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x_NeuroGenetics Review > Prenatal Genetics > Flashcards

Prenatal Genetics Flashcards

1
Q

What are some prenatal screening options for aneuploidy?

A
  • First trimester screening
  • Second trimester screening (triple, quad)
  • Ultrasound
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2
Q

What are some methods of prenatal diagnostic testing?

A

Procedures

  • Amnio
  • CVS
  • PUBS

Genetic testing options

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3
Q

What are some forms of preconception counseling?

A
  • Carrier screening
  • Review genetic causes of infertility
  • Recurrent pregnancy loss
  • PGD/PGS
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4
Q

What is prenatal screening?

A

The identification, among apparently normal pregnancies, of those at sufficient risk of a specific fetal disorder to justify subsequent invasive and/or costly prenatal diagnostic tests or procedures

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5
Q

Define the following counts:

  • True positives (TP)
  • False positives (FP)
  • True negatives (TN)
  • False negatives (FN)
A

THESE ARE COUNTS; NOT RATES

- True Positives (TP): Affected individuals correctly labeled affected

- False Positives (FP): Unaffected individuals falsely labeled as affected

- True Negative (TN): Unaffected individuals correctly labeled unaffected

- False Negative (FP): Affected individual falsely labeled as unaffected

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6
Q

Define the following rates:

  • Sensitivity
  • Specificity
  • False negative rate
  • False positive rate
A
  • Sensitivity = True Positive Rate = Detection Rate
  • Probability that an affected individual will have a positive test
  • Affected with positive test / all AFFECTEDS
  • Specificity = True Negative Rate
  • Probability that an unaffected individual will have a negative test
  • Unaffected with negative test / all UNAFFECTEDS
  • False negative rate
  • Probability that an affected individual will have a negative test (% missed by the test)
  • Affected with negative test / all AFFECTEDS
  • False positive rate
  • Probability that an unaffected individual will have a positive test (% falsely told they were positive)
  • Unaffected with positive test / all UNAFFECTEDS
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7
Q

Define these predictive values:

  • Positive predictive value (PPV)
  • Negative predictive value (NPV)
A
  • Positive Predictive Value (PPV): Probability that a positive test results indicates a true positive
  • Affected with positive test / All individuals with a positive test (affected & unaffected)
  • Negative Predictive Value (NPV): Probability that a negative test results indicates a true absence of disease
  • PPV and NPV vary considerably with prevalence of the tested condition*
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8
Q

What are we looking for in prenatal screening?

A

Most types of prenatal screening are focused on detection of:

ANEUPLOIDY

  • Down syndrome
  • Trisomy 13
  • Trisomy 18
  • Sex chromosome abnormalities

NEURAL TUBE DEFECTS

  • Open Spina Bifida (OSB)
  • Anencephaly
  • Encephalocele
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9
Q

What does prenatal screening NOT look for?

A

Structural chromosome abnormalities:

  • Translocations, Inversions , Isochromosomes, Marker chromosomes, Insertions, Ring chromosomes

Gene mutations:

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10
Q

What are methods for detecting fetal chromosomal abnormalities?

A

Traditional aneuploidy screening

  • First trimester screening
  • Second trimester screening
  • [Different combinations of first and second trimester screening]

Non-Invasive Prenatal Testing (NIPT) or screening (NIPS)?

  • Cell-free fetal DNA in maternal blood Invasive prenatal diagnosis
  • CVS or Amniocentesis?
  • Karyotype or chromosomal microarray?
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11
Q

What are the ACOG practice bulletin guidelines for screening for fetal chromosomal abnormalities?

A
  • Screening and invasive testing should be discussed with and be available to all patients regardless of age
  • 1st TM screening using NT and biochemical markers is preferred over 2nd TM screening due to higher DR at the same FPR
  • Women at increased risk of aneuploidy with 1st or 2nd TM screening should be offered genetic counseling and option of CVS or amnio.
  • Sonographers obtaining NT measurements should be credentialed by NTQR or FMF
  • Serum integrated screening is a useful option if NT not obtainable
  • NTD screening (by MsAFP screening ONLY) should be offered in 2nd TM to women who elect only 1st tm screening.
  • After 1st TM screening, 2nd TM DS screening is not indicated unless it is being performed as a component of the integrated, sequential, or contingent sequential test.
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12
Q

What are components of 1st TM screening?

A

Blood sample

  • PAPP-A – pregnancy associated plasma protein
  • Free b-hCG
  • Levels of these markers are compared to an ‘average’ pregnancy with 1.0 MoM used as the average value

Ultrasound = nuchal translucency measurement

  • Echo-free area at the back of the fetal neck
  • The larger the nuchal translucency the higher the risk
  • (tri 13,18,21 and 45,X)
  • Uniform ultrasound skills
  • certification
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13
Q

When is 1st TM screening performed?

A

11 w0d to 13w6d

  • Blood can be sampled as early as 9w0d
  • Screens for Down syndrome and trisomy 18
  • Cannot screen for neural tube defects
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14
Q

Increased nuchal translucency corresponds to what?

A
  • Significant risk chromosome abnormality: 30-50%
  • Increased risk of congenital heart defects (33% of cardiac defects have elevated NT)
  • >100 different developmental disorders/syndromes have been associated with increased NT
  • Genetic syndromes
  • Skeletal dysplasias
  • Cardiac defects
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15
Q

What are the methods for screening for the following conditions that are performed IN THE 1st TM:

  • Down syndrome
  • Trisomy 18
  • Trisomy 13
A
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16
Q

What are some serum screening methods in the 2nd TM?

