The Role of Genetic Testing in Autism
By Jessica Gold, MD, PhD
Precision medicine, which uses genetic information to direct personalized medical care, is rapidly gaining clinical utility. A genetic result can influence recommendations for medications, preventative health, surveillance, and psychosocial support.(1) Integration of precision medicine has impacted how we treat many common conditions such as cancer, heart disease, liver disease, primary immunodeficiency, and eye disease.(2-8) Individualized healthcare, tailored to a person’s specific genetic variants, has led to improved health outcomes and reduced healthcare costs, and is poised to revolutionize how our approach to medicine.(9)
We are also beginning to realize the potential impact of a genetic diagnosis in neurodevelopmental disorders, such as autism spectrum disorder (ASD).(10-15) ASD is an overarching clinical diagnosis for a range of neurological disorders that present with deficits in social interaction and communication, alongside restricted and repetitive behaviors and interests.(16) Many individuals with ASD also experience overlapping medical conditions, such as epilepsy, intellectual disability, and developmental delay. (16, 17) The global prevalence of ASD is 1-4%, though this estimate flattens the significant heterogeneity of this condition. (18,19) The causes of ASD are likely as multivariate as the condition itself. Yet, the role for genetic testing in ASD remains underrecognized.
“New discoveries of non-coding RNA causing neurodevelopmental disorders are opening new avenues for genetic diagnosis. These results suggest a larger genetic role in the development of ASD and reinforce the need for broad genetic testing in the evaluation of these individuals.”
Genetic testing looks for differences in a person’s DNA. DNA acts as the blueprint for our bodies. It uses a code of four letters (A, C, G, and T) to communicate the information needed for development, growth, and function. In humans, DNA is stored on 46 chromosomes, arranged in 23 pairs – with half of each pair, or 1 chromosome, inherited from each parent. Protein-coding genes make up 1-2% of DNA. These short sequences act as the recipe for the proteins that act as the building blocks of cells. Around 20,000 genes have been identified in human DNA and 4,000-7,000 of these genes have been connected to a Mendelian or monogenic medical condition. (20) The remaining DNA sections contain regulatory elements, including instructions on when and where to make a specific protein, components that help with replicating DNA, and sequences with unknown structure and function. While most genetic testing looks at the sequence or structure of DNA, differences in epigenetics, the processes of DNA regulation, have also been shown to cause human disease.
For the last decade, investigations into the genetics of autism have estimated a diagnostic yield from 8-25% and revealed widely variable molecular etiologies with 400-1000 genes related to autism susceptibility. (10,14,17, 21-23) Individuals with ASD have been found to have large chromosome imbalances, such as three copies of chromosome 21 in Down Syndrome. Smaller chromosomal duplications and deletions have been found, such as duplication of the short arm of chromosome in dup16p11.2 or deletion of a section of the long arm of chromosome 22 in 22q11.2 deletion syndrome. Single letter spelling changes have been reported in many genes, including AUTS2, PTEN, or MECP2, the causative gene for Rett Syndrome. Fragile X syndrome is caused by an expansion of repeating 3 letter codes in a specific section of the FMR1 gene. Epigenetic differences, such as those in Angelman syndrome, have also been connected with ASD. New genetic disorders, including those related to ASD, are being discovered at an annual rate of 50-60 disorders. Further, we are starting to identify neurodevelopmental disorders caused by DNA that is not translated into proteins. New discoveries of non-coding RNA causing neurodevelopmental disorders are opening new avenues for genetic diagnosis.(24, 25) These results suggest a larger genetic role in the development of ASD and reinforce the need for broad genetic testing in the evaluation of these individuals.
