Genetics Flashcards

(166 cards)

1
Q

What testing is recommended for all people?

A

Aneuploidy screening, CF, SMA

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2
Q

What are the components of a first trimester screen?

A

PAPP-A
Free B-hCG
AFP
Nuchal translucency

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3
Q

What is the technique for an NT scan?

A
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
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4
Q

Differential diagnosis for NT of 4.0mm

A
Chromosomal malformations (aneuploidy)
Structural malformations (heart, skeletal dysplasia)
Other genetic syndromes (noonans, SLOS)
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5
Q

How do you counsel a patient with a thickened NT?

A
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
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6
Q

What would you offer a patient with an NT of 4.0mm?

A

Invasive testing (karyotype / microarray)
Noonans
Targeted early anatomy
….

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7
Q

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?

A

95%

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8
Q

How do you counsel a patient about prenatal genetic testing options?

A

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.

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9
Q

In your practice, for whom do you recommend cell free DNA screening?

A

All patients

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10
Q

How do you counsel the low risk patient who desires cell free DNA screening?

A

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.

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11
Q

What is sensitivity of cell free DNA for T21?
What is the sensitivity of cf DNA for T18?
T13?

A

T21: 99%
T18: 97%
T13: 97%

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12
Q

For a 35 yo, What is PPV of cell free DNA for T21?
T18?
T13?

A

80%
40%
20%

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13
Q

For a 35 yo, What is NPV of cell free DNA for T21?
T18?
T13?

A

> 99% for all

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14
Q

How does age impact the PPV of cell free DNA screening for T21?

A

Increases with increasing gestational age, due to an increasing prevalence

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15
Q

When you perform an amniocentesis for genetic testing, what do you order?

A

microarray

other testing as needed

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16
Q

What is a microarray?

A

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.

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17
Q

What is the benefit of a microarray on top of a karyotyoe in an anomaly?

A

6% more abnormal genetic findings when we look at microarray

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18
Q

What is the significance of a cell free DNA result that states “low fetal fraction”?

A

Can be an abnormality the test cannot pick up

Can also have a false negative

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19
Q

What is fetal fraction dependent on?

A
Gestational age
BMI
Medication exposure (lovenox, decreases it)
Maternal conditions
Singletons / Twins
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20
Q

How do you counsel regarding invasive testing / aneuploidy screening?

A

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

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21
Q

Describe how you perform an amniocentesis?

A

Skin cleansed with iodine based solution
Ultrasound guidance used continuously
Transabdominal aspiration of fluid (20-30cc)

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22
Q

At what gestational age can you perform an amniocentesis?

A

15-16 or higher (when chorion and amnion fuse)

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23
Q

What are the risks of amniocentesis?

A

Infection
Rupture of membrane
Bleeing
Pregnancy loss (1/1000)

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24
Q

Advantages of CVS?
Disadvantages ?
Timing?

A

Advantages; Earlier information

Disadvantages:
Confined placental mosaicism
Cannot test for NTDs
Maternal cell contamination
Cannot examine methylation (fragile x)