  • What do they measure?
  • What conditions are they looking for?
A

Quadruple Marker Screening

  • AFP (alpha fetoprotein)
  • hCG (human chorionic gonadotropin)
  • uE3 (unconjugated estriol)
  • DIA (dimeric inhibin A)

Performed 15-21 weeks gestation

  • Optimal from 16-18 weeks
  • Value converted into a multiple of the median (MoM)

Risk calculated for

  • Neural tube defects such as spina bifida
  • Down syndrome
  • Trisomy 18
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17
Q

Describe Quad screening results for the following conditions:

  • Down syndrome
  • Trisomy 18
  • ONTD
A
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18
Q

What is integrated screening?

  • Pros/cons
A
  • Age, NT, 1st TM biochemistry, and 2nd TM biochem integrated for one risk in 2nd TM
  • Higher detection rates (92-95%) but wait for results
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19
Q

What is sequential screening?

  • Pros/cons
A
  • Age, 1st TM biochem and 2nd TM biochem If 1st TM risk > 1 in 50, informed of positive result and option of diagnostic testing
  • If risk less than 1 in 50, proceed to 2nd TM blood draw
  • Detection rates for Down syndrome and trisomy 18 90% with lower false positive rate of 3%
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20
Q

What is NIPT?

A

Non-invasive prenatal testing

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21
Q

What is cell-free fetal (cff) nucleic acid?

A

Method of non-invasive prenatal testing

  • Originates from trophoblast cells of the placenta
  • Released into maternal bloodstream as small DNA fragments (150-200bp)
  • Comprises approximately 3-13% of total cell free maternal DNA
  • Reliably detected after 5 weeks gestation
  • Undetectable within hours of delivery
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22
Q

_____ has revolutionized non-invasive prenatal testing for chromosomal aneuploidy from cell-free fetal DNA in maternal plasma

A

Massive Parallel Sequencing has revolutionized non-invasive prenatal testing for chromosomal aneuploidy from cell-free fetal DNA in maternal plasma

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23
Q

How does Non-invasive prenatal testing for aneuploidy by cff-DNA MPS work?

A
  • 7-15 mL Maternal blood sample
  • Separate plasma fraction from cells
  • Extract DNA from plasma fraction
  • PCR to quantify total and fetal cff DNA fraction (~5% - 10% of total)
  • Prepare sequencing library (cff DNA already fragmented)
  • Massive parallel shotgun sequencing (MPSS) 
  • Millions of 30-60bp fragments
  • Map fragments to the human genome (bin by chromosomal origin)
  • Count the fragments (N) from each chromosome:
  • N is proportional to the size of the chromosome
  • N is consistent from sample to sample
  • N is consistent from patient to patient
  • If there is fetal trisomy, there is a relative small increase in the number of fragments from that chromosome
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24
Q

What are the overall performances in samples from HR populations by NIPT

  • Trisomy 21
  • Trisomy 18
  • Trisomy 13
A

Detection rate best for 21 > 18 > 13

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25
Q

T/F: NIPT is not diagnostic

A

TRUE

Recognized benefits to NIPT, but…

  • Currently not diagnostic: “Advanced screening test”
  • Confirmation with invasive testing is needed
  • Requires comprehensive genetic counseling

- Should only be used in validated populations (= high risk)

  • Not recommended in low risk women (validation studies needed
  • For women at increased risk to have a child with a prenatally diagnosable disorder (i.e., Mendelian disorder, microdeletion syndrome), amnio or CVS still indicated
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26
Q

How should you manage Trisomies 21, 18, and 13 if you get positive ccfDNA results?

A

(If negative with normal US, no further assessment)

  • If positive with confirming US: offer invasive testing
  • If positive without confirming US: offer invasive testing
  • If negative results with abnormal US findings: offer invasive testing; consider microarray analysis
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27
Q

Why might you get discrepant results in NIPT?

A

- Confined placental mosaicism ~1%

  • NIPT measures the genome of the entire cytotrophoblast
  • True fetal mosaicism
  • Maternal sex chromosome abnormality
  • May increase with age - Maternally inherited marker chromosome
  • Maternal deletion on chromosome 21
  • Maternal tumor with high levels of cffDNA
  • Co-twin demise
  • Lab error
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28
Q

What are the nuances for using NIPT with twins?

A
  • Fetal fraction for each twin may be lower
  • May affect detection rate and ability to classify
  • Cannot differentiate between twins
  • Chorionicity does not appear to play a role
  • No good data on vanishing twin and NIPT
  • Not offered by all companies
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29
Q

__% of all screen positive are not T21, T13, or T18

A

2% of all screen positive are not T21, T13, or T18

  • Nearly 1/3 of abnormalities found after 1st TM screening are different than expected: 10 yr experience from a single center
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30
Q

Invasive diagnostic testing for aneuploidy should be available to all women, regardless of maternal age.

A

yay

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31
Q

What are methods of prenatal DIAGNOSIS?

A

– Chorionic Villus Sampling (CVS)

– Amniocentesis

– Other options (less common)

  • Early amniocentesis
  • PUBS – Percutaneous Umbilical Cord Sampling (also called cordocentesis)
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32
Q

What is the method behind CVS?

  • When is it done
A
  • Performed 10-14 weeks gestation
  • Ultrasound to locate premature placenta
  • Transcervical or transabdominal
  • 5-40 grams of chorionic villi
  • Placental cells obtained (fetal in origin)
  • Full bladder
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33
Q

Describe transcervical CVS

A
  • Speculum (or tenaculum) to open cervix
  • Antiseptic prep of external genitalia and cervix
  • Catheter inserted using US guidance
  • Aspiration of the villi
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34
Q

What are C/I for transcervical CVS?

