Genetics Flashcards
What testing is recommended for all people?
Aneuploidy screening, CF, SMA
What are the components of a first trimester screen?
PAPP-A
Free B-hCG
AFP
Nuchal translucency
What is the technique for an NT scan?
Margins of NT clear Fetus in mid-sagittal plane Fetus occupies majority of image Fetal head in neutral position Fetus observed away from amnion Calipers used Horzontal crossbars placed correctly (perpendicular to long axis) Measurement at widest NT space Measure 3x and report largest measurement CRL 45-84mm
Differential diagnosis for NT of 4.0mm
Chromosomal malformations (aneuploidy) Structural malformations (heart, skeletal dysplasia) Other genetic syndromes (noonans, SLOS)
How do you counsel a patient with a thickened NT?
Increased risk of: genetic disorders structural malformations miscarriage fetal demise If genetic testing, echo, and anatomy are normal, then 95% will have a normal outcome
What would you offer a patient with an NT of 4.0mm?
Invasive testing (karyotype / microarray)
Noonans
Targeted early anatomy
….
In patients with a thickened NT, but normal karyotype/array/noonan, normal anatomy and normal fetal echo. What is the likelihood of a normal outcome?
95%
How do you counsel a patient about prenatal genetic testing options?
Serum screening is non diagnostic and can have both false positives and false negatives
Women who desire definitive information about chromosomal conditions in their pregnancy should be offered the option of amniocentesis or CVS.
In your practice, for whom do you recommend cell free DNA screening?
All patients
How do you counsel the low risk patient who desires cell free DNA screening?
cfDNA is a screening test, and both false positive and false negative results occur.
This is particularly true in lower risk women, in whom a positive test is more likely to be a false positive.
Women who desire definitive information about chromosomal conditions in their pregnancy should be offered the option of amniocentesis or CVS.
What is sensitivity of cell free DNA for T21?
What is the sensitivity of cf DNA for T18?
T13?
T21: 99%
T18: 97%
T13: 97%
For a 35 yo, What is PPV of cell free DNA for T21?
T18?
T13?
80%
40%
20%
For a 35 yo, What is NPV of cell free DNA for T21?
T18?
T13?
> 99% for all
How does age impact the PPV of cell free DNA screening for T21?
Increases with increasing gestational age, due to an increasing prevalence
When you perform an amniocentesis for genetic testing, what do you order?
microarray
other testing as needed
What is a microarray?
It is high resolution whole genomic sequencing technique using DNA primers to bind complimentary DNA
Can identify problems detected by conventional karyotype as well as small micro deletions or duplications.
What is the benefit of a microarray on top of a karyotyoe in an anomaly?
6% more abnormal genetic findings when we look at microarray
What is the significance of a cell free DNA result that states “low fetal fraction”?
Can be an abnormality the test cannot pick up
Can also have a false negative
What is fetal fraction dependent on?
Gestational age BMI Medication exposure (lovenox, decreases it) Maternal conditions Singletons / Twins
How do you counsel regarding invasive testing / aneuploidy screening?
Discuss the risks and benefits of diagnosis
Compare other screening tests
Discuss the detection rate of aneuploiides other than T21
and the type and prognosis of the aneuploidies likely to be missed by serum screening
Describe how you perform an amniocentesis?
Skin cleansed with iodine based solution
Ultrasound guidance used continuously
Transabdominal aspiration of fluid (20-30cc)
At what gestational age can you perform an amniocentesis?
15-16 or higher (when chorion and amnion fuse)
What are the risks of amniocentesis?
Infection
Rupture of membrane
Bleeing
Pregnancy loss (1/1000)
Advantages of CVS?
Disadvantages ?
Timing?
Advantages; Earlier information
Disadvantages: Confined placental mosaicism Cannot test for NTDs Maternal cell contamination Cannot examine methylation (fragile x)
Timing: 10-14 weeks
What are the risks of CVS?
What are the risks of performing a CVS prior to 10 weeks?
Bleeding
Rupture of membranes (<1%)
Infection (<1%)
Pregnancy loss (1/200-1/300)
Prior to 10 weeks: limb defects
Contraindications to transcervical CVS?
