Making Sense of Genetic Testing Flashcards
1
Q
Different types of Lab tests. What falls under the following:
- Cytogenic
- DNA
- Metabolic
A
Cytogenic
- G-bands
- CMA: Oligo, SNP
DNA:
- Sequence
- Methylation
- Southern
- NGS; WholeExome disorder panel
Metabolic
- Mass spec
- Analyte
2
Q
What genetic test is done for (known) Down syndrome child?
A
- Chromosome analysis/karyotype (to know recurrence test)
3
Q
What is seen here?
A
46,XY,der(21;21)(q10;q10)
- This causes Down syndrome phenotype
- 21q21q translocation
- If the parent has this translocation, recurrence risk is 100%
- Parent would possibly be 45,XY,der(21;21)(q10;q10)
4
Q
What is seen here?
A
45,XY,der(21;21)(q10;q10)
- Translocation carrier for 21q21q
- 100% recurrence risk of Down’s in children
5
Q
What are take home points for Down syndrome testing
A
Always get a chromosome analysis (G-banded)
- Clinical diagnosis and/or array CGH are NOT good enough Recurrence risk for t(21;21) carrier is 100%
6
Q
T/F: The prognosis for child with Down’s due to translocation is slightly different form non-translocation type
A
False; same prognosis
7
Q
What is the resolution of G-banded chromosomes?
A
Really only ~4MB
- Less for duplications
8
Q
What is FISH?
- Mechanism
- When is it used/what can it detect
A
Fluorescence in situ hybridization (FISH)
- Fluorescent probes bind to specific sequences of DNA
- Under a special microscope these probes glow
- Can detect deletions, duplications (to a lesser extent), and translocations.
- ONLY at regions of PROBE of INTEREST!
9
Q
What is Rapid FISH?
- What does it detect
- When are results available
A
Rapid FISH (Aneuvysion)
- Can detect aneuploidy of chromosomes 13, 18, 21, X and Y chromosomes
- Results available in 2-3 days
10
Q
What is chromosomal microarray?
- Detects what
A
Array comparative genomic hybridization (aCGH)
- Oligo array
- SNP array
Detection:
- Detects extra or missing pieces of DNA
- Can detect deletion/duplication of 5-10 Kb
- Deletions and duplications detected equally well.
11
Q
What is oligo array vs. snap array?
A
- Oligo: copy number only (if 0, means copy number neutral)
- SNP: copy number and AOH (absence of heterozygosity)
- AOH could be due to deletion or UPD (uniparental disomy)
- In below picture, you have no midline dots: AOH
12
Q
What genetic is testing for this child:
- Low, but normal birth weight
- Poor feeding and failure to thrive in infancy
- Developmental delay
- Behavioral problems (hyperactivity, atypical)
- Non-dysmorphic
- No congenital abnormalities
- Cognitive testing: mild ID to Borderline range
What would genetic testing find? What condition is this?
A
- Tested because of cognitive findings
- This is due to duplication 17p11.2, Potocki–Lupski syndrome
13
Q
What is the typical phenotype of Potocki-Lupski syndrome?
A
- Patients often non-dysmorphic
- Variable phenotype:
- No congenital anomalies to HLHS
- Improved learning and behaviour with therapy.
- Long term follow up for aortic root dilation.
- Heart problems may involve L heart hypoplasia; can be really bad
14
Q
What genetic testing may come back normal for Potocki-Lupski syndrome?
A
Typically normal:
- Chromosomal analysis
- FISH
15
Q
What is the genetic cause of Potocki-Lupski syndrome?
A
Duplication 17p11.2
16
Q
Case)
- A 36-year-old woman undergoes a CVS in the 12th week of pregnancy.
- The results of the chromosome analysis reveal 47,XY,+15 and an amniocentesis is recommended.
- The results of the amniocentesis reveal a normal 46,XY complement. The couple is reassured.
- Several months later, you receive a call from the NICU to evaluate this couple’s newborn who has severe hypotonia and requires mechanical ventilation and tube feeding
- What condition do you suspect?
- What genetic test do you want?
A
Suspect Prader-Willi/Angelman
- Methylation studies
- SNP microarray
17
Q
What does this mean for suspected Prader-Willi/Angelman kid?
A
- SNP microarray: shows LOH but COPY neutral (copy neutral means no deletion; thus this is caused by UPD)
- Thus, Prader-Willi syndrome due to maternal UPD15
18
Q
If chromosome 15 showed LOH in SNP microarray, is it more probable from maternal or paternal parent?
A
Statistically, more commonly maternal
19
Q
What genetic tests would be normal if Prader-Willi syndrome is caused by maternal UPD15 (not deletion)? Abnormal?
A
Normal:
- G-banded chromosomes
- OligoArray
Abnormal
- SNP microarray
- Methylation studies
20
Q
What is seen here?
A
Example of Methylation study
- Abnormal here (due to Prader-Will syndrome with maternal UPD15)
21
Q
T/F: Deletion causing PW/AS will have normal methylation studies
A
False
- Deletion causing PW/AS will have abnormal methylation studies
22
Q
What do you do if your diagnosis is Angelman syndrome but methylation studies are normal?
A
Look for UBE3A point mutation
23
Q
What is the “new” gene for Prader-Willi-like syndrome?
- Methylation study results?
