant pattern, OK? And this is a diagram of autosomal um Autosomal dominant inheritance. So, again, That's how this is inherited. Um, one thing is, you know, cancer testing gets complicated because there's tumor testing and so there's changes in genes that can be part of the cancer, they're not hereditary. If it's a change that is hereditary, we call it a germline change. If it's just in the cancer itself, we call it a um somatic change. OK. And then I also mentioned, I also mentioned exome, and exome. Exome is a test that we use quite frequently now. We're using it more and more. It scans through the coding regions and you remember I talked about the exons and the introns, so that the, the exome, which is a word we use to say all of, all of the exons together, the exome. OK, comprises about 1%, whoa, 1% of all the genome, OK? So it's this little slice of this apple, OK? If the whole, the apple represents the whole of the genome. Now, this is an amazing technology, um, It finds a whole lot of things. 85% of disease-causing mutations are in the exome, OK? And this, this technology is used to find single gene changes. The yield of diagnosis is approximately 40% in people who have uh uh an indication of a genetic condition, if we do exome, we find a diagnosis, but it's variable cause if you remember back when I said autism, we say it's about 25% there, but it's variable in the in the same ballpark. We use this in complex unspecified genetic disorders that have multiple differential diagnoses because it helps us get right to a diagnosis much faster. We used to have to do genes on genes and multiple tests, and this is a kind of a consolidation of many of that testing, much of that testing. A suspected genetic disorder when a specific genetic test is not available. And if previous genetic testing like chromosomes or microarray didn't find the answer. Then we use the exome. OK. So Genetic testing is complex, as I, you know, hope I've I've illustrated, you know, and so I think we go back to You know, what is the question that we're asking? What is our The diagnosis that we are considering for this individual. Um, there are many different options to consider. The type of testing is determined by the clinical situation. Um, typically, with individuals with developmental delay, we start with chromosome microRA and fragile X, and we kind of go in the order of resolution. That's how I think about it. And so we look at the chromosomes, which is packages of information, and then we go to more Specific, um, higher resolution issues with looking at genes individually or scanning through all the genes with looking at an exome, OK? Um, And genetic counseling about the limitations of testing prior to testing is essential because, um, you know, when someone has a, a result that's abnormal and maybe it's an unexpected kind of a finding, it's very much better to have reviewed the possibilities ahead of time of an uncertain result, um, We, um, And look at a lot of different things in that way. So, um, I, I think that, that genetic counseling is really an important part and having people understand the limitations of the testing and, um, You know, really think through if this is the kind of information they want is really helpful to do ahead of time. And I think that really makes a big difference and I can see that in the families, um. Who, who I talked to.