Timing: 10-14 weeks

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25
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
26
Contraindications to transcervical CVS?
Vaginal infection (Chlamydia /gonorrhea) Active herpes Low lying myoma
27
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
28
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
29
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 ```
30
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 ```
31
Which soft marker carriest the highest likelhood for T21?
Nuchal fold (LR of 11-18)
32
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 ```
33
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
34
What is the likelhood of spontaneous abortion for a fetus with T21 and hydrops?
Very high
35
What % of first trimester spontaneous abortions are related to T21?
~10%
36
Differential diagnosis for 1st trimester cystic hygroma?
``` 51% have an abnormal karyotype #1 Trisomy 21 #2 45X also possible other trisomies, triploidy, noonan ```
37
What % of fetuses with a cystic hygroma in the first trimester will be diagnosed with T21? Turners? T18?
T21: 33% Turner: 30% T18: 20%
38
Why do we use Multiples of the median?
Gives reference values across multiple gestational ages
39
Quad screen results in: T21
Increased: Inhibin A, hCG, decreased: AFP, estriol | *say Hi
40
Quad screen results in: T18
All are low
41
Quad screen results in: T13
All are low
42
Quad screen results in: Omphalocele, Gastroschisis, twins, NTD
Increased AFP
43
What condition should be suspected with exremely low Estriol (<0.15 MoM)?
Smith lemli opitz | X linked iccthyoses (Steroid sulfatase deficiency)
44
What does aneuploidy screening not find?
translocations, inversions, ring chromosomes, single gene mutation
45
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
46
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
47
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
48
Approach to a patient with Multiple aneuploidies on cfDNA with no known cancer?
Blood smear, physical exam, imaging looking for cancer
49
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
50
If fetal T21 is suspected, how do you counsel the patient regarding additional testing options?
CVS vs. amniocentesis depending on gestational age | Postnatal testing
51
Who should be offered cell free DNA screening?
All patients
52
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 ```
53
How accurate is cell free DNA screening in the detection of fetal T21?
It is the most accurate screen for trisomy 21
54
What can cause False positive results for cfDNA?
Maternal malignancy Maternal karyotype abnormality Placental mosaicism Demise of co-twin
55
What does a failed cfDNA mean?
Increased risk for aneuploidy or another genetic abnormality
56
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 ```
57
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
58
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
59
What are the most common anomalies in a fetus with T21?
AVSD
60
What causes a double bubble sign on US?
Duodenal atresia
61
Can a microarray detect T21?
Yes, by detecting copy number variants
62
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
63
What is FISH?
Fluorescence in situ hybridization | Chromosome specific probes
64
Benefits of FISH? Disadvantages?
Quick (24-48 hours) Can be performed on non-dividing interphase Disadvantages: Can have false negatives Not diagnostic
65
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
66
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
67
Most common mechanism for T21?
Meiotic nondisjunction in meiosis I
68
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)
69
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
70
What is the risk of recurrence? | 46, XX[20], 47, XX+7[10]?
Low.... | ? 24:10 left d02v05
71
What does a chromosomal microarray allow you to see?
Microdeletions / duplications
72
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
73
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
74
What test should you send for a structurally normal fetus?
Either karyotype or CMA
75
What test should you send for an IUFD?
CMA
76
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) ```
77
How do you follow a patient during pregnancy with T21?
Detailed anatomic survey Fetal echocardiogram Fetal growth Antenatal testing at 32 weeks
78
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
79
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 ```
80
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
81
How accurate is cell free DNA screening in the detection of fetal T18?
High false positives (depending on maternal age) | Low false negatives
82
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 ```
83
How do you counsel a 39 yo patient with a positive cell free DNA result for T18?
60% chance its a true positive
84
How do you counsel a 29 yo patient with a positive cell free DNA result for T18?
20% chance its a true positive
85
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 ```
86
If the patient continues the pregnancy with a T18 fetus, what complications may develop?
FGR Polyhydramnios Fetal death
87
If the fetus w/ T18 is born alive, what is the likelihood of survival?
10% to age >1
88
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.
89
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.
90
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 ```
91
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
92
Is Turner Syndrome associated with maternal age?
No
93
What are the phenotypic features of Turner Syndrome?
``` Short stature Webbed neck Coarctation of the aorta Hypoplasia left heart Renal defect Gonadal dysgenesis ```
94
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
95
How do you counsel a patient at 12 weeks with confirmed fetal Turner Syndrome and hydrops?
Very high risk of pregnancy loss / fetal death
96
What % of first trimester spontaneous abortions are related to Turner Syndrome?
10%
97
What percentage of fetuses with a cystic hygroma in the first trimester will be diagnosed with Turner Syndrome?
30%
98
How accurate is cell free DNA screening in the detection of Turner Syndrome?
Very good NPV | 40/60 PPV
99
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 ```
100
How do you follow a patient during pregnancy with fetal Turner Syndrome?
Detailed anatomy Fetal echo Serial growth u/s Weekly testing near term
101
How do you counsel a patient regarding recurrence risks for Turner Syndrome?
