Cytogenetics in Prenatal Diagnosis: karyotype & CMA

Question 1

What options are there aneuploidy testing via CVS and amnio?

Answer 1

FISH, karyotype, CMA

Question 2

Can FISH be performed on villi from CVS?

Answer 2

Yes

looks at about 400 cells

Question 3

Which probes are offered for FISH analysis and can they be ordered seperately?

Answer 3

• probes for chromsomes 13, 18, 21, X & Y
• they come as a set, you can’t order just one

Question 4

How predictive is FISH testing of the final result?

Answer 4

95%

screening tool

Question 5

What are the advantages of FISH?

Answer 5

• rapid turnaround time (2 days)
• able to look at multiple cells at one time (if concerned about mosaicism - larger sample size is helpful)

Question 6

What are the limitations of FISH?

Answer 6

• the cells evaluated are trophoblasts (if +NIPT is reason for test this could be problematic)
• still considered screening
• only looks at 5 chromosomes (unless there is a familial rearrangement not involving one of these chromosomes)
• probe binds to centromere so if there are issues outside of this region it won’t pick them up (like an imbalance)

Question 7

What is an advantage of long term culture of CVS sample?

Answer 7

can ‘culture out’ maternal cells that might contaminate the CVS sample

Question 8

If mosaicism is found on CVS then what should be offered?

Answer 8

Amnio becuase we don’t know if mosaicism is confined to the placenta

Question 9

Which 2 situations could explain mosaicism of CVS sample?

Answer 9

1. confined placental mosaicism (1-2%) (risk for IUGR)
2. true fetal mosaicism (highly variable phenotype)

Question 10

Can amniocentesis be affected by maternal cell contamination?

Answer 10

Yes, FISH and chromsoome analysis can still be impacted by maternal cell contamination with a bloody tap. Confined plancental mosaicism can be ruled out though.

Question 11

One reason for ordering parental cytogenetic testing is for a history of recurrent pregnancy losses. What is the definition of recurrent pregnancy loss?

Answer 11

2 or more clinically recognized pregnancy losses. “Chemical” pregnancies do not count towards this criteria. A chemical pregnancy is a pregnancy only detcted with an at home test.

Question 12

One reason that parental cytogenetic testing may be applicable in the prenatal setting is if there is a family history of a chromosome anomaly that could be inherited. What are two examples of these types of chromosome anomalies?

Answer 12

• translocations
• deletions

Question 13

An abnormal NIPT can be a reason to order parental cytogenetic testing. What is something that this test could pick up?

Answer 13

maternal mosaicism

Question 14

46,XX,der(14;21)+21
explain this karyotype

Answer 14

trisomy 21
inherited from a Robertsonian translocation carrier. Their chromosome 14 also has the q arm of 21 on it, leading to a trisomy 21 without an abnormal number of chromosomes
She may called this an unbalanced Robertsonian translcoation but I don’t think that’s correct usage of that term…

Question 15

For parents of a child with trisomy 21, what is the recurrence risk for future children?

Answer 15

1% for any aneuploidy

Question 16

What is the risk for having a child with trisomy 21 for a parent who is a carrier of a 14;21 translocation?

risk varies depending on which intended parent has translocation

Answer 16

intended mother: 5-15%
intended father: <3%

Question 17

What is the risk of having a child with trisomy 21 for a parent with a 21;22 translcoation?

depends which intended parent has the translocation

Answer 17

intended mother: 6%
intended father: 1-2%

Question 18

What is the risk of having a child with trisomy 21 for a carrier of a 21;21 translocation?

Answer 18

100%

Question 19

How many chromosomes do Robertsonian carriers have?

Answer 19

45

Question 20

46,XY,der(18)t(18;21)(p11.3;q22.3)
Explain this karyotype.

Answer 20

Unbalanced karyotype with
partial trisomy of chromosome
21q and partial monosomy of
chromosome 18p

Parent with balanced translocation: 46,XX,t(18;21)(p11.3;q22.3)

Question 21

46,XY,der(18)t(18;21)(p11.3;q22.3)
Explain this karyotype.

