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Role of Molecular Genetic Assessment

for Autism in Clinical Setting

Young Shin Kim, MD, MS, MPH, PhD Director

STAR Center for ASD and NDDs Psychiatric Genetic Epidemiology

Associate Professor Dept. of Psychiatry, UCSF

www.mghcme.org

Disclosures

Research Grant (Spouse): Janssen

Consultant on a non-pharmaceutical project (Spouse): Janssen

Research Support (Spouse): NIH

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Purpose of Molecular Genetic Diagnoses

• Gain access to additional resources through their insurance company or school district

• Family support groups and online communities

• Decrease parental feelings of guilt

• Better anticipatory guidance

• Better genetic counseling

• Take account of specific management guidelines, if available,

• Access specific treatment considerations, if available.

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If the genetics of breast cancer were simple, the counseling might look like this

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However, other genetic and environmental risk factors also play a role

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Known genetic risk factors only account for a small proportion of total risk

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‘High risk’ genes combine with the other risk factors to give a total risk

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Without additional insight (e.g. family history) it is very hard to interpret findings

Current genetic methods cannot reliably

determine where a person lies on this curve

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Case Study 1

• JP is a 16mth-old girl presenting with speech and

walking delay

• Born at 39/40 by LCSC 2o failure to progress; APGARs

8,10,10

• Parents describe normal development in first year. No

pediatrician concerns.

• Sat up at 6mths; cruising at 9mths; first step at 13mths,

but then ‘lost interest’

• First word at 11mths, but did not progress

• “A couple of months after her first birthday it felt like the

lights went out”

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Case Study 1

• Sequencing of MECP2 reveals missense mutation. Not observed in either parent.

• Diagnosed as ‘Rett Syndrome’.

• Important characteristics: – Female

– Regression

– Progression

• MECP2 gene test has to be ordered specifically.

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Mendelian causes of ASD

• In Mendelian disorders variants are:

– Necessary (mutation required for diagnosis)

– Sufficient (no other risk factors required)

• Known Mendelian causes account for <1% of

ASD

• Rett’s should be considered in a girls presenting

with ASD

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Case Study 2

• DS is a 3yr-old boy presenting with mild speech delay

and challenging behavior

• Born at 41/40 by NVD; Normal APGARs

• Several milestones slightly delayed: sat at 8mths; first

word at 15mths; first step at 16mths

• Still not speaking in complete sentences

• Difficult to get him to concentrate on one activity

• Easily upset around other children and can be slightly

rough

• Normal growth

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Case Study 2

• PCR of FMR1 reveals excess of triplet repeats

• Diagnosed as ‘Fragile X Syndrome’.

• Important characteristics:

– Male

– Reduced IQ/ASD

– (Anticipation)

• FMR1 gene test has to be ordered specifically.

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‘Syndromic’ causes of ASD

• Variants are necessary and specific for the syndrome

• ASD is not always a feature

• Variants can be CNVs or SNVs

• Often de novo

• Usually associated with dysmorphology or characteristic symptoms

• CNVs found by microarray; single gene testing for SNVs (often requires genetics referral)

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Syndromic forms of autism

• Trisomy 21 (Down)

• X0 or XXY (Turner, Klinefelter)

• 7q11.23 (Williams)

• 22q11.2 (diGeorge/VCFS)

• 22q13 (Phelan-McDermid)

• 17p11.2 (Smith-Magenis/ Potocki-

Lupski)

• FMR1 (Fragile X)

• TSC1/2 (Tuberous Sclerosis)

• PTEN (Cowden Disease)

• CACNA1C (Timothy)

• DHCR7 (Smith-Lemli-Opitz)

• PAH (Phenylketonuria)

• SOS1, RAF1, BRAF, KRAS, MAP2K1

(Noonan)

• CHD7(CHARGE)

• UBE3A (Angelman)

• MECP2 (Rett)

• SLC6A8 (Creatine transporter)

• HPRT1 (Lesch-Nyhan)

• MBD5 (2q31 microdeletion)

• NSD1 (Sotos)

• CNTNAP2 (Cortical dysplasia-focal

epilepsy)

• TCF4 (Ptt-Hopkins)

• MED12 (Lujan-Fryns)

• ARX (ARX-related disorders)