For many years, two genetic tests were recommended for every person with ASD. Chromosomal microarrays look for missing and extra sections of chromosomes and can detect these differences down to 20-50 kilobase pairs. (26) In contrast, karyotypes, one of our first genetic tests where we actually visualize chromosomes, can detect deletions and duplications at 10-20 megabase pairs, 10x less resolution than microarrays.(26) Microarrays lead to a diagnosis for approximately 10% of patients with autism. (27) Fragile X testing is the second recommend test. This test measures the number of trinucleotide repeats in the FMR1 gene. In most people, this 3-letter code repeats 20-40 times. In people with Fragile X, this code repeats over 200 times. (28) This test adds a diagnosis in another 1-2% of patients.(29) However, as our genetic knowledge and technology improve, tests that look genetic sequences, or the spelling of genes is become increasingly important
Recent data suggests that broader genomic-based testing has a significantly higher diagnostic rate compared to microarray and Fragile X testing alone. (11, 13, 30) Broad genomic-based testing involves either exome sequencing (ES), which looks the spelling of all identified genes that code for proteins, or genome sequencing (GS), which assesses the full complement of DNA. Genomic-based sequencing is now recommended as first line testing for individuals with epilepsy, intellectual disability, global developmental delay, or congenital anomalies, conditions that frequently cooccur with ASD. (31)
Genomic sequencing tests are far more detailed – they are able to detect a spelling change in 1 letter that may cause a genetic disease. However, the increased scope of testing is met by greater complexity in its process. Genomic sequencing requires more in-depth consent process because there are more long-term implications for these results. (32). The Genetic Information Nondiscrimination Act is a federal law enacted in 2008 that protects your genetic information against discrimination by health insurance or your employers. However, it does not protect your genetic information from other forms of insurance, such as life, disability, or long-term care. (33) Genomic sequencing also looks for variants in secondary finding genes, an approximately 80-gene collection curated by the American College of Genetics to include potentially treatable inherited conditions.(34) The secondary findings list includes genes related to cancer predisposition, cardiomyopathy, arrhythmias, and inherited metabolic disorders. Therefore, it is possible to learn information about a person’s general health from this testing. Insurance coverage varies with some payors requesting detailed letters of medical necessity, or only approving testing ordered by a geneticist. Most medical professionals are not trained in the logistics around ordering and consenting for genomic sequencing, creating barriers in accessing these tests.(35)
“For now, autism is a clinical diagnosis. It is made by observing an individual interact with their environment, using a rubric to describe those interactions. Genetic testing may illuminate a potential etiology for an autism diagnosis.”
The interpretation of genomic testing also requires specialized knowledge. We all have thousands of changes in the spelling of our DNA – how can we be sure that a spelling change found on genomic sequencing is the one causing ASD? We typically send genomic sequencing as a trio, meaning that parents are requested to provide a sample. The parental results are used to analyze and interpret DNA variants. In a trio test, each spelling variant is categorized as inherited from a parent or de novo, new in the patient. The American College of Medical Genetics has created a rubric to classify spelling changes to aid with interpretation.(36) Each spelling change, or variant, is graded using the data on prevalence in the population, functional impact, presence in other family members – either healthy or affected. These grades are used to classify each variant as benign (not causing disease), pathogenic (disease-causing) or a variant of uncertain significance (VUS – indeterminant result). Pathogenic variants usually lead to a diagnosis of a genetic disorder. VUS results require the most work by the interpreting provider. When I receive genomic testing that results with a VUS, my work-up doesn’t end there. I will use publicly available variant curation databases, like ClinVar, scientific literature, and knowledge of my patient to make an independent interpretation of the VUS (37, 38). My interpretation is aided by patients with confirmatory testing, such as representative patterns in laboratories, or suggesting imaging. Despite independent review, there are many times a VUS cannot be redefined, and re-evaluation in 2-3 years is recommended. This method of diagnostic interpretation is not commonly taught in medical school, and is a knowledge gap for many clinicians.
Receiving a genetic diagnosis has several benefits. We are entering an era of precision medicine where medical recommendations hinge on a molecular diagnosis. A genetic diagnosis has led to clinical management changes in nearly 30% of individuals with (Israeli cohort). Identification of a underlying syndromic cause of autism, such as individuals with variants in PTEN – a cancer predisposition gene, can trigger preventative surveillance guidelines for early detection of thyroid or brain tumors. There are new targeted therapeutics for neurodevelopmental disorders, such as Daybue, a daily oral medication for individuals with Rett syndrome. A diagnosis may lead to clinical trial eligibility, including investigations into gene therapy or gene editing. Identifying a de novo versus inherited molecular etiology can influence reproductive planning or lead to cascade testing in family members. There are also psychosocial benefits to naming a condition. Individuals with autism and their caregivers may find community through patient advocacy groups, whose resources frequently exceed the knowledge contained in published literature.
