Clinical evaluation of
microarray data
David Amor
19th June 2011
Victorian Clinical Genetics Services
Single
base
change
Microarrays Æ
3-4Mb
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What is a microarray?
Up to 106 ‘bits’ of
Information!!
Highly multiplexed FISH hybridisations.
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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%
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Normal microarray profile
A = A/T
B = G/C
BB
AB
AA
Log(2) ratio: Log(2) of 1=0
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Deletion
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Duplication
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Long continuous stretches of homozygosity
Risk of recessive disease and/or UPD
Only A and B
Alleles
ie no AB hets
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CNVs are common
• We all have many
• Key task is to ‘sort’ detected CNVs into
four main categories:
– Pathogenic
– Uncertain significance
– Unknown significance
– Benign
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Pathogenic Copy Number Change
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•
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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
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Copy Number Change of Uncertain
Clinical Significance
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•
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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
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16p11.2 Microdeletion syndrome
Shinawi M et al. J Med Genet 2010;47:332-341
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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
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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.
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Workflow used in pathogenicity
determination: BC as an example
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Probe coverage
Known pathogenic regions
VCGS data
(Red = deletions
Blue = duplications)
DECIPHER data
Haploinsufficiency predictor
Gene content
CHOP database
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(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
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The chromosome 8 deletion
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Browser shot
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Interpretation
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•
•
•
•
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?
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Clinical challenges for inherited
variants of uncertain significance
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•
•
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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?
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FOXG1 duplication in father and son
with normal intellect
• Possible explanations
– Incomplete penetrance
– Phenotype due to
other genes
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