Autism and Developmental Delay Developed by Dr. Judith Allanson, Ms. Shawna Morrison and Dr. June Carroll Last updated Nov 2014

Disclaimer This presentation is for educational purposes only and should not be used as a substitute for clinical judgement. GEC-KO aims to aid the practicing clinician by providing informed opinions regarding genetic services that have been developed in a rigorous and evidence-based manner. Physicians must use their own clinical judgement in addition to published articles and the information presented herein. GEC-KO assumes no responsibility or liability resulting from the use of information contained herein.

Objectives Following this session the learner will be able to: – Refer to their local genetics centre and/or order genetic testing appropriately for autism/developmental delay (ASD/DD) – Set appropriate expectations for a family referred for genetic consultation regarding a child with ASD/DD – Discuss the pros and cons of first tier genetic testing for ASD/DD – Find high quality genomics educational resources appropriate for primary care

Case You have known the Spencer family for several years. They have a 4 year old daughter, Alice, who is healthy and very bright. Their son, Aidan, was born 2 years ago. He has normal stature and a slightly large head. During his first year, his parents noticed that, compared to his sister, he was floppy, with more balance and coordination difficulties; he did not establish a sleep pattern well and had lots of early morning wakening. He is a very busy boy and seems hypersensitive to noise. They are most concerned about delayed language acquisition that is becoming more obvious as time passes.

Family history The Spencers, their siblings and parents are all healthy. Aidan Floppy Balance & coordination difficulties Difficulty establishing sleep pattern Hypersensitive to noise Language delay 4 2 Alice A&W Brett A&W Beverly A&W Brenda A&W Barb A&W Benjamin A&W Carl A&W Cathy A&W Cameron A&W Coral A&W

What do I need to know about the genetics of autism spectrum disorder (ASD)? ASDs are considered genetically-influenced neuro- developmental disorders with evidence pointing to dysfunction at the level of the synapse There is extensive genetic heterogeneity and perhaps hundreds of genetic variants involved A specific genetic etiology can be found in about 15% of individuals with a diagnosis of ASD

Newer genetic testing modalities may increase yield to 30-40% Identifying genetic causes of autism TestPick up rate Chromosomal microarray (CMA)*~10-20% of children with ASD will be found to have a chromosomal micro-deletion or micro-duplication (Copy Number Variant [CNV]) Fragile X syndrome testing [FMR1 gene testing] 20% of boys with FXS meet the diagnostic criteria for autism 1-6% Other rarer single gene conditions [testing a specific gene] or chromosome differences that may be seen on karyotype 5% Metabolic<1%

Chromosomal Microarray (CMA) CMA is a technology used to determine if there are small extra (micro-duplication) or missing (micro-deletion) pieces of genetic information. These gains and losses are called copy number variants (CNVs). A CNV can be: of no medical consequence; pathogenic, resulting in physical and/or intellectual consequences; or protective against disease (e.g. HIV infection). Reference DNA from control labeled Red Test DNA from patient labeled Green Glass microarray slide Denature the DNA (separate the strands) and Hybridize to slide Computer scans and analyzes signal outputs Areas of loss (deletion) Area of gain (duplication)

Who should be offered genetic testing? Any child with autistic features should first be assessed by a general or developmental pediatrician, and specialized autism testing used to provide a definitive diagnosis – Examples: Autism Diagnostic Observation Schedule [ADOS], Autism Diagnostic Interview [ADI] If autism is confirmed, a genetics referral should be offered The genetics assessment will look for unusual physical features that might point to a syndrome or specific single gene disorder. These are most commonly found when the patient has “autism-plus” or complex ASD, with overgrowth, very large head, seizure disorder, muscle weakness or ataxia, cognitive regression, pigmentary abnormalities, or multiple congenital anomalies (25%)

Initial work up: –3–3 generation family history –E–Examination with special attention to dysmorphic features –C–Consider pediatric or genetic referral First tier genetic testing: –C–Chromosomal Microarray (CMA) to look for Copy Number Variants –F–Fragile X gene analysis –I–If evidence of regression, consider metabolic* workup Second tier genetic testing if first tier uninformative: –G–Genetic testing for specific single gene conditions –P–Possibly brain imaging Who should be offered genetic testing? Metabolic evaluation might include a complete blood count, ammonia, serum amino acids, urine organic acids and mucopolysaccharide testing. Specialist advice might be needed