A
  • Cervical stenosis
  • Vaginal infection
  • Active herpes
  • Low-lying myoma
  • Use of anticoagulants (must d/c prior)
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35
Q

Describe transabdominal CVS

A
  • Double needle system
  • Single needle with syringe mounted on holder
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36
Q

What are C/I to transabdominal CVS?

A
  • Unavoidable myomas
  • Posterior placenta
  • Unavoidable maternal intestines
  • Use of anticoagulants (must d/c prior)
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37
Q

What are advantages/disadvantages of CVS?

A
  • Allows for earlier information
  • Tissue taken allows for certain biochemical analysis not possible on amniocytes
  • Can be “like a pap smear
  • Operator experience and learning curve
  • Cannot test for NTDs: MSAFP at 16 weeks
  • Maternal cell contamination
  • Higher chance of mosaic result
  • Confined placental mosaicism
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38
Q

What are indications for amniocentesis?

A
  • Genetic studies: karyotype, FISH, CMA, mutational analysis, metabolic studies
  • AFAFP and acetylcholinesterase
  • Pulmonary maturity
  • Infections
  • Isoimmunization
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39
Q

Describe the method of performing an amnoicentesis

  • When is it done
A

• May be performed >15 weeks

  • Majority 16-18 weeks
  • Skin cleansed with iodine-based solution
  • Few centers use local anesthetic
  • Ultrasound with continuous visualization (not always used)
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40
Q

__% of pregnancies miscarry in mid TM

  • Attributable to procedures?
A

3-4% of pregnancies miscarry in mid TM

  • Typically NOT attributable to procedure (1/1600 in FASTER, 1/770 in Odibo, 1/4000 in ACOG)
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41
Q

When is early amniocentesis done?

  • Describe the procedure
  • Risks
A

< 15 wks

  • Remov 10-14 cc of amniotic fluid

Risks

  • Tenting of membranes: incomplete fusion of amnion and chorion
  • Risk of SAb may be higher (2-3%?)
  • Increased chance of culture failure?
  • Risk for club foot
  • 2ndary to decreased fetal mvt during a key phase in foot/ankle devo when fluid is removed that early on
  • This risk is highest if there is additional leakage of fluid
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42
Q

What is PUBS?

  • When is it indicated?
A

Percutaneous Umbilical Blood Sampling (PUBS)

  • Aka cordocentesis

Indications:

  • Mosaicism detected from amnio
  • Rapid karyotype
  • Late prenatal care
  • 2nd or 3rd trimester anomalies
  • Fetal infections
  • Hematologic
  • Hemoglobinopathies
  • Fetal blood type and Rh
  • Oligohydramnios/Anhydramnios
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43
Q

Describe the process of performing PUBS

  • When is it done?
A

Transabdominal needle introduction

– Direct ultrasound guidance

– Umbilical cord (vein) near placental insertion or fetal hepatic vein

– MCV of sample to confirm fetal origin (higher)

Performed 18-23 weeks (depending upon operator)

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44
Q

What are the risks of PUBS?

A

1-3% fetal loss rate

Rate is higher with a compromised fetus

– Fetal growth restriction

– Karyotypic abnormality

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45
Q

What are diagnostic tools/genetic TESTS used to diagnose chromosomal and/or genetic anomalies?

A

Cytogenetics

  • Analysis of banded metaphase chromosomes
  • Looks at all chromosomes at one time

Fluorescent in situ hybridization (FISH)

  • Targets specific chromosomes or specific areas of a chromosome

Chromosome microarray/Comparative Genomic Hybridization

Molecular testing

WES

NGS Panels (not many in prenatal)

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46
Q

Pros/cons of cytogenetics/chromosome analysis as a diagnostic tool?

A

IDs all chromosomal aneuploidies and structural chromosomal abnormalities that are microscopically visible and at least 4-5MB in size

Limitations:

–Low resolution

–Does not detect point mutations

–Need for cell culture à longer TAT (10-14 days)

–Subjective interpretation

–Requires a fresh sample containing live cells

–Samples without live cells - cannot be used for chromosome analysis

  • Serum, mature red blood cells, biopsies which put into formalin or other preservatives
  • Some tissue samples from miscarriages may no longer be viable when fetal demise is discovered
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47
Q

Describe FISH as a diagnostic tool

A

Chromosome specific probes

– Can be performed on non-dividing interphase cells without prior cell culture or on metaphase spreads from dividing cells

– Interphase FISH

  • Quicker TAT (24-48 hours)
  • Typically used prenatally for rapid detection of common aneuploidies

Locus specific probes

– Regions known to be duplicated or deleted in specific syndromes

– Used with proband at increased risk for a particular syndrome based on clinical findings or family setting

  • i.e., del22q probe
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48
Q

Describe CMA/aCGH as a diagnostic tool

A
  • Looks at entire genome for copy number variants (CNVs)
  • Different array types
  • Oligonucleotide
  • SNP
  • BAC
  • Combination platforms

• Cell culture not always needed à faster TAT

CMA/aCGH detects CNVs

  • Aneuploidies
  • UNBALANCED chromosome rearrangements
  • Copy number changes from an entire chromosome down to a few kb in over 500 specific disease regions
  • Loss of heterozygosity (SNP platforms)
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49
Q

What are the classifications of CNV?

A
  • Pathogenic variant – known to be disease causing
  • Benign variant – known to be a polymorphism
  • Variant of uncertain clinical significance
  • Likely benign
  • Likely pathogenic
  • Unknown
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50
Q

What are the types of abnormal results in CMA?