Vaginal infection (Chlamydia /gonorrhea)
Active herpes
Low lying myoma
35 yo G1 with increased NT
CVS shows 46,XX [10], 47,XX +14 [20]
How do you counsel her about this test result?
Can be normal with placental mosaicism
Can be abnormal
Or baby could be mosaic
How do you counsel a patient with suspected mosaic trisomy of fetus?
Cannot be sure which cells are mosaic (skin, brain, heart, etc…)
So we don’t know the severity
Can be anywhere from as severe as a full trisomy vs. a milder form
No way to be sure
What are the phenotypic features of T21?
Flattened face Small ears Short neck Outside corners of eyes are pointed upward Narrow high arch palate Single crease across the palms Sandal gap feet
What are soft markers for T21 on US?
Thickened nuchal fold Absent nasal bone Short limbs Pyelectasis Echogenic bowel Echogenic intracardiac focus Single umbilical artery
Which soft marker carriest the highest likelhood for T21?
Nuchal fold (LR of 11-18)
How do you counsel a patient at 12 weeks with confirmed T21?
Expectant management verses pregnancy termination Increased risk of pregnancy loss Increased risk of anomalies Varying degree of intellectual ability Increased risk of Leukemia
How do you counsel a patient at 12 weeks with confirmed T21 and hydrops?
Prognosis is grave, 90% risk of fetal death.
Offer termination of pregnancy
What is the likelhood of spontaneous abortion for a fetus with T21 and hydrops?
Very high
What % of first trimester spontaneous abortions are related to T21?
~10%
Differential diagnosis for 1st trimester cystic hygroma?
51% have an abnormal karyotype #1 Trisomy 21 #2 45X also possible other trisomies, triploidy, noonan
What % of fetuses with a cystic hygroma in the first trimester will be diagnosed with T21?
Turners?
T18?
T21: 33%
Turner: 30%
T18: 20%
Why do we use Multiples of the median?
Gives reference values across multiple gestational ages
Quad screen results in: T21
Increased: Inhibin A, hCG, decreased: AFP, estriol
*say Hi
Quad screen results in: T18
All are low
Quad screen results in: T13
All are low
Quad screen results in: Omphalocele, Gastroschisis, twins, NTD
Increased AFP
What condition should be suspected with exremely low Estriol (<0.15 MoM)?
Smith lemli opitz
X linked iccthyoses (Steroid sulfatase deficiency)
What does aneuploidy screening not find?
translocations, inversions, ring chromosomes, single gene mutation
If CfDNA shows mosaic for 46xx and 45xo, what are the possible reasons?
(1) Fetus with mosaic monosomy x
(2) Mom with mosaic monosomy x
(3) Confined placental mosaicism
What is the recurrence risk of a fetus with Mosaic 45Xo?
Test the mom and dad for mosaicism
If negative, discuss the risk of gonadal mosaicism
What is the best aneuploidy screening test for a patient with leg cancer?
Amniocentesis
if not, can do quad screen
With active cancer, can have aneuploid cell turnover
Approach to a patient with Multiple aneuploidies on cfDNA with no known cancer?
Blood smear, physical exam, imaging looking for cancer
Can you do cell free DNA in twins?
Yes, but there are limitations
Positive results but cant be sure which baby is affected
No method of aneuploidy screening that includes a serum sample is as accurate in twin gestations as it is in singleton pregnancies
If fetal T21 is suspected, how do you counsel the patient regarding additional testing options?
CVS vs. amniocentesis depending on gestational age
Postnatal testing
Who should be offered cell free DNA screening?
All patients
Limitations of cell free DNA screening?
Low fetal fraction Confined placental mosaicism Co-twin demise (vanishing twin, false results) Tumors Sex discordance maternal deletion/duplication maternal mosaicism
How accurate is cell free DNA screening in the detection of fetal T21?
It is the most accurate screen for trisomy 21
What can cause False positive results for cfDNA?
Maternal malignancy
Maternal karyotype abnormality
Placental mosaicism
Demise of co-twin
What does a failed cfDNA mean?
