Clinical evaluation of microarray data David Amor 19 th June 2011
Single base change Microarrays 3-4Mb
What is a microarray? Up to 10 6 bits of Information!! Highly multiplexed FISH hybridisations.
Microarray Supercedes: FISH Karyotype (detection rate of 3%) The investigation of choice for: Developmental delay/ intellectual disability Autism Congenital abnormalities Pathogenic copy number changes detected in approximately 7000 referrals = 15%
Normal microarray profile A = A/T B = G/C BB AB AA Log(2) ratio: Log(2) of 1=0
Deletion
Duplication
Long continuous stretches of homozygosity Risk of recessive disease and/or UPD Only A and B Alleles ie no AB hets
CNVs are common We all have many Key task is to sort detected CNVs into four main categories: Pathogenic Uncertain significance Unknown significance Benign
Pathogenic Copy Number Change This is a well established pathogenic copy number change Already described and verified in the literature These include common microdeletion and microduplication syndromes, e.g. Prader-Willi syndrome Angelman syndrome 22q11 microdeletion syndrome (VCFS) Cri-du-chat syndrome
Copy Number Change of Uncertain Clinical Significance Known association with phenotypic abnormality But Also be found in phenotypically normal parents/healthy controls. Therefore likely to be a contributing factor but not in itself sufficient to cause the abnormality 16p11.2 deletion IQ low normal/ mild ID Language difficulties Overweight 16p11.2 duplication Found in normal individuals Increased risk of in dev delay and psychiatric disorders 15q13.3 deletion Found in normal individuals Increased risk of ID, seizures, autism, schizophrenia
16p11.2 Microdeletion syndrome Shinawi M et al. J Med Genet 2010;47:332-341
Novel Copy Number Change of Unknown Significance This is a change which has not been described and verified in the literature, but which contains genes, therefore is potentially relevant. Information to be considered: Size of CNV Inherited vs. de novo If inherited, does it track with phenotype in family? Gene content Information from databases
Benign Copy Number Change These are changes found in phenotypically normal individuals (we all have these) Often located in highly variable regions often containing segmental duplications or repetitive sequences. No known clinical significance Reported as NORMAL.
Workflow used in pathogenicity determination: BC as an example
Probe coverage Known pathogenic regions VCGS data (Red = deletions Blue = duplications) DECIPHER data Haploinsufficiency predictor Gene content CHOP database (2000 normals)
Eur J Med Genet 2009 52: 88-93 Same chromosome region as VCFS/DiGeorge, includes TBX gene Most have mild learning difficulties Some have heart defect/clefting, urogenital abnormalities Some individuals essentially normal Often inherited from a parent Uncertain clinical significance
The chromosome 8 deletion
Browser shot
Interpretation De novo deletion Small number of genes 1 similar case in DECIPHER: SZ, hypotonia No published cases FBXO25 gene widely expressed in brain (animal studies) More information likely to become available in the future, but little prognostication possible for now What is the effect of having two abnormalities?
Clinical challenges for inherited variants of uncertain significance How robust are the data? What is normal? two hit hypothesis Entering field of complex genetics, but only seeing a fraction of contributing genetic factors What is the role of cascade testing Is prenatal diagnosis appropriate?
FOXG1 duplication in father and son with normal intellect Possible explanations Incomplete penetrance Phenotype due to other genes