A

1 – Easy: Gain or loss of no clinical consequence:

  • Benign – reassuring: repeatedly observed in healthy individuals
  • Likely benign – reassuring but with some caution: in gene-devoid region, inherited, present in other healthy, not known to be associated with disease

2 – Harder: Established clinically significant gain or loss:

  • Aneuploidy, loss or gain in known disease region – consistent phenotype
  • Uniparental (iso)disomy causing known disease
  • Unbalanced translocation

3 – Very challenging: Variant of uncertain clinical significance:

  • Continuing = known phenotype but incompletely penetrant or variable
  • Temporary = del or dup in region not known to be associated with clinical disease – phenotype not yet well-described
    • –Dup of known deletion syndrome region – phenotype not yet well-described
51
Q

What are limitations of CMA?

A

– Cannot detect truly balanced chromosomal rearrangements (i.e. translocations, inversions, triploidy, polyploidy)

– Does not detect all cases of mosaicism

– Does not detect point mutations or intragenic mutations

– CNV of uncertain significance (<2%)

Limitations specific to prenatal CMA

– Often no prenatal phenotype for known chromosomal abnormalities (dels/dups) or other genetic defects

– Prenatal presentation and spectrum of anomalies associated with mutations in known disease genes is not always known

– Penetrance of known genetic defects when detected prenatally in “asymptomatic fetus” is not always known

52
Q

Describe CMA vs. NIPT

A
  • Amniocentesis or CVS with CMA will detect a clinically significant abnormality if no other finding is present in ~1:60 of cases
  • Currently offered Sequencing-based NIPT tests on cell-free fetal DNA will detect a clinically significant abnormality in ~1:500 cases
53
Q

If there are still abnormal US findings, but haven’t found anything else, what are we missing?

A

• Diagnostic procedure with karyotype and CMA:

  • Detects a clinically significant chromosomal abnormality in ~6-7% with single major anomaly and ~10% with multiple anomalies
  • This means that we do not have a genetic diagnosis in at least 90% of the cases
  • Many well-known syndromes caused by single-gene mutations, but not all aspects of these phenotypes are prenatally detectable
  • In pediatric patients the incremental benefit of whole-exome sequencing in unresolved cases is 25%
  • Many had more extensive work-up than CMA prior to WES

• Supports that there will be benefit to single-gene mutation detection methods: WES or NGS panels

54
Q

Describe molecular single gene testing

  • What does it look for
  • When is it used
A
  • Look for small DNA mutations
  • Indirect mutation analysis or linkage analysis
  • Used when the location of a gene is known, although the gene itself and its function are not, or when the gene is known but the mutations are too heterogeneous to make direct analysis practical
  • Often requires more than one affected individual in more than one generation.

• Direct mutation analysis

  • Used when gene responsible for the condition has been ID AND specific mutations w/in the gene have been characterized
55
Q

Describe NGS panels as a diagnostic tool

A
  • Multi-gene, NGS panels to provide addtl diagnostic options for certain common and rare genetic disorders
  • Some disorders challenging to diagnosis due to overlapping, non0psecifi features that make targeting a specific gene difficult of impossible
  • Can be more cost-effective than single gene testing
  • Prenatal examples: Skeletal dysplasia panel (Greenwood), increased NT
56
Q

Describe Whole Exome Sequencing (WES) as a diagnostic tool

A
  • Not currently offered in prenatal
  • The EXOME is 1.5-2% of the whole GENOME, but makes up the part of the genome we best understand
  • Exons are short, functionally important sequences of DNA which represent the regions in genes that are translated into protein
57
Q

What is Whole Exome Sequencing (WES)?

  • What is it looking for
A
  • Test that “captures” or selects the coding regions or exons throughout the whole genome to then be sequenced nucleotide by nucleotide to a depth of coverage necessary to build a consensus sequence with high accuracy.
  • This consensus sequence is then compared to standards and references of what is normal in the population
  • Once identified through WES variations in an individual’s DNA sequence can be related back to the individual’s medical concerns in an effort to diagnose the cause of the medical disorder.
58
Q

What is the goal of clinical WES?

A
  • Obtaining a diagnostic result
  • Improve preventive care through identification of medically actionable result
  • Probable cost-effectiveness
59
Q

Pros/cons of WES?

A

PROS:

  • WES is an efficient method of analyzing a patient’s DNA to discover the genetic cause of diseases or disabilities because it analyzes the exons of tens of thousands of genes at the same time.
  • The exome is the part of the genome currently best understood
  • Ideal to help us understand highly penetrant allelic variation and relationship to a given phenotype
  • Less expensive and less data generated as compared to WGS and also takes less machine time

CONS

  • Laboratory/Interpretation challenges: How to classify VUS, How to handle secondary findings?
  • Can be difficult to counsel
  • Identifying the genetic cause of the disease may not change medical management or help predict prognosis
60
Q

What are limitations of WES?

A
  • Due to technology limitations does not cover 100% of the exome. Coverage ranges from ~90%-95% depending on methodology.
  • Depth of coverage varies across exome
  • Not well detected: Triplet repeat expansions, large deletions & duplications
  • Detection of small indels may not be as accurate as detection of base substitutions
  • The mitochondrial genome is not sequenced by capture method
  • Genes that have closely related pseudogenes are not uniquely captured by this method
61
Q

What can high resolution US be used for?

A
  • Fetal age
  • Number of fetuses
  • Fetal viability
  • Structural abnormalities
  • Increased risk of fetal aneuploidy
  • Genetic syndromes
  • Fetal sex

(Not all US are created equal!)