Increased risk for aneuploidy or another genetic abnormality
What are possible explanations for cell free DNA results indicating high risk for T21?
Mosaic placenta Aneuploid placenta Aneuploid fetus Mosaic mom False positive Resorbed twin Maternal malignancy
How do you counsel a 39 yo patient with a positive cell free DNA result for T21?
High likelihood its a true positive >90%
Can confirm with invasive testing
How do you counsel a 29 yo patient with a positive cell free DNA result for T21?
Medium likelhood its a true positive 50-60%
Can confirm with invasive testing
What are the most common anomalies in a fetus with T21?
AVSD
What causes a double bubble sign on US?
Duodenal atresia
Can a microarray detect T21?
Yes, by detecting copy number variants
What is cytogenetic analysis?
Need live rapidly growing cells (WBCs or amniocytes)
Culture
Stimulate cells to divide
Arrest in metaphase
Treat with solution to break open cells
Chromosomes fixed, spread on slides and stained
What is FISH?
Fluorescence in situ hybridization
Chromosome specific probes
Benefits of FISH?
Disadvantages?
Quick (24-48 hours)
Can be performed on non-dividing interphase
Disadvantages:
Can have false negatives
Not diagnostic
What are the benefits/ disadvantages of a Karyotype?
Chromosomal rearrangements
Large deletions / duplications
Balanced structural rearrangements
Disadvantages:
Miss microdeletions / microduplications
Need live cells that are able to grow
What advantages does a fetal karyotype have over microarray in a fetus with T21
Microarray cant tell you if you have 3 separate copies or 2 copies attached to each other, and this is important for recurrence counseling
Most common mechanism for T21?
Meiotic nondisjunction in meiosis I
What are the types of translocations?
Reciprocal/Balanced: two pieces switch
Robertsonian: rearrangement with two acrocentric chromosomes (so get one chromosome with 2 q arms)
How do you interpret this cvs result?
46, XX[20], 47, XX+7[10]?
Next steps?
Mosaicism with additional chromosome 7
Could be fetal mosaicism
Confined placental mosaicism
Could be maternal mosaicism
Next step: Test amniocytes
Rules out confined placental mosaicism
What is the risk of recurrence?
46, XX[20], 47, XX+7[10]?
Low….
? 24:10 left d02v05
What does a chromosomal microarray allow you to see?
Microdeletions / duplications
Karyotype vs Microarray, pros /cons
Karyiotype detects: large del/dup, balanced translocations, triploidy
Karyotype cannot detect: small dels/dups
Microarray detects: microdels/microdups, unbalanced translocation, triploidy (snp based), areas of homozygosity
Microarray cannot detect: Balanced translocations
What test should you offer for a major structural anomaly?
CMA (replaces the need for fetal karyotype)
6-7% more detection than a normal karyotype
What test should you send for a structurally normal fetus?
Either karyotype or CMA
What test should you send for an IUFD?
CMA
You are seeing a consultation of history of fetal demise at 30 weeks. She chose limited autopsy with no specific finding and now you have microarray results:
VUS in WNT gene
What are your next steps in analysis and how do you counsel the couple?
Parental testing (targeted microarray) Cannot be sure if this is the reason the baby died. Counsel that VUS can be associated with adverse outcomes, but there is no clear information about this variants at this time. If none of them has this abnormality, it is unlikely to recur because it was a de novo mutation If one of them does have it, but has a normal phenotype, then there is a higher chance its a non pathogenic variant (but cant be sure)
How do you follow a patient during pregnancy with T21?
Detailed anatomic survey
Fetal echocardiogram
Fetal growth
Antenatal testing at 32 weeks
How do you counsel a patient regarding recurrence risks for T21?
Non-inherited extra chromosome -> 1% recurrence (or age dependent)
Translocated Down syndrome -> 50% recurrence
What ultrasound findings would lead you to suspect T18?
