A Study in DNA: The Adventures of a Clinical Geneticist

Genetic disorders often present with a puzzling array of symptoms, making diagnosis challenging. Fortunately, clinical geneticists are on the case! Dr. Marjan Nezarati takes us through the process of providing her patients and their families with answers.

Meredith Laver & Alex Margaritescu

Dr. Marjan Nezarati, M.D., RCPSC Specialist. Photo courtesy of Marjan Nezarati.

The Clinical Genetics department at NYGH sees a wide variety of cases that span a few main categories. Generally, a person is referred to clinical genetics if they are suspected of having a genetic disorder, either because of a family history, or because they are presenting symptoms. Children are often referred for developmental delay combined with one or more dysmorphic features. Prenatal cases are referred when a parent has an unusual screening test such as an ultrasound, or a family history of genetic disorders. NYGH also runs a hereditary cancer clinic which sees individuals with a familial history of cancer. Dr. Nezarati laments lengthy wait times and explains that they “really don’t have the resources”, given the number of referrals they receive. After a referral is accepted, the patient is scheduled to see a clinical geneticist like Dr. Nezarati. She then gets a detailed picture of the patient’s family history and gives a preliminary overview of possible findings. Most cases require additional testing to elucidate physical symptoms, or to investigate genetic causes. 

Figure 1 – Process of diagnosing genetic disorders in prenatal, child, adolescent or adult patients. All cases begin with a visit to a physician, who may write a referral to a genetics clinic if the findings suggest the possibility of a genetic disorder. At the clinic, a geneticist re-examines the patient’s physical symptoms and family history, and orders appropriate genetic testing. Image created in BioRender.

Dr. Nezarati has access to a toolkit of genetic tests to help identify the molecular causes of disease. Genetic tests look for the presence of potentially disease-causing changes in a patient’s DNA. Prenatal cases receive either non-invasive prenatal screening (NIPS) or invasive prenatal testing (IPT). Prenatal testing is time-sensitive as parents must make informed decisions and prepare for health challenges before a child is born. Although IPT is faster and provides more information, some parents opt for NIPS first because of the small risk of miscarriage associated with IPT4. One of two common IPT methods, chorionic villus sampling (CVS) or amniocentesis, is used to acquire a sample of fetal DNA. CVS harvests a small tissue sample of the chorion which is a membrane enveloping the fetus, and amniocentesis harvests the amniotic fluid which surrounds the fetus4. The DNA derived from these samples can then be tested for common disease-causing mutations and chromosomal abnormalities.

In contrast, children and adults who present with suspected genetic syndromes usually receive microarray testing of blood samples. Microarrays detect duplications or deletions of specific genomic regions. If a particular condition is suspected, a microarray is ordered which tests at sites at which duplications or deletions are known to cause that condition. Since microarrays have become fairly common tests, geneticists are now trying to encourage family physicians and specialists to order them independently, instead of submitting a genetics referral.

If microarray testing doesn’t reveal a diagnosis, and a genetic syndrome is still suspected, Dr. Nezarati will often order either a gene sequencing panel or whole exome sequencing (WES). Sequencing identifies the DNA sequence of a portion of the genome. Gene panels involve sequencing only the genes which are commonly associated with a specific disorder or symptom, and are typically used to confirm a clinical diagnosis. WES looks at the entire exome, which is the portion of the genome that contains instructions to make cellular products such as proteins. Although the exome makes up only 1% of the genome, approximately 85% of disease-causing mutations are located in these areas5. It can be much more cost effective to sequence the entire exome than to run multiple gene panels if the first is inconclusive, making WES a good diagnostic test for patients whose clinical diagnosis remains elusive5.

In some cases, the usual genetic tests fail to identify a causative mutation, leaving patients and families without answers. Geneticists can bridge the gap between emerging research and clinical practice by submitting these especially puzzling cases to research studies. This practice helps to provide patients with a diagnosis, and uncover new molecular signatures of disease. Dr. Nezarati is the primary investigator at NYGH for two research studies which use expanded testing methods to investigate undiagnosed cases: Care4Rare–SOLVE and EpiSign.