62
Q

Describe US screening for chromosome abnormalities

  • What can be screened for?
A

Down syndrome

– Approximately 50% have a finding

  • Congenital defect (heart, duodenal atresia)
  • Soft markers (nuchal fold, pyelectasis)

– 50% will not have a finding

– Cannot see dysmorphic features on ultrasound

Trisomy 13 & 18

– Approximately 80-85% have a finding

– Incidence of structural malformations higher

NTDs (Neural Tube Defects)

– 90-95% spina bifida seen by ultrasound

  • Splayed vertebrae
  • Abnormal shape of cerebellum (banana) and front of skull (lemon)

– >99% of anencephaly seen on ultrasound

– As with all, position of fetus, size of defect, and maternal habitus play role

63
Q

What should you think about when you see: duodenal atresia?

A

30% association with Down syndrome, but may also be seen with various other genetic, chromosomal, and sporadic syndromes

64
Q

What should you think about when you see: omphalocele?

A

25% have aneuploidy, especially trisomy 13 or trisomy 18. Also think about Beckwith-Wiedemann (esp. if macrosomia, macroglossia, etc.)

65
Q

What should you think about when you see: diaphragmatic hernia?

A

20-25% aneuploidy risk (esp. tri 18, 13, 21, and Turner). Also described with Fryns, Cornelia de Lange, and multiple other single gene disorders

66
Q

What should you think about if you see congenital heart defects (CHDs)?

A
  • Multiple possible etiologies, usually multifactorial
  • Aneuploidy risk anywhere from 5-30%, depending on study
  • Some CHDs, such as AV canal defects, have stronger associations (40-70% Down syndrome risk)
  • May also be the result of a chromosome microdeletion or microduplication syndrome, such as 22q11 deletion (DiGeorge syndrome)
  • Environmental factors – teratogens (Lithium, alcohol, etc.) and maternal medical conditions (uncontrolled diabetes)
67
Q

What falls under the blanket of “ambiguous genitalia”?

  • Cuases
  • Describes internal or external genitalia?
A
  • Hypospadias, micropenis, clitoromegaly, cryptorchidism
  • Various causes
  • Chromosomal – 22q deletions and duplications, 9q subtelomere deletions
  • Microdeletions/microduplications
  • Single gene disorders – SLO, CAH, SRY deletions, partial androgen insensitivity syndromes, etc.

• Only describes external genitalia, not always appropriate to describe the abnormality

  • Genital tubercle (not penis/clitoris)
  • Labioscrotal folds (not labia or scrotum)
  • Gonads (not testes or ovaries)
68
Q

What do you do after seeing an US anomaly?

A
  • Look for other anomalies, as some tend to go together (e.g. hydrocephalus and ONTDs)
  • Refer for genetic counseling
  • Full family history, discussion of possible etiologies, inheritance pattern(s), and recurrence risks if isolated

• Refer for a level II ultrasound with an MFM

  • From there, may need MRI, fetal echo, pedi surgery, etc.

• Offer invasive diagnostic testing

69
Q

What are soft US findings?

A
  • Not considered malformations, but may indicate an increased risk for fetal trisomy
  • Characteristics
  • nonspecific
  • common in normal fetuses
  • often transient

• Significance of isolated soft ultrasound findings is unclear

70
Q

What are examples of soft US findings?

A

• nuchal thickening

• choroid plexus cysts

• echogenic bowel

• shortened long bones

• echogenic intracardiac foci

• fetal pyelectasis

  • mild ventriculomegaly
  • single umbilical artery
71
Q

Describe nuchal thickening

A
  • Nuchal fold measuring 5-6mm (or >6mm) between 14-21 weeks gestation
  • Different than nuchal translucency (NT) in the first trimester
72
Q

Describe echogenic bowel

A
  • Bowel with similar or greater echogenicity than surrounding bone
  • Diagnosed in 0.6 – 2.4% of second-trimester ultrasounds
  • Associations
  • normal variant
  • vaginal bleeding
  • cystic fibrosis
  • in utero infection
  • chromosome abnormalities
73
Q

Describe intracardiac echogenic foci (ICEF/EIF)

A
  • Structures within the fetal heart which represent reflections from calcifications of the papillary muscle, with echogenicity similar to bone
  • Overall Incidence
  • 0.5% - 30.4%
  • Incidences may vary based on ethnicity
    • Asian = 30.4%
    • Caucasian = 10.5%
    • African American = 5.9%
74
Q

Describe fetal pyelectasis

A
  • Dilation of the fetal renal pelvis of >4mm in the transverse A-P diameter
  • Diagnosed in 0.7 – 2.9% of second-trimester ultrasounds
75
Q

What genetic counseling should be done for soft US findings?

A

If isolated soft finding:

– Assess other risk factors for aneuploidy

– Address risk in terms of ultrasound findings, maternal age, and serum screen results

– Discuss option of invasive and non-invasive testing including a comparison of risks for aneuploidy vs. risk for procedure-associated complications

  • In the absence of additional risk factors, offering invasive testing for an isolated finding is controversial and varies among different practices/clinics

If non-isoalted:

– In conjunction with other ultrasound findings or additional risk factors for aneuploidy, invasive testing should be offered.

76
Q

Describe the detection rates across screening options for:

  • Down syndrome
  • Trisomy 18
  • Trisomy 13
  • Neural Tube Defects
A
77
Q

What are some factors to consider for carrier screening?

A

• Ethnicity based carrier screening

  • ACOG and ACMG guidelines
  • Family history based carrier screening
  • Universal/expanded genetic screening
78
Q

What are the ethnicity considerations for Cystic Fibrosis?