MORE Micrognathia Omphalocele Rocker bottom feet Ears low set Cephalic -Brachycephaly (strawberry head) Celes (omphalocele/ meningomyocele) Clenched hands overlapping digits Choroid plexus cyst Cleft lip/palate CDH Cardiac defect Posterior fossa abnormalities Nuchal translucency verses cystic hygroma
If fetal T18 is suspected, how do you counsel the patient regarding additional testing options?
Recommend diagnostic testing with amniocentesis or CVS
NIPT if patient declines diagnostic testing
How accurate is cell free DNA screening in the detection of fetal T18?
High false positives (depending on maternal age)
Low false negatives
What are possible explanations for cell free DNA results indicating high risk for T18?
Mosaic placenta Aneuploid placenta Aneuploid fetus Mosaic mom False positive Resorbed twin Maternal malignancy
How do you counsel a 39 yo patient with a positive cell free DNA result for T18?
60% chance its a true positive
How do you counsel a 29 yo patient with a positive cell free DNA result for T18?
20% chance its a true positive
How do you counsel a patient about prognosis with confirmed T18?
Poor prognosis ( 50% IUFD, 20% survive beyond 1st month 5-10% survive beyond 1st year Can consider termination of pregnancy
If the patient continues the pregnancy with a T18 fetus, what complications may develop?
FGR
Polyhydramnios
Fetal death
If the fetus w/ T18 is born alive, what is the likelihood of survival?
10% to age >1
Do you offer c/s for fetuses with T18?
Discuss a shared decision making model, explain to patient that cesarean section puts her at risk and that a t18 fetus has a low probability of survival.
Will you perform intrapartum fetal monitoring for fetuses with T18?
Shared decision making, explain to them that we may find heart rate abnormalities that cause us to intervene and that they may not improve the ability of the fetus to survive.
What US findings would lead you to suspect Turner Syndrome?
Cystic hygroma Coarctation of aorta in female fetus Pelvic Kidneys Fetal edema Horseshow kidney Non-immune hydrops
How does Turner Syndrome occur?
Instability of the Y chromosome in the sperm. 80% occur when an egg fertilized with sperm lacking a X chromosome
Is Turner Syndrome associated with maternal age?
No
What are the phenotypic features of Turner Syndrome?
Short stature Webbed neck Coarctation of the aorta Hypoplasia left heart Renal defect Gonadal dysgenesis
How do you counsel a patient at 12 weeks with confirmed fetal Turner Syndrome?
Increased risk of miscarriage
There is an increased risk of cardiac and other anomalies
High risk of fetal loss prior to delivery
How do you counsel a patient at 12 weeks with confirmed fetal Turner Syndrome and hydrops?
Very high risk of pregnancy loss / fetal death
What % of first trimester spontaneous abortions are related to Turner Syndrome?
10%
What percentage of fetuses with a cystic hygroma in the first trimester will be diagnosed with Turner Syndrome?
30%
How accurate is cell free DNA screening in the detection of Turner Syndrome?
Very good NPV
40/60 PPV
What are possible explanations for cell free fetal DNA results indicating high risk for Turner Syndrome?
Mosaic placenta Aneuploid placenta Aneuploid fetus Mosaic mom False positive Resorbed twin Maternal malignancy
How do you follow a patient during pregnancy with fetal Turner Syndrome?
Detailed anatomy
Fetal echo
Serial growth u/s
Weekly testing near term
How do you counsel a patient regarding recurrence risks for Turner Syndrome?
Low risk because it is sporadic
How is Noonan Syndrome inherited?
Autosomal Dominant (PTPN 11 gene mutation) - Usually De Novo
What is the classic phenotype of Noonan syndrome?
Short stature Webbed neck / lymphedema Pulmonary stenosis (sometimes Pulm HTN) Cardiomyopathy Micrognathia Wide spaced eyes Delayed puberty Pectus carinatum or excavation Developmental delay Spine
What US findings are suspicious of Noonan syndrome?
Thickened NT >4.0
What is the most common cardiac defect with Noonan syndrome?
Pulmonary stenosis
Idiopathic cardiomyopathy
What is the prognosis for a fetus diagnosed with Noonan syndrome?
Related to presence or absence of cardiac abnormalities.