Learning more about the intersection of genetic conditions and ASD is helpful for general medical care as well. Individuals with ASD are at risk for healthcare disparities due communication barriers, and unusual presentations of common conditions. Diagnosing a genetic condition with specific surveillance recommendations could alleviate miscommunication, prevent delays in care, and target medical evaluation. For example, I recently recommended exome sequencing for a nonverbal patient with ASD. His exome sequencing did not result with a cause of his ASD, but did return a pathogenic variant in a gene associated with the connective tissue disorder. People with this syndrome are at risk for aortic dilation and rupture occurring in the fourth to fifth decade of life. For this patient, an aortic event could be catastrophic. He would be unable to use the phrases typically ascribed to these events – “a tearing pain that radiates to the back.” He would be at risk for misdiagnosis due to anchoring bias – abdominal pain in ASD is commonly attributed to constipation – or based on his age; the average age of aortic rupture in this connective tissue disorder is much younger than the average age in the general population. Instead, this patient will undergo interval surveillance echocardiograms and be referred for surgery when indicated. We are also able to learn about how ASD can lead to uncommon presentations of uncommon disease. I follow a young adult with ASD and Fabry disease, a lysosomal storage disorder that causes peripheral neuropathy and heat intolerance. He struggles to control his nerve pain, especially in the summer months. However, learning more about his neurodivergence has been revelatory for him. He realizes that his ASD causes him to feel pain more acutely, which has led us to be more proactive in offering him medical and disease-specific treatment.
“While I strongly advocate for genetic testing in ASD, I must acknowledge that controversy around its role exists in the larger ASD community.”
Genetic testing will not give or take away a diagnosis of autism. For now, autism is a clinical diagnosis. It is made by observing an individual interact with their environment, using a rubric to describe those interactions. Genetic testing may illuminate a potential etiology for an autism diagnosis. It may identify differences in how neurodevelopmental processes are regulated, affecting the instruction manual for brain development. It may provide an answer to parents that this change was a random occurrence and there wasn’t anything they did or didn’t do during pregnancy or infancy that led to an autism diagnosis. Similarly, receiving a genetic diagnosis does not guarantee an ASD diagnosis, but rather, acts as a risk factor. We are learning that many genetic disorders occur on a spectrum and presentations vary between individuals. Genetic testing should enhance, but not replace traditional evaluations for autism.
Barriers to obtaining genomic testing for ASD persist. Medical geneticists and genetic counselors play a primary role in the evaluation of genetic disease and performance of genomic sequencing.(39) Access to these specialists is frequently impeded by clinician knowledge gaps, geographic limitations, and lengthy waitlists, leading to prolonged diagnostic odysseys and exacerbating healthcare disparities (40, 41). Integrating genetic testing into primary care, a process known as mainstreaming, has been successfully trialed for breast and ovarian cancer, polycystic kidney disease, and prostate cancer. (42-45). These disorders have well-defined causative genes, making it possible to send gene-based panels that include 2-50 genes.(46) Mainstreaming broad-based testing like exome and genome sequencing has not been trialed. It represents an appealing model, where complex care or developmental medicine specialists could receive directed training on consenting for and interpreting genomic testing.
Alternatively, a genetic counselor could be embedded in high-risk clinics and facilitate testing, result interpretation, and referral to genetics when indicated. Referral to genetics is already limited by health disparities and knowledge gaps on the role of genetics evaluation. Patients from minoritized backgrounds or from lower socioeconomic statuses are less likely to be seen in a genetics clinic.(47) More clinician-, patient-, and caregiver-facing education is needed on the benefits for genetic testing in ASD, especially for underserved communities.
“As a geneticist, I am a strong advocate for improving access to genomic testing for all individuals with ASD. They should receive counseling on genomic testing from qualified providers, with benefits and risks outlined in a developmentally-appropriate manner.”
