Transcript Genetics of TSC - Tuberous Sclerosis Alliance

Genetics of Tuberous
Sclerosis Complex
David A. Stevenson
Associate Professor
Division of Medical Genetics
Stanford University
Outline of Presentation
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Overview of Medical Genetics
Genetics 101
TSC genes
Genetic Testing Methods
Mosaicism
Genotype-phenotype correlations
What is a Medical Geneticist?
• Physician (residency in Medical Genetics)
• Traditionally prenatal and pediatric areas
• In past 15 years expansion into various medical specialties (oncology,
cardiology, etc.)
• Diagnose, help patients understand disorder, arrange proper
treatment, explain recurrence risks
Why genetic counseling
• Better understand the risks within your family
• Decide whether to undergo genetic testing and learn
about the implications of your test results
• Life planning: medical management, reproductive
plans
• Genetic counseling does not mean you MUST
undergo genetic testing – it can help you decide
Genes
• A gene is a segment of DNA on a chromosome that tells the body how to make a
certain protein.
• 1 gene = 1 protein
Examples of Mutations
THE CAT ATE THE RAT
THE KAT ATE THE RAT
Silent
The meaning of the sentence is the
same.
THE CAT ATE THE RAT
THE HAT ATE THE RAT
Substitution (Missense)
The sense of the sentence is changed.
THE CAT ATE THE RAT
THE CAA TET HER AT
THE CAT ATE THE RAT
THE ECA TAT ETH ERA T
THE CAT ATE THE RAT
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Frameshift:
-insertion
-deletion
The sentence makes no sense.
Whole gene deletion
No sentence made
Genetics 201
(it gets more complicated)
• Some genes cause symptoms in everyone, while others cause
symptoms in a minority
• Penetrance
• Changes in the same gene can cause different effects in different
people
• Variable Expression
• Many conditions are caused by changes in more than one gene – this
can make testing more complicated
• Occasionally a condition (like TSC) can happen for the first time in an
individual (“de novo”)
• Environment and behaviors may influence clinical symptoms
Tuberous sclerosis complex due to changes in one of two genes: TSC1 and TSC2.
TSC1 gene
• 30% of those with TSC with identifiable mutation
• <1% with large deletions or duplications
• TSC1 gene encodes for the protein “hamartin”
• On chromosome 9
TSC2 gene
• 70% of those with TSC with identifiable mutation
• ≈6% with large deletions or duplications
• TSC2 gene encodes for the protein “tuberin”
• On chromosome 16
Recurrence risks
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50% recurrence risk if affected
1/3 have an affected parent
2/3 de novo (spontaneous mutation)
Risk to sib (depends on status of the
parent)
If there are Clinical
Diagnostic Criteria why do
genetic testing?
The genetic testing process
• Think in advance about what you may or may not learn (It’s
not “just a blood test”)
• Would I do anything differently?
• Medically – surveillance, treatments
• Life planning
• Insurance planning
• Reproductive planning
How can genetic testing help?
• YOU
• Reproductive decision making (preimplantation genetics)
• Genetic testing can help if clinical symptoms are unclear
• But only if there is a positive result. If negative, the
uncertainty may remain…
• Family members
• Genetic testing can clarify recurrence risk
• Can help plan ahead and receive appropriate surveillance
Prenatal Genetics
• Testing of fetus:
• Amniocentesis, chorionic villus sampling (CVS)
• Preimplantation
• Selecting embryo without specific genetic change.
Testing strategies
Test a relative who is known to be affected first,
so that results are most informative
•Positive results
• Medical management, planning ahead
•Negative results
• True negative if mutation known in family
• Family members’ risks cannot be adjusted
•Uncertain results
• Uninformative – you don’t know if you are positive or
negative
Variant of unknown clinical
significance
The results you get back sometimes demonstrate a “variant”
that is not clearly a pathogenic mutation.
What does this mean?
• May lead to more frustration and anxiety
• Do you presume it is causing the disease and change
management?
Ways to detect genetic changes
Sanger Sequencing
Multiplex Ligation-dependent probe amplification
(MLPA)
Other: Next generation sequencing, comparative genomic hybridization array, real-time PCR
Molecular testing difficult for TSC
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Two genes
Large size of the genes
Many different disease-causing mutations
Somatic mosaicism
In TSC2 there are more large deletions and
rearrangements (need more than just sequencing)
Genetic Testing in TSC
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sequence analysis of TSC1 and TSC2 gene
looking for DNA changes;
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test to look if the whole gene is deleted.
Laboratory testing
Various Labs (e.g.)
• Prevention Genetics
• GeneDx
• Emory
• Athena
• Transgenomic
• UAB Medical Genomics
Different combination of tests
• Comprehensive (TSC1/2 sequencing and panel)
• Each gene individually
• Deletion/duplication testing
• Sequencing with reflex to deletion/duplication
• Targeted familial testing
Turn-around time
2-8 weeks
Price
$250-$6000
What if no mutation is identified?
Approximately 85% of individuals with a definite clinical diagnosis of
TSC have an identifiable mutation.
What about the other 15%?
• Problems with molecular testing method
-human error
-medium size deletions
-unscreened changes (Promoter/enhancer regions, intronic)
• variants of unknown significance (might be pathogenic but don’t know yet)
• other not yet discovered genes
• mosaicism
Mosaicism
Cells within the same person have a
different genetic makeup
(happens after conception)
Gonadal Mosaicism
Gonadal (or germline) mosaicism:
mutation only in the eggs or sperm
• Rose et al (1999) reported about 5% of families with more than two
affected children with TSC with unaffected parents had confirmed
gonadal mosaicism
Somatic Mosaicism
Somatic (“relating to the body”):
cells except sperm and eggs
• Described in numerous individuals with TSC
• Difficult to test (low levels of mosaicism; tissue specific)
Genotype-Phenotype Relations
i.e. does the specific genetic change (genotype) correlate
with the physical findings (phenotype)
• TSC1: In general thought to have milder symptoms
compared to TSC2
• TSC2: reports of more hypomelanotic macules, earlier
onset of seizures, tubers, retinal findings, and learning
disability/cognitive impairment
• TSC2/PKD1 contiguous gene deletion (renal cysts)
Variability of disease
Each individual has variable presentation of features
Twin studies (same exact gene)
• Some studies show variability in cognitive and behavior
symptoms indicating role of seizures in this development
• too few reports to draw conclusions
“Second Hit”
• Hypothesized that some of the clinical variability
is due to “second hits”; somatic mutations in the
other gene copy.
• May also help explain lack of genotypephenotype correlations
Pathway
and Therapies
20 clinical trials listed on
clinicaltrials.gov