Making Sense of Genetic Testing Flashcards
Different types of Lab tests. What falls under the following:
- Cytogenic
- DNA
- Metabolic
Cytogenic
- G-bands
- CMA: Oligo, SNP
DNA:
- Sequence
- Methylation
- Southern
- NGS; WholeExome disorder panel
Metabolic
- Mass spec
- Analyte
What genetic test is done for (known) Down syndrome child?
- Chromosome analysis/karyotype (to know recurrence test)
What is seen here?
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)
What is seen here?
45,XY,der(21;21)(q10;q10)
- Translocation carrier for 21q21q
- 100% recurrence risk of Down’s in children
What are take home points for Down syndrome testing
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%
T/F: The prognosis for child with Down’s due to translocation is slightly different form non-translocation type
False; same prognosis
What is the resolution of G-banded chromosomes?
Really only ~4MB
- Less for duplications
What is FISH?
- Mechanism
- When is it used/what can it detect
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!
What is Rapid FISH?
- What does it detect
- When are results available
Rapid FISH (Aneuvysion)
- Can detect aneuploidy of chromosomes 13, 18, 21, X and Y chromosomes
- Results available in 2-3 days
What is chromosomal microarray?
- Detects what
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.
What is oligo array vs. snap array?
- 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
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?
- Tested because of cognitive findings
- This is due to duplication 17p11.2, Potocki–Lupski syndrome
What is the typical phenotype of Potocki-Lupski syndrome?
- 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
What genetic testing may come back normal for Potocki-Lupski syndrome?
Typically normal:
- Chromosomal analysis
- FISH
What is the genetic cause of Potocki-Lupski syndrome?
Duplication 17p11.2
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?
Suspect Prader-Willi/Angelman
- Methylation studies
- SNP microarray
What does this mean for suspected Prader-Willi/Angelman kid?
- 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
If chromosome 15 showed LOH in SNP microarray, is it more probable from maternal or paternal parent?
Statistically, more commonly maternal
What genetic tests would be normal if Prader-Willi syndrome is caused by maternal UPD15 (not deletion)? Abnormal?
Normal:
- G-banded chromosomes
- OligoArray
Abnormal
- SNP microarray
- Methylation studies
What is seen here?
Example of Methylation study
- Abnormal here (due to Prader-Will syndrome with maternal UPD15)
T/F: Deletion causing PW/AS will have normal methylation studies
False
- Deletion causing PW/AS will have abnormal methylation studies
What do you do if your diagnosis is Angelman syndrome but methylation studies are normal?
Look for UBE3A point mutation
What is the “new” gene for Prader-Willi-like syndrome?
- Methylation study results?
Schaaf-Yang syndrome
- Normal methylation results
- Still unknown % due to MAGEL2 point mutation
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
Would want to make clinical diagnosis and do analyte testing
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
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
What is the inheritance pattern for S-L-O?
- Recurrence risk
- Autosomal recessive
- Recurrence risk 25%
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%!!!
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
What genetic testing do you want to do for Fragile X?
Southern blot- used for trinucleotide repeats
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
What is seen here?
Ex of Fragile X Southern Blot
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
What are nuances of exam you want to do with “Non-accidental trauma” suspected in pt?
- Ophthalmic exam
- Skeletal survey
Contact CPS
What genetic test do you want to do here (not suspecting MCA syndrome), but rather a metabolic disorder?
Analyte testing!
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
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
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
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
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
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
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
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)
What is the diagnosis with the following exome sequencing results:
- Gene: PTPN11- protein-tyrosine phosphatases nonreceptor-type 11
Noonan syndrome
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
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
Relative genetic testing costs?