Low risk because it is sporadic
102
How is Noonan Syndrome inherited?
Autosomal Dominant (PTPN 11 gene mutation) - Usually De Novo
103
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 ```
104
What US findings are suspicious of Noonan syndrome?
Thickened NT >4.0
105
What is the most common cardiac defect with Noonan syndrome?
Pulmonary stenosis | Idiopathic cardiomyopathy
106
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
107
What diseases should ashkenazi jews be screened for?
CF Tay sachs Familia dysautonomia Canavan disease
108
What is Fragile X syndrome?
CGG trinucleotide repeat, that expands and can lead to intellectual disability when it reaches full mutation.
109
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
110
What are the phenotypic features of Fragile X syndrome?
``` Mental retardation (most common inherited intellectual disability) Prominent jaw Long face Large ears Macroorchidism ```
111
What phenotype do women express who are pre-mutation carriers for Fragile X syndrome?
They can have premature ovarian failure | and/or ataxia syndrome
112
What is the inheritance of Fragile X syndrome?
X-linked dominant
113
Can a female with a full mutation have Fragile X syndrome?
Yes, but it is usually milder thru skewed X inactivation
114
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)
115
How do AGG triplets affect Fragile X?
Intervening AGG makes it more stable, and reduces the risk of expansion
116
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
117
What gene is affected with Fragile X syndrome?
FMR1 gene
118
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
119
What are other examples of trinucleotide expansion repeat disorders?
myotonic dystrophy | huntingtons
120
Is Fragile X syndrome inherited through the mother or the father?
Both, but increased risk when comes from the mom
121
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
122
How do you test a fetus to see if has full mutation?
CVS or Amnio (PCR or Southern blot)
123
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
124
What is myotonic dystrophy?
AD inherited trinucleotide repeat disorder which can cause cataract, hypotonia, muscle weakness.
125
What ultrasound features can be identified in a fetus with myotonic dystrophy?
Polyhydramnios
126
How is myotonic dystrophy inherited?
Autosomal dominant inheritance (CTG trinucleotide repeats)
127
Classic physical exam finding in myotonic dystrophy?
Difficulty letting go/releasing grip
128
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
129
What patients should be screened for myotonic dystrophy carrier status?
Family history of weakness / cataracts
130
Is myotonic dystrophy associated with maternal or paternal expansion of trinucleotide repeats?
Maternal
131
What is a pre-mutation carrier for myotonic dystrophy?
38-49
132
Phenotype of huntingtons?
Progressive neurodegnative condition Chorea movements Dementia
133
What is the full mutation cutoff for huntingtons?
40
134
In huntingtons, is expansion risk greater with paternal or maternal inheritance?
Paternal
135
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.
136
What is the phenotype for Prader-Willi Syndrome?
``` Hypotonia Poor cry Lethargy Small penis Small hands/feet Childhood hyperphagia (obesity) Cognitive impairment ```
137
Which chromosome is involved in Prader-Willi Syndrome?
Chromosome 15 - loss of dads (prader no father)
138
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.
139
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
140
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
141
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
142
If Prader-Willi Syndrome develops as a result of UPD, are there two copies of the maternal or paternal chromosome?
Maternal
143
How is prader-willi syndrome tested for?
Parent specific - DNA methylation analysis on PW region of chrom 15
144
What US findings may be associated with Prader-Willi Syndrome?
None really
145
What is the phenotype for Angelman syndrome?
Happy puppet Dev delay Seizures Ataxia
146
Which chromosome is involved in Angelman syndrome?
Chrom 15
147
What are the 3 explanations for how Angelman syndrome occurs?
(1) Deletion of maternal (2) Paternal uniparental disomy (3) Imprinting defect on Chrom 15
148
If Angelman syndrome develops as a result of UPD, are there two copies of the maternal or paternal chromosome?
Paternal
149
What is the prognosis for Angelman syndrome?
Severe developmental delay Speech limitations Motor dificulties Normal life spans
150
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
151
What US abnormalities would make you suspect a 22q11 deletion?
Congenital heart defects (conotruncal most specific, Tetralogy most common) Cleft palate
152
How is a 22q11 deletion syndrome inherited?
Autosomal Dominant (usually de novo)
153
If you perform an amniocentesis, what studies will you send on the amniotic fluid to test for 22q11 deletion syndrome?
Direct FISH CMA
154
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.
155
What percentage of fetuses with 22q11 Deletion syndrome will have a cardiac defect on US?
75%
156
What is the most common cardiac defect in 22q11 deletion syndrome?
Tetralogy
157
What non-cardiac issues can be found in individuals with 22q11 deletion syndrome?
Learning disabilities Immune issues (thymic hypoplasia) Cleft palate
158
What are the classic US findings in Beckwith Wiedemann Syndrome?
Polyhydramnios Large for gestational age Omphalocele Macroglossia
159
What are the genetics of Beckwith Wiedemann Syndrome?
Epigenetic changes (methylation) in embryos in media, imprinted regions of 11
160
What is the prognosis for a fetus with Beckwith Wiedemann Syndrome?
Good prognosis, normal lfe expectancy | They grow up to be healthy adults
161
If you suspect a fetus of having Beckwith Wiedemann Syndrome, what testing will you perform on the amniotic fluid?
DNA Methylation testing
162
What clinical findings are there in patients with CF?
Respiratory: Bronchiectasis Pancreas: Pancreatic insufficiency Sweat glands: Increased Na in sweat (dehydration) Infertility
163
What testing do we do to assess risk for CF?
CFTR mutation panel
164
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
165
Clinical findings in patients with Spinal muscular atrophy (SMA)?
Hypotonia Absent DTRs Respiratory compromise #1 genetic killer of children <2
166
Can you be a carrier for SMA if you have 2 copies of SMN1?
Yes, if they are in cis configuration