  • Screen what ethnic groups
  • How is screening accomplished
A

Highest prevalence in Caucasians

  • However, ACOG standards are to rpovide info about CF screening to ALL couples (since increasingly difficult to assign single ethnicity)
  • Carrier screening by panel of at least 25 of the most common DNA mutation analysis (not sequencing!)
79
Q

What are issues/residual risks for ethnicity based carrier screening in CF?

A

– Decreased carrier frequency and detection rate

– Potential to detect an “affected” person through screening (i.e. person having two mutations and mild or no symptoms, like CBAVD)

– Prenatal testing for women who are carriers when father of baby not available for carrier testing

– Rare chance of uncovering non-paternity

80
Q

Describe the prevalence of CF in different ethnic groups

  • Carrier frequency
  • Detection rates
  • Carrier risks
A

Highest carrier frequencies in:

  • N European/Caucasian (1/25 - 1/29)
  • Ashkenazi Jewish (1/25-1/29)
  • S European Caucasian (1/29)
  • Hispanic (1/46)
  • African American (1/65)
  • Asian (1/90)

Detection Rate highest in:

- Ashkenazi Jewish (97%)

- N European Caucasian (85-90%)

  • S European Caucasian (70-80%)
  • African American (72%)
  • Hispanic (57%)
  • Asian (30%)

Carrier risk after negative test highest in:

  • Hispanic (1/105)
  • S European Caucasian (1/97-1/140)
  • African Americans (1/210)
  • N European Caucasian (1/250)
  • Ashkenazi Jewish (1/800)
81
Q

What are ACOG standards for ethnicity based carrier screening in Ashkenazi Jewish individuals? ACMG standards?

A

ACOG: Standard of care to offer to persons of AJ background or their partners prior to conception or during 1st trimester:

  • Cystic fibrosis (1/25)
  • Canavan Disease (1/40)
  • Familial Dysautonomia (1/30)
  • Tay Sachs Disease (1/30)

ACMG: recommend CF, Canavan, Familial dysautonomia, and Tay Sachs, PLUS:

– Bloom syndrome (1/100)

– Gaucher Disease (1/13)

– Nieman Pick Disease type A (1/90)

– Fanconi Anemia, Type C (1/89)

– Mucolipidosis, Type 4 (1/122)

Additional disorders considered if AR, >90% DR or allele frequency of >1% in the AJ population

82
Q

What are the ethnicity based carrier screening guides for Hispanic/Latina individuals?

A

There is no standard protocol for carrier testing

  • CF carrier rate is 1/46
  • CBC and/or hemoglobin electrophoresis
  • Risk varies greatly depending on country of origin
83
Q

What are the ethnicity based carrier screening guides for East/Southeast Asian individuals?

A

Standard to review MCV

– If < 80, screen for thalassemia w/quantitative Hb electrophoresis and ferritin:

  • Alpha-thalassemia carrier rates up to 1/20
    • MCV < 80, Hb electrophoresis nl, serum ferritin nl
    • DNA testing required for prenatal diagnosis
  • Beta-thalassemia carrier rates 1/30 (SE Asian) to 1/50
    • MCV < 80, Abnl peripheral blood smear with nucleated red blood cells, Normal iron studies, ↓ HbA2, ↑ HbF (after 12m)
    • DNA testing required for prenatal diagnosis

Cystic fibrosis –carrier rate 1/90 or less

– Detection rate is very low (~ 30%)

84
Q

What are the ethnicity based carrier screening guides for African and African-American individuals?

A

Hemoglobin Electrophoresis with quantitative A2 (regardless of MCV)

  • Will screen for:
    • Sickle cell (carrier freq 1/10-1/12)
      • Do NOT use sickle dex
    • Beta-thalassemia (1/75)
    • Other hemoglobinopathies

CF carrier rate about 1/65

85
Q

What are the ethnicity based carrier screening guides for French Canadian/Cajun individuals?

A

Tay Sachs ENZYME testing*

  • Different mutations than in the AJ population

CF

86
Q

What are the ethnicity based carrier screening guides for Mediterranean individuals?

A

CBC and hemoglobin electrophoresis

– Beta-thalassemia trait (1/20 – 1/30)

– Alpha thalassemia trait (1/30 – 1/50)

– Sickle cell trait (1/3 – 1/50)

CF

87
Q

What are the ethnicity based carrier screening guides for Middle Eastern/S Central Asian individuals?

A

CBC and hemoglobin electrophoresis

– Beta-thalassemia trait (0.5 – 5.5%)

– Alpha thalassemia trait (variable)

– Sickle cell trait and other hemoglobin variants (variable)

CF

88
Q

What is universal/expanded genetic screening?

A
  • A new concept of carrier screening
  • Aka Expanded Multi-disease genetic carrier screening panel, aka Next generation carrier screening; all in one carrier screening
  • Allows to screen for hundred-ish conditions at once at reduced cost
  • Can be applied to all ethnicities
89
Q

Universal/expanded carrier screen Counsyl does NOT include screening for what?

A
  • Hemoglobinopathies/thalassemias à still need to following ethnicity/CBC guidelines
  • Tay Sachs enzyme testing

BUT the platform is customizable

  • Can screen only for AJ diseases
  • Opt in/out of disease
  • If include opt in diseases, 40% of pts will screen (+) for at least 1 condition (frequency of MTHFR in general population)
  • If opt out of additional diseases, 20% of pts will screen (+) for at least 1 condition
90
Q

What are typical opt-ins for universal/expanded carrier screening at BCM/TCH/BTGH?