Answer 21

Unbalanced translocation
resulting in partial trisomy 9 and
partial trisomy 21

balanced parent: 46,XX,t(9;21)(q22;q22.3)

Question 22

46,XX,inv(9)(q2.1q34.3)
Explain this karyotype

Answer 22

• this is balanced
• paracentric inversion of chromosome 9
• Resulted in the birth of a child with dicentric recombinant chromosome 9 but these births are RARE

Question 23

What are the risks for live births for babies that inherit paracentric inversions?

Answer 23

• usually these babies do not live to term
• LOW risk for abnormal live birth (0.1- 0.5%)
• this is because they form acentric and dicentric fragments in the inversion loop that are not usually viable (none or 2 centromeres during crossing over/recombination)

Question 24

How is a paracentric inversion usually found in an intended parent?

Answer 24

history of infertility and/or recurrent miscarriage

Question 25

What factor affects risk related to pericentric inversions?

Answer 25

- the size of the inversion - smaller = more likely to lead to live birth

Question 26

How can marker chromosomes be detected?

Answer 26

CMA

Question 27

What er percentage of marker chromosomes are familial vs de novo?

Answer 27

familail: 20% & generally benign de novo: 80% associated with abnormal phenotype 13-16% of the time

Question 28

Besdies whoel chromosome aneuploidy and known del/dup syndromes, what finding has the highest risk of resulting in an abnormal live born?

Answer 28

marker chromsomes identified in prenatal diagnostic testing

Question 29

When a de novo marker chromosome is identified on prenatal diagnostic testing, what are the risks for an abnormality in the child?

Answer 29

- overall: 13-16% of the time will be assocaited with an abnormal phenotype - if the marker chromosome is derived from a non-acrocentric chromosome the risk for abnormal phentoype = 28.6% - if the marker chromosome is dervied from an acrocentric chromosome the risk for an abnormal phenotype = 7-11% - marker chromosomes that are de novo and derived from non-acrocentric chromosomes have the highest risk for an abnormal phenotype ## Footnote acrocentric = 13, 14, 15, 21, 22, & Y

Question 30

There are two CMA techniques used in identifying submicroscopic imbalances: comparative genomic hybridization (CGH) and single nucleotide polymorphisms (SNP). Which one do we use at URMC?

Answer 30

Single Nucleotide Polymorphisms (SNP) Analysis uses high-density oligonucleotidebased arrays in which target probes are chosen from DNA locations known to vary between individuals by a single base pair

Question 31

What is SNP array?

Answer 31

DNA (fetal) is labelled and hybridized to the SNP array. Copy number changes are determined by measuring the absolute fluorescence probe intensities of the patient sample compared with the intensities of multiple normal controls that were independently hybridized (in silico comparison)

Question 32

What are the advantages of the SNP Array for CMA?

Answer 32

In addition to detecting copy number variants, uniparental disomy (UPD), mosaicism, zygosity, maternal cell contamination, parent of origin and consanguinity can all be identified. Triploidy, which cannot be detected by aCGH, can be identified by SNP array. ## Footnote CMA can't be used to test for UPD, but sometimes it shows up in teh results

Question 33

Which CMA technique can detect triploidy: aCGH or SNP?

Answer 33

SNP

Question 34

When is it recommened to order a CMA in the prenatal setting?

Answer 34

- 1+ structural abnormalities on US & undergoing invasive testing. Can replace karyotype - structurally normal fetus undergoing invasive diagnostic testing: karyotype or CMA is appropriate (remember that CMA will have lots of benign findings) - IUFD or stillbirth (balanced translocations won't be identified but this doesn't matter)

Question 35

What is the turnaround time for CMA on direct array vs cultured cells? ## Footnote direct array = able to use collected sample without amplification (almost never happens with CVS and if amnio is close to 16 weeks)

Answer 35

- direct array: 7-10 days - cultured cells: 4 weeks (2 weeks to culture and 2 weeks for analysis)

Question 36

CMA testing of parents to check on a VUS from fetal CMA. Is this testing covered by insurance?

Answer 36

NOPE it'll be over $1,000 please. for each parent.

Question 37

When should you consider skipping right to an array?

Answer 37

- ultrasound anomalies in the presence of normal NIPT (unlikely to be trisomy 13, 18, or 21) - known familial del/dup that is submicroscopic - known chromosomal rearrangement previously identified with CMA only (i.e. cryptic rearrangements/very small) - US anomalies found close to date of termination being allowed