A
Schaaf-Yang syndrome
- Normal methylation results
- Still unknown % due to MAGEL2 point mutation
24
Q
What is your genetic test for Multiple Congenital Anomalies as indicated by:
- 4 yo male with devo delay and dysmorphic features
- PMH: failure to thrive, poor feeding
- PSH: VSD repair, hypospadius repair, orchiopexy, removal of 6th finger L hand, syndactyly
- FHx of stillborn and SAb
A
Would want to make clinical diagnosis and do analyte testing
25
What condition are you thinking with these features:
- 4 yo male with devo delay and dysmorphic features
- PMH: failure to thrive, poor feeding
- PSH: VSD repair, hypospadius repair, orchiopexy, removal of 6th finger L hand, syndactyly
- FHx of stillborn and SAb
Smith-Lemli-Opitz syndrome
26
How do you diagnose Smith-Lemli-Opitz syndrome?
Clinically and then with analyte testing (rather than expensive WholeExome sequencing)
- Defect in cholesterol biosynthesis
* Sterol profile abnormal
* d7-dehydrocholesterol reductase mutation analysis for carrier/prenatal
27
What is the inheritance pattern for S-L-O?
- Recurrence risk
- Autosomal recessive
- Recurrence risk 25%
28
What are the take home points for malformation syndromes/SLO?
- Not all malformation syndromes are “chromosomal”
- Family history (miscarriages) may provide a clue to mode of inheritance
- Rapid testing necessary when patient not stable:
- ANALYTE TESTING: STEROL ANALYSIS SINGLE GENE SEQUENCING
- Recurrence risk for SLO is 25%!!!
29
What condition are you thinking with:
- 4 yo boy with DD, hypotonia
- Chromosome analysis and aCGH sent by PCP are normal
- Metabolic studies and WES sent by neuro are normal
- Genetics takes family history
Thinking this is Fragile X syndrome
30
What genetic testing do you want to do for Fragile X?
**Southern blot**- used for trinucleotide repeats
31
What is the process of southern blot testing?
- PCR
- Enzymes cleave DNA into smaller pieces
- Electrophoresed on a gel (larger pieces move more slowly)
- Radio-labeled primers added that bind to target DNA sequences
32
What is seen here?
Ex of Fragile X Southern Blot
33
What condition are you thinking for:
- 7 mo girl w/ progresive macrocephaly
Physical examination
- alert and playful infant
- fontanelle soft
- mild generalized hypotonia
- normal CNs; normal DTRs CT of brain shows large bilateral subdural hematomas
**Glutaric aciduria type I**- this is a metabolic disorder
34
What are nuances of exam you want to do with "Non-accidental trauma" suspected in pt?
- Ophthalmic exam
- Skeletal survey
Contact CPS
35
What genetic test do you want to do here (not suspecting MCA syndrome), but rather a metabolic disorder?
Analyte testing!
36
What are basic and specialized components of analyte testing (done for suspected metabolic disorders)
_Basic_
- Ammonia
- Lactate
_Specialized_
- Plasma amino acids
- Urine organic acids
- Acylcarnitine profile
37
What does plasma AAs test detect
- Diagnostic for what conditions
Detects the levels of AAs in the blood
Diagnosis of some inborn errors of metabolism:
- Maple Syrup Urine Disease (MSUD)
- PKU
- Tyrosinemia
- Urea Cycle Disorders
38
What does urine organic acid test detect
- Diagnostic for what conditions
Detects presence of organic acids in the urine
Diagnoses some inborn errors of metabolism
- Organic acidemias
- Propionic Acidemia
- Methylmalonic Acidemia
- Isovaleric Acidemia
39
What does an acylcarnitine profile detect?
- Diagnostic for what conditions
Detects levels of acylcarnitines (fatty esters bound to carnitine)
Diagnoses fatty acid oxidation disorders
- MCAD
- VLCAD
- Primary carnitine deficiency
40
What are expected labs for Glutaric aciduria type I?
Urine organic acids:
- High glutaric acid
- High 3-OH-GA
- High glutaconic acid
Low plasma carnitine
41
Describe Glutaric aciduria type I
- Inheritance pattern
- Incidence
- Presentation
- Symptoms
- Prognosis
**- Autosomal recessive**
- 1/30,000 (1/300 Amish & Ojibway-Cree)
- NBS panel, but may be negative
- Typically presents **6-18 months** macrocephaly; poor feeding; irritable mild hypotonia; dystonia; dyskenesia
- Mild manifestations may be overlooked
- Prognosis variable
42
Take home points for Glutaric aciduria type I
- Glutaric aciduria is sneaky
- Can be missed on NBS
- Will be diagnosed on Urine Organic Acids
- Can be asymptomatic in infancy
- Can mimic NAT
- Sometimes misdiagnosed as “CP” Is treatable
- Carries a 25% recurrence risk
43
What are you thinking with:
- 3.5 yo female
- “looks like skeletal dysplasia”
- Macrocephaly, short stature
- Chiari I malformation, obstructive hydrocephalus
- Pulmonary valve stenosis
- Myopia
- FGFR3 normal What tests do you want?
Uncertain, Yet Likely “Genetic” Cause
- Whole Exome Sequencing Results (not necessary anymore once more research was done on this condition)
44
What is the diagnosis with the following exome sequencing results:
- Gene: PTPN11- protein-tyrosine phosphatases nonreceptor-type 11
Noonan syndrome
45
Describe the genetics of Noonan sydnrome
- Gene: **PTPN11**- protein-tyrosine phosphatases nonreceptor-type 11
- Mutation:
* c.922A\>G (p.N308D)
* NGS call: 0/1:108:86:194
- Heterozygous
* Confirmed by Sanger sequencing as heterozygous
46
Describe Noonan syndrome
- Inheritance pattern
- Symptoms
- Dysmorphic features
**- Autosomal dominant**
- Hypertelorism, downward eyeslant, and low-set posteriorly rotated ears, short stature, a short neck with webbing or redundancy of skin, cardiac anomalies, epicanthic folds, deafness, motor delay, and a bleeding diathesis
47
Relative genetic testing costs?
48