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Some Mendelian/syndromic disorders are

potentially treatable

• PKU – dietary avoidance of phenylalanine

• Mutation in BCKDK

– inactivates amino acid breakdown

– treatment by high amino acid diet

• Usher syndrome – hearing and vision

• Cohen syndrome – vision and infection

• MECP2, AFF2 – current trials

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Case Study 3

• NP is a 6yr-old girl with a long-standing diagnosis of ASD

• Unremarkable birth history

• Presented at 2yrs of age with speech delay and mild

motor delay

• In mainstream school with support

• Head on 85th centile despite weight and height on 40th;

no overt dysmorphic features

• Microarray analysis was recently ordered

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Case Study 3

• Microarray reveals 500kb deletion in 16p11.2 region

• Diagnosed as ’16p11.2 microdeletion syndrome’

• Important characteristics:

– ‘Typical’ ASD presentation

• Microarray analysis picks up all large deletions

and duplications

– Misses inversions, translocations, and small CNVs

– ~5% diagnostic yield

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CNVs Associated with Autism

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Who should have a microarray?

• Everyone with developmental delay

without a clear genetic diagnosis

• Low IQ and dysmorphic features are not

clinically predicitive

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Case Study 4

• JT is a 7yr-old boy with a being followed up after a

recent diagnosis of ASD

• Born spontaneously at 36/40; no NICU required

• Presented at 5yrs due to concerns about social

interaction raised by kindergarten

• Coping well at school, above average performance in

some subjects

• Father is an engineer who has few social interests and

collects bottle caps

• Mother has good social interaction

• Microarray shows 200kb duplication at 19q13.41

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Case Study 4

• 19q13.41 duplication contains two genes: – MYADM - myeloid-associated differentiation marker

– NLRP12 - NLR family, pyrin domain containing 12 • “Mutations cause familial cold autoinflammatory syndrome

type 2”

• Rare (no other reported cases)

• Inherited from the mother

• Variant of unknown significance (VOUS)

• Hard to act on clinically

• But, always check the latest research

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Complex Genetics

• No clear segregation patterns in families

• Genetic heterogeneity

• Allelic heterogeneity

• GxG, GxE

• Low penetrance, variable expressivity

• Common polymorphism and rare variant

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Whole exome/genome sequencing

• Use of next-gen sequencing genome-wide – 3-4 x 10-6 per genome

• ‘Exome’ approaches target only coding – 10,000 per exome

• Challenge = analysis! [and $$$$]

• Other findings (~2% actionable)

– 100 LoF, 20 ko, 75 ‘pathogenic’, 50 unique

• Current estimated yield – Autism ~10%

• Recessive, X-linked, de novo

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Data from two studies leads to 50 genes (FDR <10%)

FOXP1 GIGYF1 KMT2E

MED13L DIP2A WAC

TCF7L2 KDM5B

CHD2 WDFY3 TNRC6B KDM6B DSCAM

PHF2 RIMS1

NCKAP1 ANKRD11

CTTNBP2 BCL11A

TRIO MLL3

APH1A ASXL3 MIB1 VIL1 RELN

CDC42BPB MYT1L CUL3

NR3C2 ASH1L ETFB

SYNGAP1 CACNA2D3

GABRB3 SETD5

SUV420H1 NAA15 PTEN

MYO9B

POGZ ADNP CHD8 TBR1

KATNAL2 GRIN2B ANK2 SCN2A ARID1B DYRK1A

(23) (17)

(10)

Iossifov et al, Nature, 2014 De Rubeis et al, Nature, 2014

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Case Study 5

• NP is an 8yr-old boy diagnosed with ASD, intellectual

disability and attention problems

• Unremarkable birth history

• Head circumference on 90th centile; height on 75th;

weight on 50th

• Subtle dysmorphic features

• Severe sleep disruption – often goes 72hrs without sleep

• One afebrile seizure, but not on medication

• Recurrent constipation

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Case Study 5

• Exome sequencing reveals de novo CHD8 nonsense

mutation

• Important characteristics:

– ‘Typical’ ASD presentation

– Sleep/GI problems (but not reliably)

– Large head (but not reliably)

• Exome sequencing picks up many single gene

disorders

– ~10% diagnostic yield

– Not routine practice yet...

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Your Next Case in Psychiatry

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Take Home Message

• Autism is predominantly a genetic disorder

• Accurate diagnoses of ASD, family history, physical examination are essential

• Every child with autism should have: – MECP2/FMR1/PKU testing

– Microarray

– Referral to clinical geneticist if syndromic features

• Genetic diagnosis should be revisited every 2-3 years

• Exome sequencing likely to be routine soon

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Molecular Genetic Examination of Autism

www.mghcme.org

Role of Molecular Genetic Assessment

for Autism in Clinical Setting

Young Shin Kim, MD, MS, MPH, PhD Director

STAR Center for ASD and NDDs Psychiatric Genetic Epidemiology

Associate Professor Dept. of Psychiatry, UCSF