Can have issues as baby but usually improve and lead mostly normal lives
failure to thrive
Learning disability/ Mild intellectual impairment
Delayed puberty
What diseases should ashkenazi jews be screened for?
CF
Tay sachs
Familia dysautonomia
Canavan disease
What is Fragile X syndrome?
CGG trinucleotide repeat, that expands and can lead to intellectual disability when it reaches full mutation.
What patients should be screened for their Fragile X syndrome carrier status?
Relatives with intellectual disability
Early menopause
Personal/family history of intention tremor and cerebellar ataxia
What are the phenotypic features of Fragile X syndrome?
Mental retardation (most common inherited intellectual disability) Prominent jaw Long face Large ears Macroorchidism
What phenotype do women express who are pre-mutation carriers for Fragile X syndrome?
They can have premature ovarian failure
and/or ataxia syndrome
What is the inheritance of Fragile X syndrome?
X-linked dominant
Can a female with a full mutation have Fragile X syndrome?
Yes, but it is usually milder thru skewed X inactivation
What is a premutation carrier for Fragile X syndrome?
55-200, increaased risk of expansion to a full mutation
Can have some associated issues (Premature ovarian failure, tremor/ataxia syndrome)
How do AGG triplets affect Fragile X?
Intervening AGG makes it more stable, and reduces the risk of expansion
What does it mean to say someone carries the full mutation for Fragile X syndrome?
The expansion from anticipation of the repeat has reached a critical level where the features of the disease begin to show
What gene is affected with Fragile X syndrome?
FMR1 gene
How does methylation of the FMR1 gene lead to Fragile X syndrome?
FMR1 protein is important for neurons, with expansion of the CGG, there is methylation which causes less producton of this protein
What are other examples of trinucleotide expansion repeat disorders?
myotonic dystrophy
huntingtons
Is Fragile X syndrome inherited through the mother or the father?
Both, but increased risk when comes from the mom
Explain the concept of anticipation?
Increasing repeats with every generation, at a certain level (>200 in fragile x) its enough to cause instability and can stop transcription resulting in disease
How do you test a fetus to see if has full mutation?
CVS or Amnio (PCR or Southern blot)
Why is amnio preferred for Fragile X testing?
If there are indeterminate results, and methylation needs to be done
Methylation testing can only be done with amnio because CVS is placental
What is myotonic dystrophy?
AD inherited trinucleotide repeat disorder which can cause cataract, hypotonia, muscle weakness.
What ultrasound features can be identified in a fetus with myotonic dystrophy?
Polyhydramnios
How is myotonic dystrophy inherited?
Autosomal dominant inheritance (CTG trinucleotide repeats)
Classic physical exam finding in myotonic dystrophy?
Difficulty letting go/releasing grip
What is the phenotype of myotonic dystrophy?
> 50 CTG: Mild: cataract , myotonia ,late onset
Moderate: muscle weakness, cataracts, onset at 20-30yrs
1000 CTG: severe: congenital, polyhydramnios, developmental delays, hypotonia
What patients should be screened for myotonic dystrophy carrier status?
Family history of weakness / cataracts
Is myotonic dystrophy associated with maternal or paternal expansion of trinucleotide repeats?
Maternal
What is a pre-mutation carrier for myotonic dystrophy?
38-49
Phenotype of huntingtons?
Progressive neurodegnative condition
Chorea movements
Dementia
What is the full mutation cutoff for huntingtons?
40
In huntingtons, is expansion risk greater with paternal or maternal inheritance?
Paternal
What is exclusion testing?
If a grandparent has a disease like huntingtons, can test to see whether child is inheriting that gene area from the affected grandparent (without specifying whether its the affected one or unaffected one) or the unaffected grandparent.
This allows excluding disease without testing / telling the parent about their status.
What is the phenotype for Prader-Willi Syndrome?
Hypotonia Poor cry Lethargy Small penis Small hands/feet Childhood hyperphagia (obesity) Cognitive impairment
Which chromosome is involved in Prader-Willi Syndrome?