A

Opt-in for common “milder” conditions and fragile X syndrome

  • Testing can be performed on blood or saliva sample
91
Q

What are benefits and limitations of expanded carrier screening?

A

Benefits

– Finds most common mutations for conditions tested

– Negative result lowers risk for affected child

– >75 condition typically included

– Can have full reproductive testing options if tested preconceptionally

– Cost is similar or less than most single gene tests

Limitations:

– Does not test for all mutations

– Does not cover some of the more common disorders (ex. CAH)

– Some results are for mild conditions and can cause anxiety and confusion

– Proprietary technology can prevent independent validation

– Depending on lab can be expensive

– For some condition there may be a more accurate less expensive screen

92
Q

What is responsible for most of the rare/orphan diseases affecting Americans?

A

Most are single gene disorders; they account for

  • 10% of pediatric admissions (US)
  • 20% of infant mortality (US)
93
Q
A
94
Q

What are some benefits and limitations of carrier screening through sequencing?

A

Benefits

– Negative screening provides much more significant risk reduction, particularly in ethnicities where genotyping panels have low detection rates

– Good option for couples where one member has already been found to be a carrier for a condition

Limitations

– Will not eliminate carrier risk

– If lab reports all changes detected this may results in reporting of variants of uncertain significance

– Will not pick up gene deletions or duplications

– Still does not screen for all genetic conditions

95
Q

What are female factors contributing to infertility?

A
  • Ovulation problems (25%)
  • Tubal or peritoneal problems (35%)
  • Age
  • Cervical problems
  • Uterine problems
  • Polycystic ovary syndrome (PCOS)
  • Congenital adrenal hyperplasia (CAH)
  • Low ovarian reserve (high FSH or estradiol levels)
  • Premature ovarian failure (POF)
  • Translocation carrier/other chromosome abnormality (~5%)
  • Idiopathic
96
Q

What is premature ovarian failure (POF)?

  • Diagnostic criteria
  • Prevalence
  • Associated with
A

Cessation of menses for > 6 months before age 40

  • Affects approximately 1% of women
  • Increased incidence of fragile X syndrome premutations
  • 13-16% of familial cases
  • 1-3% of sporadic cases
97
Q

What is Classic CAH? Non-classic?

  • Symptoms
  • Inheritance pattern
A

Classic CAH (21-hydroxylase deficiency)

  • Virilized females
  • Salt wasting
  • Autosomal recessive

Non-classic CAH

  • Hirsuitism, amenorrhea, PCOS
  • Compound heterozygotes (2/3 of affected females have “severe” CAH mutation)
98
Q

What are male factors contributing to infertility?

A
  • Semen abnormalities (volume, motility, morphology)
  • Varicocele or obstruction
  • Translocation carrier/other chromosome abnormality
  • Y chromosome microdeletion
  • CBAVD
99
Q

What are normal semen variables?

  • Volume
  • pH
  • Sperm concentration
  • Motility
  • Morphology
  • WBC
A
  • Volume – 2+ mL
  • pH – 7.2 - 8
  • Sperm concentration – 20 X 106 per mL
  • Motility – ≥50%
  • Morphology - ≥30% normal
  • WBC - ≤ 1 x 106 per mL
100
Q

Define:

  • Oligospermia
  • Azoospermia
  • OAT
A
  • Oligospermia: < 20 million sperm
  • Azoospermia: NO sperm in semen analysis
  • OAT (Oligo-astheno-teratospermia): problems with count, motlity, and morphology
101
Q

What are chromosome abnormalities that may be male factors in infertility?

A

Chromosome abnormalities in men (including in those with 47,XXY and 46,XX cell lines) may result in oligospermia or azoospermia

– 5-7% of men with oligospermia

  • usually structural rearrangement

– 15-20% of men with azoospermia

  • usually sex chromosome abnormality

The prevalence of karyotypic abnormalities in men with hypergonadotropic hypogonadism is approximately 15%, with 47,XXY being the most common and 46,XX the second most common abnormality

Balanced translocations have been identified in 1% to 2% of men with severe oligospermia and azoospermia, whether or not hypogonadism is present.

102
Q

Y chromosome microdeletions occur in __% of men with azoospermia or severe oligospermia

  • Most have deletions in _____
  • There is a correlation between specific deletion and presence of _____
  • Prognostic implications
A

Y chromosome microdeletions occur in 3-18% of men with azoospermia or severe oligospermia

  • Most have deletions in AZFc
  • There is a correlation between specific deletion and presence of spermatozoa in testes
  • AZFc deletion: good prognosis
  • AZFb deletion: no spermatozoa
103
Q

What is CBAVD in terms of male factors contributing to infertility?

  • Prevalence
  • Genetic mutation
  • Associations
  • Symptoms
A

Congenital bilateral absence of vas deferens

  • 1-2% of men with infertility
  • Significant proportion of men with CBAVD have one or two mutations in the CFTR gene
  • Increased risk of having a child with cystic fibrosis
  • Sons may have similar fertility problem
  • 5T splice variant in intron 8 of the CFTR gene

Men with CBAVD have azoospermia but they usually have normal testicular sperm

  • Epididymal or testicular aspiration may provide sperm for ICSI of oocytes at the time of IVF
104
Q

Recurrent pregnancy loss (RPL) can present how?

A
  • Infertility
  • Recurrent early pregnancy loss
105
Q

2-3 recurrent pregnancy losses is an indication for what?

