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Cytogenetics Exam > Prenatal diagnosis and screening > Flashcards

Prenatal diagnosis and screening Flashcards

1
Q

CVS advantage

A

early diagnosis

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2
Q

CVS disadvantages

A

higher risk for maternal cell contamination (MCC) than amniocentesis & confined placental mosaicism

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3
Q

When can you perform an amniocentesis?

A

Usually 15-20 weeks, but can be wider

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4
Q

How much amniotic fluid is collected in amniocentesis

A

20-30 ml, first draw is discarded due to risk of maternal cell contamination

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5
Q

What kinds of cells come from amniocentesis?

A

Contains cells of fetal origin

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6
Q

Indications for prenatal diagnosis via invasive testing?

A

advanced maternal age, abnormal screening results, structural abnormalities identified by ultrasound, previous fetus or child with autosomal or sex chromosome aneuploidy, parental carrier of chromosome rearrangement, family hx of genetic disorders

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7
Q

Cytogenetics testing for prenatal diagnosis

A

karyotype, FISH, CMA, etc

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8
Q

Turn around time for karyotype

A

7-14 days

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9
Q

Turn around time for FISH (direct preparation - interphase)

A

24-48 hrs

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10
Q

Turn around time for FISH - cultured cells (metaphase)

A

7-14 days

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11
Q

Turn around time for CMA

A

3-5 days (direct testing), 10-14 days (cultured cells)

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12
Q

Conditions detected on karyotype

A

chromosomal abnormaliites >5-10 Mb

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13
Q

Conditions detected for FISH (direct preparation - interphase)

A

Rapid assessment of major aneuploidies (chromosomes 13, 18, 21, X, and Y)

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14
Q

Conditions detected for FISH (cultured cells - metaphase)

A

microdeletions and duplications

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15
Q

Conditions detected for CMA

A

Copy number variants >50-200 Kb

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16
Q

FISH analysis - quick overview

A
  1. Fast (24-48 hours)
  2. Interphase cells - cell culture not needed
  3. Screening test for common aneuploidies and microdeletion syndromes - chromosomes 13, 18, 21, X, and Y & DiGeorge Syndrome
  4. Can be used for known family hx of conditions
  5. Detects abnormalities of target regions, integrate with karyotype or CMA results
17
Q

Karyotype quick facts

A
  1. Diagnostic test
  2. Identifies >99% aneuploidies and chromosomal rearrangements >5-10Mb
  3. Relies on metaphase analysis of cultured cells, results are available in two weeks.
  4. Culture failure is common when testing cells from fetal death or still birth.
18
Q

ACMG standards and guidelines for testing

A

A minimum of two cultures should be analyzed on each case whenever possible. FISH analysis for the chromosome of interest can be done on uncultured amniotic fluid cells in addition to chromosome analysis of cultured cells.

19
Q

CMA overview - pros

A
  1. Includes CGH array and SNP array
  2. High resolution, detects submicroscopic duplications/deletions
  3. first tier test for invasive prenatal diagnostic testing
  4. DNA-based test, can be performed on uncultured tissue. Preferred for cases of fetal death or still birth.
  5. SNP array is useful to detect UPD and consanguinity
20
Q

What should be the primary test for patients undergoing prenatal diagnosis for indication of fetal structural abnormality detected by ultrasound?

A

CMA

21
Q

Next generation sequencing (NGS) overview

A
  1. Multigene panel, WES, and WGS
  2. Emerging test
  3. Pre and post-test counseling are required
  4. Diagnostic yield - similar to postnatal WES cases (trio > singleton)
  5. Lack of solid evidence from large cohort studies
22
Q

GC issues regarding invasive testing

A
  1. Culture failure
  2. Mosaicism
  3. False positive or false negative results caused by CPM or MCC
  4. VUS
23
Q

Prenatal screening overview

A
  1. Used to determine the chance for genetic conditions, esp aneuploidies
  2. No risk to pregnancy as it involves ultrasound and blood work
  3. NOT diagnostic, just screening
  4. Available for all pregnant women
  5. Multiple options
24
Q

Traditional screening

A
  1. Biomarkers in maternal serum or amniotic fluid - pregnancy-associated plasma protein A, human chorionic gonadotrophin, unconjugated estriol, alpha-fetoprotein
  2. Soft markers identified by ultrasound - increased nuchal translucency, structural fetal anomalies
25
Q

NIPS

A

A screening method that analyzes cell-free fetal DNA.

26
Q

What is cell-free fetal DNA (cff-DNA)?

A

small fragments of DNA (~170bp), comes from placenta trophoblasts, present after 10 weeks of gestation, cleared within hours, compromises about 10-15% of total cell-free DNA in maternal circulation

27
Q

Two types of NIPS

A

Parallel shotgun sequencing, genomewide & SNP-based, targeted sequencing

28
Q

Pros of NIPS

A

High sensitivity, specificity, and PPV; non invasive; early screening

29
Q

Why is NIPS not diagnostic?

A

Possible false positive and false negatives, risk assessment is limited to common aneuploidies, does not assess risk of fetal anomalies such as neural tube defects

30
Q

Causes for false positive results or incidental findings

A

Confined placental mosaicism, vanishing twins, maternal chromosomal abnormalities, low level mosaicism, aneuplodies, multiple chromosomal abnormalities inidicating for maternal malignancies, medical condition or treatment affecting quality of cff-DNA

31
Q

Causes for false negatives

A

CPM, low fetal fraction, multiple gestations

32
Q

Goals of prenatal diagnosis and screening

A

Determine the risk or outcome of the pregnancy, manage the remaining weeks of the pregnancy, plan for possible complications with the birth process, and evaluate the risk for genetic disorder in future pregnancies

33
Q

What are some prenatal diagnostic methods?

A

Invasive testing - chorionic villus sampling (CVS) and amniocentesis
Non-invasive testing - ultrasound

34
Q

When can a CVS be performed?

A

1st trimester (10-13 weeks)

35
Q

CMA overview - cons

A
  1. Does not detect form of chromosome rearrangements and low mosaicism.
  2. Does not reveal underlying genetic mechanisms.
36
Q

Challenges for nextgen sequencing?

A

concerns for maternal cell contamination and confined placental mosaicism. Lack of phenotypes for prenatal cases in the literature, postnatal onset diseases, incomplete penetrance, and turnaround time

Cytogenetics Exam (6 decks)

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