Chromosome 15 - loss of dads (prader no father)
What is the prognosis for Prader-Willi Syndrome?
not life-threatening, but compulsive eating and weight gain can cause young adults with the syndrome to develop serious obesity-related conditions such as: type 2 diabetes.
What is an imprinting disorder?
Epigenetic phenomenon that causes genes to be expressed or not depending on whether they are inherited from the mother or the father
What are 3 explanations for how Prader-Willi Syndrome occur?
(1) Paternal deletion chrom 15
(2) Maternal UPD chrom 15
(3) Imprinting defect on chrom 15
What is uniparental disomy? Increases risk of?
Getting 2 copies of a chromosome from one parent (6,7,11,14,15)
At first you get two from one parent 1 from the other and trisomic rescue occurs to kick out one of them, leading to a cell with 2 of a certain chromosome from one parent.
Increased risk of imprinting disorders
If Prader-Willi Syndrome develops as a result of UPD, are there two copies of the maternal or paternal chromosome?
Maternal
How is prader-willi syndrome tested for?
Parent specific - DNA methylation analysis on PW region of chrom 15
What US findings may be associated with Prader-Willi Syndrome?
None really
What is the phenotype for Angelman syndrome?
Happy puppet
Dev delay
Seizures
Ataxia
Which chromosome is involved in Angelman syndrome?
Chrom 15
What are the 3 explanations for how Angelman syndrome occurs?
(1) Deletion of maternal
(2) Paternal uniparental disomy
(3) Imprinting defect on Chrom 15
If Angelman syndrome develops as a result of UPD, are there two copies of the maternal or paternal chromosome?
Paternal
What is the prognosis for Angelman syndrome?
Severe developmental delay
Speech limitations
Motor dificulties
Normal life spans
What is the classic phenotype of Di George Syndrome?
Congenital heart defects (conotruncal most specific, Tetralogy most common)
Abnormal facies
Thymic hypoplasia (Decreased T cell immunity)
Cleft palate
Hypoparathyroid
What US abnormalities would make you suspect a 22q11 deletion?
Congenital heart defects (conotruncal most specific, Tetralogy most common)
Cleft palate
How is a 22q11 deletion syndrome inherited?
Autosomal Dominant (usually de novo)
If you perform an amniocentesis, what studies will you send on the amniotic fluid to test for 22q11 deletion syndrome?
Direct FISH CMA
What are the pitfalls of using cell free DNA screening in cases of suspected fetal 22q11 deletion syndrome?
Most of these microdeletions are extremely rare. Given the very low prevalence of these conditions, most positive test results will be false positives, and the positive predictive value of the test is very low.
What percentage of fetuses with 22q11 Deletion syndrome will have a cardiac defect on US?
75%
What is the most common cardiac defect in 22q11 deletion syndrome?
Tetralogy
What non-cardiac issues can be found in individuals with 22q11 deletion syndrome?
Learning disabilities
Immune issues (thymic hypoplasia)
Cleft palate
What are the classic US findings in Beckwith Wiedemann Syndrome?
Polyhydramnios
Large for gestational age
Omphalocele
Macroglossia
What are the genetics of Beckwith Wiedemann Syndrome?
Epigenetic changes (methylation) in embryos in media, imprinted regions of 11
What is the prognosis for a fetus with Beckwith Wiedemann Syndrome?
Good prognosis, normal lfe expectancy
They grow up to be healthy adults
If you suspect a fetus of having Beckwith Wiedemann Syndrome, what testing will you perform on the amniotic fluid?
DNA Methylation testing
What clinical findings are there in patients with CF?
Respiratory: Bronchiectasis
Pancreas: Pancreatic insufficiency
Sweat glands: Increased Na in sweat (dehydration)
Infertility
What testing do we do to assess risk for CF?
CFTR mutation panel
Limitations of CFTR mutation panel?
Tests the most common mutations
In negative results, it doesnt rule out a mutation, just rules out the mutations tested
Clinical findings in patients with Spinal muscular atrophy (SMA)?
Hypotonia
Absent DTRs
Respiratory compromise
#1 genetic killer of children <2
Can you be a carrier for SMA if you have 2 copies of SMN1?
Yes, if they are in cis configuration