Care4Rare is a consortium that was founded in 2011 to unite researchers and clinicians across Canada in providing care for individuals with rare diseases6. The current iteration of the project is called Care4Rare–SOLVE and is focused on identifying the molecular causes of rare genetic conditions6. Clinical researchers like Dr. Nezarati collect and share data to help expedite patient diagnosis and the classification of new disorders. Patients enrolled in Care4Rare receive access to whole exome and genome sequencing, as well as expanded testing methods which include RNA sequencing6. Dr. Nezarati signed a young girl up for an early form of Care4Rare after a battery of standard tests failed to produce a diagnosis. They entered the patient’s phenotype and genotype data into a knowledge sharing database called Matchmaker Exchange and suddenly the pieces began falling into place. There was “someone from Australia and another person from the US, and they [had] patients with mutations in the same gene.” Researchers and clinicians around the world were able to work together to formally classify a new rare genetic disorder and begin to build a knowledge base7. Around half of the individuals enrolled in Care4Rare have received a diagnosis for their rare disease6. A formal diagnosis can help patients and families to seek appropriate healthcare, inform family planning decisions, and allow them to connect with others through shared experiences. 

Even advanced DNA testing methods can sometimes fail to produce a diagnosis. In these cases, patients can be enrolled in EpiSign for epigenetic analysis. Genetic and environmental differences create changes in the way that DNA regions are packaged and read. Epigenetics is a branch of genetics that looks at how these differences impact gene expression. Certain genetic disorders such Fragile X, Prader-Willi, or Kabuki Syndromes are associated with recognizable epigenetic signatures8. EpiSign analyzes a patient’s epigenetic pattern in order to identify these signatures and connect them to a diagnosis8.

So how does a patient qualify for submission to a research study? “Really, it’s when we are highly suspicious…that it’s a syndromic diagnosis that we’re not catching by routine testing. And sometimes it’s individuals who have a clinical diagnosis”, Dr. Nezarati explains. “So I’m looking at this person and I think they have Kabuki syndrome, let’s just say, and we do the [sequencing] panel of Kabuki genes and we don’t find a hit. Then that would be a case where you could say, well, let’s submit this to Care4Rare–SOLVE or even to EpiSign to see if the epigenetic signature matches the epigenetic signature for Kabuki syndrome.” The interest and consent of the family is also paramount – “if they don’t want to do it, that’s the end of the discussion.”

In some cases, clinical geneticists are able to collaborate with researchers around the world to help assess the impact of new mutations. “I find most of the time when I’ve reached out to people internationally, even big names… I hear back from them”, Dr. Nezarati recounts. “Geneticists are generally… very, very generous with their time.” One couple who had lost multiple pregnancies was looking for an answer. Often in these cases, recurrent mutations in the fetus are responsible. Genetic testing identified mutations in the fetus and parents in a gene which had not been formally recognized as disease-causing. Dr. Nezarati reached out to a group researching the gene to help solve the case. The researchers recreated the mutations in yeast and found that this particular combination of mutations completely disabled the gene. Fortunately, the couple was able to receive prenatal testing for these mutations in future pregnancies.

Nevertheless, a clinical geneticist’s job isn’t all thrilling detective work and happy endings. Even if a diagnosis can be found, many genetic disorders lack therapy options which address the root cause; patients rely on treatments to manage each individual symptom. Families may also face hurdles from the medical system; Dr. Nezarati describes how one child’s mother “had to really fight to get a referral.” Nonetheless, Dr. Nezarati finds that many patients and families take comfort in understanding their situation, and in feeling understood. “Sometimes I really find I’m sort of just a listener. Sometimes I make very little difference and it’s just the willingness, and having the time to sit and listen to someone. That may be all I can do for them, but sometimes that’s helpful.”

References

1. Baird, P. A., Anderson, T. W., Newcombe, H. B. & Lowry, R. B. Genetic disorders in children and young adults: a population study. Am J Hum Genet 42, 677–693 (1988).

2. Basel, D. Dysmorphology in a Genomic Era. Clin Perinatol 47, 15–23 (2020).

3. About CORD | Canadian Organization for Rare Disorders. https://www.raredisorders.ca/about-cord/.

4. Beta, J., Zhang, W., Geris, S., Kostiv, V. & Akolekar, R. Procedure-related risk of miscarriage following chorionic villus sampling and amniocentesis. Ultrasound in Obstetrics & Gynecology 54, 452–457 (2019).

5. Choi, M. et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106, 19096–19101 (2009).

6. Osmond, M. et al. Outcome of over 1500 matches through the Matchmaker Exchange for rare disease gene discovery: The 2-year experience of Care4Rare Canada. Genetics in Medicine 24, 100–108 (2022).

7. White, S. M. et al. A DNA repair disorder caused by de novo monoallelic DDB1 variants is associated with a neurodevelopmental syndrome. Am J Hum Genet 108, 749–756 (2021).

8. Sadikovic, B. et al. Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders. Genet Med 23, 1065–1074 (2021).

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