Special consideration should also be given to adults with ASD. Overall, medical genetics is biased towards children – most clinical geneticists are dual-trained in pediatrics and genetics. Some insurance policies, both commercial and public payors, do not cover genomic testing for anyone over age 18. However, the benefits of a genetic diagnosis are not age-limited. Adults with ASD are at risk for a cascade of health disparities, due to inadequate management of comorbid conditions, lack of preventative care, and limited access to care, (48) which could be disrupted by genetic diagnosis. A genetic diagnosis may also provide benefit to the community overall by defining the natural history of the disease. During my time as a rare disease primary care physician in an adult developmental medicine clinic, I evaluated 2 siblings with cerebral palsy. Their genetic testing returned with a diagnosis of Vici syndrome, a disorder of autophagy, that causes differences in the brain, heart, eyes, and immune syndrome.(49) The life expectancy of Vici syndrome is commonly cited as 4-5 years. Yet, here I was, caring for adolescent patients aged 16 and 18 years. Their genetic diagnosis expanded our understanding of this condition and changed how we will counsel families about prognosis. Even adults who underwent genetic testing in childhood would likely benefit from re-evaluation due to the enormous technological advances in genetics over the last five years.
While I strongly advocate for genetic testing in ASD, I must acknowledge that controversy around its role exists in the larger ASD community. Caregivers for children with ASD report strongly positive attitudes toward genetic testing. (50, 51) However, a recent survey of adults with ASD by Byres et al showed overall negative perceptions of genetic testing. (52) Nearly half of respondents reported that genetic testing should not be done at all for ASD. Only 15% of participants rate genetic testing as “only beneficial, while 40% rated genetic testing as “only harmful.”
Concerns about genetic testing included lack of impact on ASD diagnosis, supports received, or familial understanding. Participants were concerned that negative genetic testing would negate their ASD diagnosis. They also expressed reservations about performing testing on individuals who could not independently consent. This survey, which was distributed via social media, was limited to respondents who could navigate the internet and complete an electronic form. It likely represents only a small section of the spectrum of autistic individuals and those with comorbid intellectual disability are likely underrepresented. Notably, only 5% of respondents had personally completed genetic testing and the survey did not collect information about their results. It is possible that gaps in education and communication are influencing these negative perceptions, and more outreach should be directed to those with the lived experiences of ASD. Future work should address the disparate opinions between individuals with ASD and their caregivers to ensure that those living with ASD receive optimal care.
As a geneticist, I am a strong advocate for improving access to genomic testing for all individuals with ASD. They should receive counseling on genomic testing from qualified providers, with benefits and risks outlined in a developmentally-appropriate manner. The ASD community should be engaged with how genetic testing is integrated into their healthcare to ensure best practices. People with ASD are already at disproportionate risk for poor health outcomes and inequitable health care. A genetic diagnosis has the potential to disrupt these disparities and improve health outcomes.
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About the Author
Dr. Jessica Gold is an assistant professor of pediatrics in the division of Clinical Genetics and director of newborn screening at Cohen Children’s Medical Center and Northwell Health. With board certifications in pediatrics, internal medicine, clinical and biochemical genetics, she is dedicated to addressing healthcare disparities for individuals with rare disease across their lifespan. Dr Gold completed her MD and PhD at Thomas Jefferson University. She then opted to pursue a combined internal medicine and pediatrics residency at the University of Chicago prior to completing clinical genetics and medical biochemical genetics training at the Children’s Hospital of Philadelphia. As principal investigator on projects funded by the American College of Medical Genetics Foundation, University of Pennsylvania’s Orphan Disease Center, and the Maple Syrup Urine Disease Family Support Group, Dr Gold has described significant barriers to healthcare for adults with genetic conditions, including knowledge gaps for adult clinicians on inherited metabolic disorders and the unique needs for adults with inherited metabolic disease.
Her current work on reproductive healthcare for women with inherited metabolic disorders is supported by an Innovation Grant from the Katz Institute of Women’s Health. Dr Gold is currently a National Academy of Medicine Scholar in Diagnostic Excellence where she will be leading a study on mainstream genomic testing in primary care for adults with intellectual and developmental disabilities.