What sorts of chromosomal microarray results might I receive? Normal – Excludes a micro-deletion/micro-duplication (CNV) within the limits of resolution of the test (typically very high) Cannot completely rule out a CNV in all areas of the genome Cannot exclude a syndrome caused by a mutation within a single gene Cannot detect balanced chromosome differences Pathogenic micro-deletion or micro-duplication (CNV) – CNV previously described and associated with a known phenotype, autism or other Variation of unclear clinical significance (VUS) – Not every CNV in the genome is pathogenic – A variant that has not been described in the literature is challenging to interpret and benefits from knowledge of parental status – Parental samples should be obtained and analysed – Next steps*before a referral to the Genetics clinic is initiated CNV – Copy Number Variant

VUS identified in child  Test parents Both parents have normal CMA results One parent has same CMA result as child Finding in child is new, de novo Likely pathogenic Finding in child is new, de novo Likely pathogenic Finding in the child is normal familial variant Not pathogenic Finding in the child is normal familial variant Not pathogenic Finding in the child is pathogenic, but parent displays reduced penetrance (not everyone with the CNV will have symptoms), variable expressivity (individuals with this CNV have varied presentation) A second predisposing factor is needed to cause problems Finding in the child is pathogenic, but parent displays reduced penetrance (not everyone with the CNV will have symptoms), variable expressivity (individuals with this CNV have varied presentation) A second predisposing factor is needed to cause problems

What do these results mean for the recurrence risk of autism spectrum disorder (ASD)? If no genetic cause is identified – Empirical studies suggest sibling recurrence risk (RR) is 10-18% If the sex of the next child is male his risk will be on the higher end – If two siblings in one family are affected RR is 25-35% If a de novo pathogenic mutation/CNV is found – RR is 1% to account for rare gonadal mosaicism When a ASD ‘risk variant’ with incomplete penetrance and/or variable expressivity is identified on CMA – If de novo, RR of the CNV itself is <1%, but the empirical RR for ASD is more difficult to predict. Empirical risks similar to simplex families – If inherited from a normal parent, RR is very difficult to decide as CNV may not be the sole cause for the child’s ASD, however the CNV increases the ASD risk by indeterminate amount CMA – Chromosomal Microarray CNV – Copy Number Variant

How do I order the genetic test? Genetic testing is generally performed on a blood sample Specifics will depend on your region – Details can be found at

How will genetic testing help you and your patient? A specific diagnosis allows: – Better understanding of etiology, natural history and prognosis – Informed treatment decisions – Specific anticipatory guidelines – Accurate recurrence risk information de novo pathogenic CNV versus ASD risk variant Single gene disorder: disorder-specific risk depending on mode of inheritance and whether de novo or not – Prenatal diagnosis CNV – Copy Number Variant

Are there harms or limitations of genetic testing? Potential harms – Insurance discrimination Genetic testing may affect an individual’s ability to obtain life, disability, critical illness, long-term care and/or extended health insurance if the test reveals a predisposition to other medical issues, e.g. increased cancer risk – CNVs may be identified that are unrelated to the health/developmental problems in the child, but could possibly cause other health problems in the future – CMA is unable to detect single gene disorders (e.g. Fragile X) or balanced chromosome rearrangements, such as a translocation – Normal result does not rule out the possibility of a genetic cause for an individual’s health and/or developmental concerns – Non-paternity could be disclosed CMA – Chromosomal Microarray CNV – Copy Number Variant

Aidan Floppy Balance & coordination difficulties Difficulty establishing sleep pattern Hypersensitive to noise Language delay 4 2 Alice A&W Brett A&W Beverly A&W Brenda A&W Barb Menopause at age 38 Benjamin A&W Carl A&W Cathy A&W Cameron A&W Coral A&W Adam Developmental delay First tier genetic testing CMA = Negative Fragile X testing = Positive Refer to genetics (if not already done) Consider carrier testing for family members- can have health and reproductive implications

Key points If autism is suspected – refer for definitive diagnosis When autism or ASD is confirmed – Initial investigations (family history, examination, referral) – Refer to pediatrics or arrange first tier testing – Refer to genetics for dysmorphology examination and further testing Pearls: – The child with autism who has, in addition, overgrowth, a seizure disorder, muscle weakness or ataxia, cognitive regression, pigmentary abnormalities, or multiple congenital anomalies is the one most likely to be diagnosed with a single gene disorder – If the genetic cause of autism (spectrum) is diagnosed, family testing may be extremely important to establish risks for other relatives

References Carter M, Scherer SW. Autism spectrum disorder in the genetics clinic: a review. Clin Genet 2013; 83(5): Schaefer GB, Mendelsohn NJ. Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions. Genet Med 2013; 15: Flore LA, Milunsky JM. Updates in the genetic evaluation of the child with global developmental delay or intellectual disability. Semin Ped Neurol 2012; 19: