paediatric neurogenetics - rch.org.au
TRANSCRIPT
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Paediatric Neurogenetics
Prof Martin Delatycki
Clinical Genetics Austin Health
Bruce Lefroy Centre for Genetic Health Research, MCRI
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What will be covered
• Dynamic mutations
• NF
• Tuberous sclerosis
• Prenatal diagnosis and preimplantation diagnosis
• Genetic disease searches
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Genes- Nuclear and Mitochondrial
• Nuclear- most genes
(~23,000)
• Mitochondrial- 37 genes- 13
encode proteins
– No introns
– 93% of mitochondrial
genome is coding DNA
(nuclear 2%)
– Mitochondrial DNA
maternally inherited
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Dynamic mutations
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DYNAMIC MUTATIONS
• = a mutation which changes upon transmission
• Trinucleotide repeat disorders are the best example
• = three nucleotides which are present in increased number
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TRINUCLEOTIDE REPEATS
• Normal
• Disease causing when expanded beyond a certain
threshold
• Below that threshold they are stable both in mitosis and
meiosis
• Beyond a certain number the repeat can be unstable in
meiosis ± mitosis
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DYNAMIC MUTATIONSREPEAT DISEASES INHERITANCE PARENTAL
GENDER BIAS
CGG/GCC FRAX A, E XL MATERNAL
GAA FRIEDREICH ATAXIA AR MATERNAL
CTG MYOTONIC
DYSTROPHY, SCA8?
AD MATERNAL
CAG HD, DRPLA, SCA
1,2,3,6,7, 17 (TBP),
SBMA,
AD, XL PATERNAL
12 MER PROGRESSIVE
MYOCLONUS
EPILEPSY
AD
5 MER SCA 10 AD
CCTG DM2 AD
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SITE OF TRINUCLEOTIDE REPEAT
5’
ATG
TAA
3’
CCG GAA CAG CTG
FRAXA
CAG
SCA 12
FRDA HD
SBMA
SCA1,2,3,6,7
DM
?SCA8
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DYNAMIC MUTATIONS
• INTERGENERATIONAL INSTABILITY
• ANTICIPATION
• PREMUTATIONS
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INTERGENERATIONAL INSTABILITY
• REPEAT CHANGES IN SIZE FROM PARENT TO
OFFSPRING
• SEX OF TRANSMITTING PARENT IMPORTANT
• SOME MORE UNSTABLE FROM FATHER, OTHERS
FROM MOTHER
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ANTICIPATION
• MORE SEVERE PHENOTYPE WITH SUCCESSIVE
GENERATIONS
• BEST EXAMPLE IS MYOTONIC DYSTROPHY
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MYOTONIC DYSTROPHY
• Worse with succeeding generations= anticipation
• Most severe= congenital myotonic dystrophy
• Very floppy, may need ventilator
• If survives, intellectual disability
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ANTICIPATION
Myotonic dystrophy
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MYOTONIC DYSTROPHY
• CTG repeat
• <37- no problem
• >50- disease
• 50-100- generally mild
• Congenital form often >1000
• Congenital form almost always maternally inherited
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PREMUTATIONS
• REPEAT SIZE WHICH IS UNSTABLE BUT DOES NOT
RESULT IN A PHENOTYPE
• BEST EXAMPLE IS FRAGILE X SYNDROME
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Fragile X syndrome
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Fragile X syndrome
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FRAGILE X SYNDROME
• CGG repeat
• <55- normal and no risk for offspring (45-54 grey zone)
• 55-200= premutation- normal intellect but risk to offspring of
females
• >200- males have intellectual disability but intellect in
females is variably affected
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FRAGILE X PREMUTATION
• Not truly a premutation because female premutation
carriers have a higher rate of
– premature ovarian failure
– “shy” personality
• Males and females with a premutation are at higher risk of
late onset cerebellar tremor/ ataxia syndrome (FXTAS)
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FRAXA Cerebellar Tremor/ Ataxia Syndrome
• Progressive action tremor, ataxia, cognitive decline
• 45% males, 17% females >50yrs
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GENOTYPE- PHENOTYPE
• For most dynamic mutation disorders, the larger the repeat,
the earlier the onset
• CANNOT use the repeat size to predict phenotype with
accuracy
• eg: myotonic dystrophy prenatal
• Huntington disease predictive test
• NOT true for all dynamic mutations- eg: CCTG repeat in
DM2
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Friedreich Ataxia
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Friedreich Ataxia
Autosomal Recessive
Commonest Hereditary Ataxia
Prevalence 1:30 000 based on molecular data
Carrier Frequency 1:85
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Friedreich Ataxia
• Clinical Features
» progressive ataxia of limbs
» absent lower limb reflexes
» reduction in vibration and proprioception
» extensor plantar responses
» scoliosis
» foot deformity
» cardiomyopathy
» diabetes mellitus
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Friedreich Ataxia
9q13 - q21.1
GAA triplet repeat in intron 1 of FXN gene
98% of affected alleles have an expansion of this trinucleotiderepeat
Normal 7-36
Affected 67-1300
Point mutations and deletions in FXN described
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12345a
Intron 1
GAAn
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Friedreich Ataxia
• FXN produces frataxin
• Nuclear encoded, mitochondrial localisation
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GAA Expansion
0
5
10
15
20
25
30
35
100 300 500 700 900 1100 1300 More
GAA repeat number
Num
ber
of a
llele
s in
ran
ge
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0
510
15
2025
30
0 500 1000 1500
GAA repeat size of smaller allele
Ag
e o
f o
nse
t
Age of onset v GAA size smaller allele (R2=0.39)
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P- value: complication v small allele size
FEATURE Delatycki Dürr Filla Montermini
Wheelchair 0.02 - <0.01 <0.0001
Cardiomyopathy 0.11 <0.05 <0.05 NS
Diabetes 0.08 NS <0.001 NS
Scoliosis 0.0001 <0.005 - -
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Iron in FRDA
• Knockout of the yeast frataxin homologue leads to
mitochondrial iron accumulation
• Iron deposits found in the myocardium of FRDA patients
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Iron levels in whole cells- FRDA v control (p=0.55)
0
0.5
1
1.5
2
2.5
3
3.5
FRDA Control
ng
Fe
/ ce
ll x
10000
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Mitochondrial iron/protein (p=0.01)
0
1
2
3
4
5
6
FRDA Control
ug
Fe
/ u
g p
rote
in x
10000
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Mitochondrial copper/protein (p=0.77)
0
0.2
0.4
0.6
0.8
1
1.2
FRDA Control
ug
Cu
/ u
g p
rote
in x
10000
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Pathogenesis
• Frataxin involved in iron sulphur cluster synthesis
• Fe-S crucial in various protein including some respiratory chain
proteins
• Deficiency leads to increased susceptibility to oxidative stress
• Increased Fe results in oxidative damage 2 to Fenton chemistry
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FRDA Treatment - Iron chelation
Must preferentially remove mitochondrial rather than cytosolic iron
Desferioxamine not successful (Kaplan unpublished data)
Deferiprone (L1) has shown promise (Boddaert, Cabantchik Blood, 2007)
Reduced dentate nucleus Fe with six months treatment with 20-30 mg/kg/day deferiprone
? Improved neurological parameters- open label
Des Richardson- mitochondrial specific chelators
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Deferiprone trial
• Placebo controlled, 3 doses- 20, 40, 60 mg/kg
• International multi-centre- Europe, Australia, Canada
• Recruited 10 subjects here
• High dose group permanent stop
• 20 and 40mg/kg – improved cardiac parameters, 40mg/kg
worse neurology scales
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FRDA Treatment - Anti-oxidants
• Treats down-stream effects
• Idebenone, mitoquinone, CoQ10, vitamin E
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Idebenone
Late 90’s shown to reduce cardiac hypertrophy in some
Buyse et al Neurology 2003- improved cardiac strain and strain rate
Di Prospero et at Lancet Neurology 2007
Phase II placebo controlled multi dose
Subjects < 18 years
12 subjects per arm- placebo, 5mg, 15mg, 45mg/kg/day
Trend to dose dependent response as measured by ICARS
Two phase III trials
USA- 6/12 trial no benefit
Europe- 12/12 trial- no benefit but close and 12% of placebo subjects took idebenone!
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Idebenone trial
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Upregulation of FXN
In FRDA normal frataxin produced but at low levels
An increase in frataxin production should ameliorate
disease
A few-fold increase in frataxin may stop disease
progression
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Upregulation of FXN
Erythropoietin
HDAC inhibitors
Resveratrol
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Dynamic Mutations-Practical Implications
• Diagnosis
• Predictive testing
• Therapeutic implications
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PREDICTIVE TESTING
• Testing people at increased risk for a disease prior to the
clinical onset of that disease
• Huntington disease= greatest experience
• Over 5000 predictive tests for HD done worldwide
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PREDICTIVE TESTING
• Process
– 1) discussion of genetics
– 2) neurological examination
– 3) counselling regarding what a positive and negative result
may mean for that person
– 4) result given
– 5) post-result counselling as required
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PREDICTIVE TESTING- UPTAKE
• Prior to availability- 75%
• Reality- less than 20%
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Predictive testing in minors
• Guidelines recommend against this
• Evidence is scarce
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Neurofibromatosis Type 1
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Neurofibromatosis Type 1- facts
• Incidence about 1:3000
• Affects all ethnic groups
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Neurofibromatosis Type 1- diagnostic criteria
• Require two or more of the following:
– 6 café au lait patches (>5mm prepubertal; >1.5cm
postpubertal)
– 2 neurofibromas or 1 plexiform neurofibroma
– Axillary and/or inguinal freckling
– Optic glioma
– 2 Lisch nodules
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Neurofibromatosis Type 1- diagnostic criteria
(cont)
– Distinctive osseous
lesion inc: sphenoid
wing dysplasia,
thinning of long bone
cortex ±
pseudoarthrosis
– A 1st degree relative
with NF1 by the
above criteria
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Plexiform neurofibromas
• 30%
• Severe lesion of head or neck- 2%
• Majority of disfiguring plexiform neurofibromas evident by 2
years
• Variable natural history
• Can undergo malignant transformation
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Plexiform Neurofibromas- Rx
• Surgery of limited value- regrowth
• Medical treatment-
– 2interferon
– cis-retinoic acid
– thalidomide
– farnesyl protein transferase inhibitor
– etoposide
• Problem of assessing efficacy
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Neurofibromatosis Type 1- complications
• Learning difficulties- 50%. Mean full scale IQ- 88.5 (51-
129):
– severe (IQ< 70)- 6%
– about 45% require special educational assistance
– UBOs (T2 weighted MRI signal)- ? association with learning
difficulties
• Seizures- 4.4%
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Neurofibromatosis Type 1- complications
• Symptomatic CNS tumours including optic nerve gliomas-
2% Subclinical optic nerve gliomas- 15%
• Peripheral nerve malignancy- 10%- often in a pre-existing
plexiform
• Scoliosis:
– requiring surgery- 4.4%
– mild- 5.2%
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Optic Nerve Gliomas
• Asymptomatic 15%
• Symptomatic 2%
• F:M= 2:1
• Often regress
• Association with eyelid plexiform
• Treatment with carboplatin successful in some with
symptomatic lesions
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UBOs
• Hyperintense regions on T2 MRI images
• Present in about 2/3- cerebellum> brainstem> internal
capsule
• Increase in size till about 10yrs then often disappear
• Benign
• ? Should be added to diagnostic criteria
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CNS Tumours
• 5x more common in NF1 than in general population but
after 10 years 100x
• Apart from optic nerve gliomas CNS tumours are not very
common (but increased compared to people without NF1)
• Include
– non-optic nerve gliomas
– meningiomas
– astrocytomas
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CNS tumours
• Childhood astrocytomas tend to be low grade
• Adult astrocytomas often high grade
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Spinal Cord
• Spinal neurofibromas
• Malignant peripheral
nerve sheath tumour
infiltrating the spinal
canal
• Rare
• Children> Adults
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Aqueduct Stenosis
• Increased incidence in NF1
– tumour
– idiopathic
• Childhood or adult presentation
• Responds well to shunting
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Malignant Peripheral Nerve Sheath Tumours
(MPNST)
• Neurofibrosarcoma
• Lifetime risk about 10%
• Most arise in deep plexiform neurofibromas and fewer in
superficial cutaneous plexiform neurofibromas
• Present with pain and rapid growth
• PET scanning useful for diagnosis
• Risk increased by radiotherapy
• Treatment- surgical
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Neurofibromatosis Type 1- complications
• Hypertension- 6%
– Renal artery stenosis- 1.5%
– Phaeochromocytoma- 0.7%
• Disturbances of puberty- rare and when present usually
associated with a CNS lesion
• Mortality- mean age at death 54 (males), 59 (females) cf:
gen pop 70, 74
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Timeline for Complications
• 0-2: Café au lait, plexiform neurofibromas
• 1-6: Symptomatic optic nerve glioma, skinfold freckling
• Preschool onwards: learning difficulties
• > 2: hypertension
• >6: neurofibromas, neurofibrosarcomas
• 6-16: scoliosis
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Neurofibromatosis Type 1- genetics
• Autosomal dominant
• 30-50% are new mutations
• Due to mutations in a gene called NF1
• Product= neurofibromin= tumour suppressor gene
• Huge gene!
• Numerous mutations
• Virtually 100% penetrant by 5 years
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Neurofibromatosis Type 1- diagnosis
• Clinical
• Gene too big with too many mutations to be able to use
mutation detection as a clinical tool
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Neurofibromatosis Type 1- clinical evaluation
• The vast majority of children with multiple café au lait
patches will go on to fulfil the diagnostic criteria for NF1
although a few families with dominant café au lait patches
exist
• Disease severity CANNOT be predicted in a child. There is
great intrafamilial variability including identical twins.
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Neurofibromatosis Type 1- clinical evaluation
• Children-
– 12/12 review including:
» learning evaluation formal psychometric assessment as
necessary
» neurological assessment
» BP
» scoliosis
– 12/12 ophthalmological review
• Routine neuroimaging not recommended (controversial)
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Neurofibromatosis Type 1- genetic counselling
• Must examine parents
– to confirm diagnosis in child
– to provide risk assessments in future pregnancies
– to look for complications in them
• Prenatal diagnosis/PGD rarely requested
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Prenatal Advice
• If child inherits NF1 mutation:
– 40% medical problems
– 50% learning problems, ID- 6%
– 4.5% problem in childhood resulting in lifelong morbidity
– Malignant CNS tumour 2.3%
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Malignancies in NF1
Non nervous system
GIST 6%
Somatostatinoma ?
Phaeochromocytoma 1%
Breast cancer 8.4% < 50 years (4x background)
Rhabdomyosarcoma 0.5% (20x background)
Nervous system
Astrocytoma ?
MPNST 8-13%
Neuroblastoma ?
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Tuberous Sclerosis
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Tuberous Sclerosis
• = Bourneville disease
• 1:5000 of those < 5 years
• 1:25 000 of all ages
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Diagnostic Criteria
• Major Features
– Facial angiomas of forehead plaques
– Nontraumatic ungual or periungual fibroma
– >3 hypomelanotic macules
– Shagreen patch
– Multiple retinal nodular hamartomas
– Cortical Tuber
– Subependymal nodule
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Diagnostic Criteria
• Major features (cont)
– Subependymal giant cell astrocytoma
– Cardiac rhabdomyoma 1
– Lymphangiomyomatosis
– Renal angiomyolipoma
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Diagnostic Criteria
• Minor features
– Multiple pits in dental enamel
– Hamartomatous rectal polyps
– Bone cysts
– Cerebral white matter migration lines
– Gingival fibromas
– Nonrenal hamartomas
– Retinal achromic patch
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Diagnostic Criteria
• Minor features (cont)
– “Confetti” skin lesions
– Multiple renal cysts
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Diagnostic Criteria
• Definite TS
– 2 major OR 1 major + 2 minor
• Probable TS
– 1 major + 1 minor
• Possible TS
– 1 major OR 2 minor
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TS- Adenoma
Sebaceum-
severe
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TS- Adenoma
Sebaceum- mild
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TS-
Hypomelanotic
Macule
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TS- Periungual Fibroma
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TS- Shagreen Patch
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TS- Forehead plaque
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TS- MRI showing a
tuber and
subependymal
nodules
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TS-
Hyperpigmented
macule= café au
lait
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TS- Enamel
pits
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CNS
• 85% CNS complication
– Seizures
– Intellectual disability
– Behavioural problems
– Tumours
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Seizures
• 75%
• Infantile spasms (20% will have TS)
• Myoclonic, partial, GTCS
• Presence in 1st 2yrs- association with MR- particularly
infantile spasms
• Can be refractory to treatment
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Development and Behaviour
• About 50% have intellectual disability- mild- severe
• 30% profound ID
• Behaviour- ADHD, autistic like, sleep problems
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Tumours
• >75% have a brain abnormality inc:
– tubers
– subependymal glial nodules
– white matter radial migration
• Giant cell astrocytomas- highest risk is late childhood/
adolescence but can affect adults
• Usually cause hydrocephalus
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Skin
• Depigmented patches may only be visible using a Woods
lamp- UV light- present in nearly all
• Adenoma sebaceum= angiofibromata- butterfly distribution-
present in >75%
• Forehead plaque- 25%
• Shagreen patch- “leathery”- 60%
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Ophthalmology
• Retinal phakoma- rarely affect vision
• “mulberry” lesions
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CVS
• Cardiac
rhabdomyomata
• Mostly asymptomatic
• Rarely to arrhythmia
or CCF
• Tend to regress
spontaneously
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Renal complications
• Commonest cause of TS related death
• Angiomyolipomata
– Generally bilateral and multiple (~80% of adults with TS)
– Usually asymptomatic
– Increase in frequency and severity with age
– Can bleed
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Renal complications
• Renal cysts (contiguous gene deletion TSC2 and PKD1)
• Renal cell carcinoma ~3%
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Respiratory
• Lymphangiomyomatosis
• F>>M
• Poor prognosis
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Genetics
• Autosomal dominant
• 2/3 sporadic, 1/3 inherited
• 2 genes
• TSC1- 9q34
• TSC2- 16p13.3
• Tumour suppressor genes
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Gene
% of Probands
with Definite TSC
and an
Identifiable
Mutation in This
Gene
Mutation Detection Frequency by
Gene, Family History, and Test
Method
Familial Cases Simplex Cases
TSC1 ~31% ~30% ~15%
TSC2 ~69% 51% ~60%-70%
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mTOR inhibitors in TSC
• mTOR = mammalian target of rapamycin
• mTOR activated by mutations in TSC1 and 2
• Sirolimus, mTOR inhibitor, used for 12 months, resulted in
a reduction in size of angiomyolipomas and improved PFTs
in some with lymphangiomyomatosis
• Everolimus treatment reduced the size of subependymal
giant cell astrocytomas and reduced seizure frequency
• Topical rapamycin shown to reduce size of facial
angiofibromas
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Genetics
• TSC1:TSC2= 1:1 in families
• TSC2:TSC1= 5:1 in sporadic cases
• ?TSC2 more severe than TSC1
• TSC1- hamartin
• TSC2- tuberin
• No homology between the two
• Appear to function in the same pathway
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Genetics
• Mutations tend to cluster but the majority are family specific
• Not widely available
• US$2000
• Mutation found in about 80%
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Genetic Counselling
• Parent with TS- 50% risk to offspring
• If affected about 50% chance MR- therefore 25% risk MR
• 75% risk epilepsy
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Genetic Counselling
• Apparent sporadic case
• MUST assess parents
– Skin examination including Woods lamp
– CT ± MRI brain
– Renal ultrasound
– Ophthalmology
• If normal, recurrence risk 2% (gonadal mosaicism)
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Prenatal diagnosis
Preimplantation diagnosis
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Prenatal Options
• Traditional prenatal diagnosis
– Chorionic villus sampling
– Amniocentesis
• Preimplantation genetic diagnosis
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Chorion Villous Sampling (CVS)
Amniocentesis
•CVS from 11 weeks
•Amnio from 15 weeks
•Diagnosis
– Chromosome abnorm.
– DNA Studies
– Biochemical studies
•CVS 1:100 miscarriage
•Amnio 1:200 miscarriage
CVS Amnio
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Preimplantation Genetic Diagnosis- PGD
• In the context of IVF
• Testing by embryo biopsy
• Chromosomal abnormalities
• Selected single gene disorders
• Most common reason an objection to TOP or previous TOP
following PND.
• No apparent increase in birth defects
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PGD
+
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PGD
- DNA extracted and mutation
detection testing done
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Method of embryo biopsy
The hole in the zona allows
entry of a micro pipette to
aspirate 1 or 2 cells from the
embryo.
The cell can then be fixed to
a slide, or placed in solution
to allow genetic analysis.
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PGD for single gene disorders
• Requested by couples wishing to avoid TOP
• 97% diagnostic accuracy
• 20% pregnancy rate per cycle
• Cystic fibrosis most common indication
• Counselling by both Genetics and IVF team
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Next generation sequencing
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Next Generation Sequencing (NGS)
• = Massively parallel sequencing (MPS)
• Whole exome sequencing = sequencing of all ~200,000
exons (~50x106 bp)
• Whole genome sequencing = sequencing of 3x109 bp of
genome
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Whole exome sequencing
• Most disease causing mutations are in the protein coding
part of the genome (ie: exons)
• Cost ~ $1,000 but ~$3000 with interpretation
• ~40,000 variants per exome!
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AATCCGATTTCGGCTAAGCCTAAGGCTGTTACGTACCCG
AATCCGATTTTGGCTAAGCCTAAGGCTGTTACGTACCCG
AATCCGATTTCGGCTAAGCCTAAGGGTGTTACGTACCCG
AATCCGATTTCGGCTAAGCCTAAGGCTGTTACGTACCCG
AATCCGATTTCGGCTAAGCCTAAGGCTGTTACGTACCCG
AATCCAATTTCGGCTAAGCCTAAGGCTGTTACGTACCCG
AATCCGATTTCGGCTAAGCCTAAGGCTGTTACGTACCCG
AATCCGATTTCGGCTAAGCCTCAGGCTGTTACGTACCCG
AATCCGATTTCGGCTAAGCCTAAGGCTGTTACGTACCCG
AATCCGATTTCGGCTAAGCCTAAGGCTGTTACGTACCCG
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NGS- uses
• Research- gene discovery
– Now possible to identify genes for rare diseases with few
families or in one family with relatively few affected
individuals
– New genes (and old genes causing new phenotypes) being
identified daily
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Clinical uses
• It is much cheaper to do whole exome or targeted gene
sequencing and look at genes of interest than to sequence
two or more genes
• Here gene panels developed- technology focusses on the
genes of interest- targeted capture to get very high
coverage of genes of interest
– eg: Charcot Marie Tooth, Leukodystrophy, HSP, muscular
dystrophy
• ~$1000 cf TS-$2000 for 2 genes!
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Typical whole exome dataset
Statistics summary ASD1 37509-1
Total reads 27,617,622 52,616,952
Total yield (bp) 3,037,938,420 5,787,864,720
Average read length (bp) 110 110
Mappable reads (=reads mapped to human genome) 22,786,188 47,217,845
Mappable yield (bp) 2,362,112,810 4,936,651,971
% Mappable reads (out of total reads) 82.50% 89.70%
On-target reads (=reads mapped to target regions) 18,178,648 35,664,336
On-target yield (bp) 1,536,584,594 3,004,107,432
% On-target reads (out of mappable reads) 79.80% 75.50%
% On-target reads (out of total reads) 65.80% 67.80%
Target regions (bp) 62,085,286 62,085,286
% Coverage of target regions (more than 1X) 88.20% 93.20%
% Coverage of target regions (more than 10X) 66.70% 82.10%
Median read depth of target regions 20.0X 44.0X
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Whole genome sequence
• 1st human genome sequence- 13 years, $2.7 billion
• Now ~$5K (aim is for $1K)- this is for the test- more $$$ for interpretation
• 98% more data than whole exome sequence
• Much more variation
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NGS- challenges
• Generates huge volumes of data- whole exome ~40,000 variants identified per study- “separate wheat from chaff”
– Bioinformaticians are the most important people in genetics!
• Not as accurate as Sanger sequencing so generally need to confirm findings but this is changing
• Not all exons captured with current technology- very important issue- can make this technology inappropriate for some genes/conditions
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Variants of unknown significance
• = VOUS
• = unclassified variants
• Some alterations clearly pathogenic
• Some alteration clearly benign polymorphisms
• Often can’t tell which is the case
• Already a major issue in genetic testing
• With NGS being used, this will increase exponentially
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Variants of unknown significance
• Generally missense mutations (changes one amino acid for
another)
• Various programs can assist with defining pathogenicity
• Based on conservation of the amino acid across species
• Is the amino acid changed from one type to a very different
or similar type?
– Eg: large basic to small acidic v large basic to large basic
• Common in population = likely to be polymorphism
• Functional studies- can take years!
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Problems of VOUS
• 8 year old child
• Parents concerned with various symptoms
• Possibility of connective tissue disorder mentioned
• Parents went to internet
• At parent’s request, paediatrician ordered FBN1 and
COL3A1 mutation detection
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Reports
• FBN1- “probable pathogenic mutation” identified
• BUT no signs Marfan syndrome! Probable polymorphism-
test parents (who have no signs Marfan syndrome)- if one
has it, can be confident it is not pathogenic
• COL3A1- silent mutation (base substitution but no change
in amino acid sequence)- extremely unlikely to be
pathogenic (child has no signs of EDS III)- parents still
concerned- want to have testing to be sure it is inherited
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Extrapolate to WES and WGS
• 1000s of alterations
• We will quickly become better at knowing what is
pathogenic and what is not but there will always be
unknowns
• This case has taken 4 hours of clinical geneticist time
already
• Who will counsel individuals/families?
• Charge per alterations discussed??!!
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NEJM October 3 2012
• 100 people with ID where cause not known (microarray,
fraX), IQ<50, healthy parents
• Whole exome sequencing
• 765 others with ID used to assess new genes
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• 79 de novo alterations in 53 patients
• 10 autosomal mutations and 3 X-linked inherited mutations
in males previously described as pathogenic
• Potentially causative de novo mutations in 22 others
• These genes sequenced in 765 others with ID
• Mutations in 3 “new ID genes” identified in others with
similar phenotype
• No autosomal recessive mutations found
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• Overall, 16% received a diagnosis
• 19 unclassified variants
• Shows that most undiagnosed genetic ID is new dominant mutations
• Surprising how little is recessive
• This will enter clinical practice
• Will potentially diagnose as many causes of ID as microarray
• Whole genome sequencing will likely eventually replace whole exome AND microarray
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Whole genome sequencing
• Mercy Children’s Hospital Kansas- whole genome
sequencing and preliminary report in 50 hours from receipt
of sample for neonates (Stat-seq)- $13,500
• Not in clinical use yet in Australia but will be soon no doubt
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Non-invasive prenatal diagnosis
• Detects foetal DNA in maternal blood
• Utilises NGS
• Currently fairly limited in how many things can be tested
(trisomy 13, 18,21, sex chromosome disorders) but will
increase rapidly
• Likely will be able to do whole exome/genome in the
relatively near future
• Will CVS/amnio become obsolete?
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Ethical issues
• NGS can reveal things that were
not being sought
– Incest
– Mutations in other genes- eg:
BRCA
• What to do when such information
is identified?
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Ethical guidelines
• Generally say if the variant leads to preventable disease risk (eg: BRCA), the person should be told
• If the variant leads to disease that is not treatable/preventable and the disease is unrelated to the purpose of the test (eg: Huntington disease mutation in a person being tested for cause of ID) then they should not be told
• BUT what if preventions become available?
• What if families would want to use the information for avoiding future children having those mutations?
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Ethical issues
• Can people consent for the level of information they want?
– Just severe disorders (eg: always causes ID)
– Risk findings (eg: this finding gives a 15% risk ASD)
– Everything (eg: your son’s likely IQ will be 93, brown hair,
175cm, poor sporting prowess)
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Online genetics resources
• OMIM
• Genereviews
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Online Mendelian Inheritance in Man
• OMIM
• Lists practically every Mendelian condition and every gene
associated with a phenotype
• Lists some mutations
• Cross referenced to Pubmed and gene databases for those
interested in in-depth information about genes and
mutations underlying the various conditions
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Autosomal X-
Linked
Y-
Linked
Mitochondrial Total
* Gene with known sequence 13980 683 48 35 14746
+ Gene with known sequence
and phenotype
87 2 0 2 91
# Phenotype description,
molecular basis known
3962 286 4 28 4280
% Mendelian phenotype or locus
,
molecular basis unknown
1541 134 5 0 1680
Other, mainly phenotypes with
suspected mendelian basis
1732 113 2 0 1847
Total 21302 1218 59 65 22644
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Thank you!