Sharan Goobie, MD, MSc, FRCPC

Chromosome testing in 2014 Presenter Disclosure: Sharan Goobie has no potential for conflict of interest with this presentation

Objectives Review of standard genetic investigations in the child with developmental delay Understand chromosomal microarray and possible results Demonstrate the importance and limitations of chromosomal microarray

A typical referral to Medical Genetics Child with developmental delay/intellectual disability +/ dysmorphic features +/ behavioural diagnoses (ADHD, ASD, ODD, etc) +/ medical co morbidities Is there an identifiable genetic cause for the child s presentation?

Standard genetic investigations for the child with developmental delay Karyotype OLD NEWS!! Fragile X testing males or females with developmental delay/id +/ Metabolic screening work up Neurologic features (seizures, tone abnormalities, white matter disease) Episodic decompensation with illness, fasting, protein load Other red flags: developmental regression, failure to thrive

Traditional Cytogenetic Testing Karyotype Aneuploidy, translocations, rearrangements Large deletions / duplications (>5Mb) Fluorescent in situ hybridization (FISH) Looking for a specific deletion/ duplication DiGeorge syndrome 22q11.2 deletion Williams syndrome 7q11.2 deletion Smith Magenis syndrome 17p11.2 deletion

2010 Out with the old, in with the new Consensus Statement: Chromosomal Microarray Is a First Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies Miller D. et al, 2010. American Journal of Human Genetics 86, 749 764 acgh should be the first line lab investigation for the patient whose DD/MR, autism, MCA or dysmorphic features are unexplained after thorough history and physical www.ccmg ccgm.org

Chromosomal Microarray (Comparative Genomic Hybridization, array CGH) Molecular technique to detect small deletions or duplications along the chromosomes, not detectable by routine karyotyping www.genedx.com

Patient DNA Increased copy number in patient DNA CGH technique Deletion of patient DNA 1.0 (Smeets, 2004)

karyotype acgh PCR, southern blot, MLPA, sequencing >5Mb 3Mb 10kb 1kb 1bp Size of abnormality

I m a primary care provider, why do I need to understand this complex genetic test? Any physician can order this test Testing is performed at LHSC for Southwestern Ontario You may be asked to order this test on your patient while they are on our Genetics clinic waiting list You need to be able to explain the purpose of this test to your patients

CGH Results 1. Normal no copy number changes

What does it mean to have a Normal Microarray? Cause is genetic: Microarray not sensitive enough (eg., very small deletion) Point mutation in a single gene (eg. Noonan syndrome) Epigenetic (eg. Beckwith Weidemannsyndrome) Cause is NOT genetic: Environmental (eg teratogen, birth asphyxia)

CGH Results 1. Normal no copy number changes 2. Deletion/duplication detected: known syndrome = diagnosis confirmed

Case 1 5 year old with global developmental delay Autistic features Mild dysmorphic features

CGH results

Possible results 1. Normal no copy number changes 2. Deletion/duplication detected: known syndrome = diagnosis confirmed 3. Deletion/duplication detected: known polymorphism in general population = not clinically relevant 4. Deletion/duplication detected: not previously reported Variant of uncertain clinical significance (VUS)

Variant of uncertain significance (VUS) Need parental samples for further interpretation Likely pathogenic Likely benign VUS inherited from healthy parent VUS inherited from affected parent VUS contains genes with potential pathogenic role VUS contains few genes X X X X

Case 2 Adult with autism

Other anxiety provoking results Incidental findings clinically relevant result but not what you were looking for! ie: deletion/ duplication involving cancer predisposing genes Clinically important but does not explain developmental delay

Microarray Summary First line investigation for developmental delay of unknown etiology Only detects chromosomal copy number changes ie: deletions/duplications CGH does not detect: Balanced rearrangements (ie: balanced translocations) Point mutations, or small deletion/duplications within a gene Trinucleotide repeat expansions (ie: Fragile X syndrome)

Take home messages Do not order karyotype for developmental delay ; order microarray and Fragile X as first line testing Explain the types of possible results to families prior to ordering testing (info sheet in your handout) Inform parents you may require a blood sample from them Refer patients with abnormal results or VUS to Medical Genetics appointment may be prioritized

Thank you