A

Parental karyotype

  • Balanced translocations (reciprocal or Robertsonian) – seen in 2-5% of couples with RPL
  • Think of rare X-linked male-lethal disorders, e.g. incontinentia pigmenti, steroid sulfatase deficiency (miscarriage of male fetuses)
106
Q

What are methods of preimplantation genetic diagnosis/screening (PGD/PGS)?

  • What is the goal?
A

– Polar body biopsy

– Cleavage stage (blastomere) biopsy

– Blastocyst biopsy

An option for women/couples to avoid the possibility of an affected pregnancy secondary to a genetic disorder by:

– using IVF and genetic testing or screening

– implanting only embryos that do not have the genetic abnormality

(Prenatal diagnosis is still recommended)

107
Q

Describe a polar body biopsy

A
  • Pipette used to pierce zona pellucida of egg
  • Polar body removed by aspiration
  • Analysis of polar body performed
  • If testing indicates disease free, oocyte fertilized with sperm
  • Successful embryos available for transfer
108
Q

What are pros/cons of polar body biopsy?

A

Pros:

– Errors in both meiosis I and meiosis II recognized

– Samples extra-embryonic material (non-invasive for embryo proper)

Cons:

– Only detects maternally inherited mutations

109
Q

Describe a cleavage stage biopsy

A
  • An opening is made in the outer covering of the embryo using a laser or acid solution
  • One or two blastomeres are removed by suction using a pipette
110
Q

What are pros/cons of a cleavage stage biopys?

A

Pros:

– Can detect maternal and paternal abnormalities

Cons:

– Limited amount of material available for analysis

– Possible mosaicism

111
Q

Descirbe blastocyst biopsy

  • When is it done
A
  • Performed on day 5 or 6 after fertilization
  • An opening is made in the zona pellucida and multiple cells are removed from the early trophoblast
112
Q

What are pros/cons to blastocyst biopsy?

A

Pros:

– Multiple cells removed allowing more material for analysis

– Inner cell mass remains intact

– Can detect material and paternal abnormalities

Cons:

– Procedure more challenging, fewer centers currently perform

– Fewer embryos reach the blastocyst stage

  • No blastocysts are available for biopsy in up to 40% of cycles

– Allows for less time for genetic testing or requires freezing of the embryo

– Mosaicisim may still be an issue due to possible differences between the trophectoderm and inner cell mass

113
Q

When is preimplantation genetic diagnosis (PGD) done?

A

– Applies when one or both parents carry a gene mutation or balanced translocation

– Testing is performed to determine whether the specific mutation(s) or an unbalanced translocation has been transmitted

114
Q

When is preimplantation genetic screening (PGS) done?

A

– Applies when the genetic parents are known or presumed to be chromosomally normal

– Screening for aneuploidy

115
Q

What is comparative genomic hybridization? (Methods involved)

A

Metaphase (mCGH), array CGH (aCGH), and SNP array are being consdiered and examined for PGS

116
Q

Describe mCGH? aCGH?

A

mCGH:

  • Can take up to 72 hrs with additional time required for the analysis of data so this method typically requires freezing embryos
  • Has been applied at the polar body stage, cleavage stage, and blastocyst stage

aCGH:

– can be performed within 24 hours

– With cleavage-stage, biopsy embryo transfer can still be performed on day 5

–With blastocyst biopsy and/or PGD requiring transport of cells for testing, freezing the embryos may still be preferred

117
Q

What are the general advantages of CGH? Disadvantages?

A

Advantages:

  • Allows all chromosomes to be analyze instead of a subset

Disadvantages:

  • Cannot detect polyploidies, such as triploidy
  • Cannot detect balanced translocations or inversions
  • Cannot detect changes in DNA sequence
  • Cannot detect gains or losses in regions of the genome not covered by the array
118
Q

What do SNP arrays offer for PGD?

A

Additional options for testing that are not available with CGH-based analysis

– Allows for simultaneous testing of specific diseases and aneuploidy in each embryo by using haplotyping of SNPs around and within the gene of interest

– Haplotyping of various markers through the genome allows for analysis of live-born children to determine which embryo(s) implanted in any given cycle.

119
Q

What are the advantages of PGD/PGS counseling?

A

Advantages:

  • Reduction in risk of genetic disease (for single gene disorders and translocations)
  • Reduction in aneuploidy rate?
  • Increased implantation rate?
  • Reduction in pregnancy loss rate?
  • Information with which to make decisions about future IVF cycles?

Disadvantages:

  • Risk of embryo biopsy
  • Risk for misdiagnosis
  • Mosaicism
  • Only specific disorders tested
  • Does not replace prenatal diagnosis
  • Need IVF (if not infertile already)
  • Less embryos available for transfer
  • Cost
120
Q

What are the recommendations for PGD?

A

– Before PGD is performed counseling must be provided to ensure patients fully understand the risks of having an affected child and limitations of PGD for the condition.

– Prenatal diagnostic testing to confirm the results of PGD is strongly encouraged because of the limitations of PGD, including the possibility of a false negative result.

121
Q

What are the recommendations for PGS?

A
  • Before PGS is performed counseling must be provided to ensure patients fully understand the limitations of PGS, the risk of error, and the lack of evidence that PGS improves live-birth rates.
  • Available evidence does not support the use of PGS as currently performed to improve live-birth rates in patients
  • of advanced maternal age
  • with previous IVF failure
  • with recurrent pregnancy loss
122
Q

What are some ethical concerns with PGD?

A
  • Diagnostic accuracy
  • Use of IVF in fertile couples/increase in multiple births
  • Safety of biopsy
  • Access to services/high costs
  • Eugenic potential
  • Sex selection
123
Q
A

x_NeuroGenetics Review (38 decks)

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