Prenatal Chromosomal

Microarray
Developed by Dr. Judith Allanson, Ms. Shawna Morrison and Dr. June Carroll

Last updated November 2015

 Disclaimer
• This presentation is for educational purposes only and should
not be used as a substitute for clinical judgement. GEC-KO
aims to aid the practicing clinician by providing informed
opinions regarding genetic services that have been developed
in a rigorous and evidence-based manner. Physicians must use
their own clinical judgement in addition to published articles
and the information presented herein. GEC-KO assumes no
responsibility or liability resulting from the use of information
contained herein.
 Objectives
• Following this session the learner will be able to:
– Appropriately refer to their local genetics centre and/or
order prenatal chromosomal microarray
– Discuss and address patient concerns regarding prenatal
chromosomal microarray
– Find high quality genomics educational resources
appropriate for primary care
 Case 1
• 29-year-old G1P0 woman, in good health
• No significant
QF-PCR family history
is a PCR-based or history
technique of consists
that prenatal of
exposure
• amplifying markersScreening
Integrated Prenatal located on thewas
(IPS) chromosomes
negative of
interest to determine
– 1 in 2,000 versus her agethe number
related risk to of copies
have a baby of
withthose
Down
syndrome of about
chromosomes 1 in 1,095
present per cell.
• This
19 week
method fetalonly
morphology
detects ultrasound
chromosome showed ventricular
number of the
septalchromosomes
select defect (VSD), polyhydramnios
(13, 18, 21, X and and suspected cleft lip
Y), not structural
and palate
arrangement.
• Patient is seen in Genetics and offered amniocentesis with QF-
PCR* to rule out common aneuploidies (Down syndrome,
trisomy 18, trisomy 13 and sex chromosome differences)
 Case 1
• No common aneuploidy is detected (normal
male on QF-PCR)
• Patient is then offered chromosomal
microarray for further, more detailed analysis
(testing will be performed on the same
amniotic sample)
• Results take about 2-3 weeks
 Case 2
• 42-year-old G3P2 woman
• No significant family history or history of
prenatal exposure
• Integrated Prenatal Screening (IPS) was
positive
– 1 in 100 versus her age related risk to have a baby
with Down syndrome of about 1 in 61
 Case 2
• The patient is offered the options of: no further
testing, non-invasive prenatal testing, or
amniocentesis
• She chooses the diagnostic certainty of amniocentesis
• This genetics centre has implemented a new
algorithm for all prenatal invasive testing so that all
normal QF-PCR samples are sent for chromosomal
microarray testing
• Results take about 2-3 weeks
 Typical Prenatal Testing Algorithm
Offer PN screening to all pregnant women

NIPT for AMA and for Ethnicity-based

FTS/IPS/SIPS Family history
women willing to pay screening

AMA – Advanced Maternal Age,

≥40y@EDB

*for ethnicity-based
screening, if both
If negative members of the couple
If positive*
or decline are carriers of the same
condition

18-20 week fetal

morphology scan Refer to Genetics

If indicated (e.g. fetal anomalies )

 Prenatal Testing Algorithm for Women at Increased Risk

Indication
Advanced maternal age, multiple soft markers on ultrasound, ultrasound anomaly,
positive prenatal screen, etc.

Genetic counselling with testing options

Invasive Testing Screening Test

No further testing
(diagnostic) e.g. NIPT
If positive If negative
QF-PCR
Detects common aneuploidies: Down Depending on
syndrome, Trisomy 18, Trisomy 13 and sex indication:
chromosome aneuploidies •No further testing
•Consider additional
If positive testing
Karyotype If negative

Additional Testing
No further testing
e.g. Chromosomal
microarray
 What is chromosomal microarray (CMA)?

• A cytogenetic test used to determine if there

are chromosomal imbalances, either large
(e.g. whole extra or missing chromosomes,
also detected by standard karyotype) or
smaller extra (micro-duplication) or missing
(micro-deletion) pieces of genetic information,
also called copy number variants (CNV)
Single Nucleotide Polymorphism Array
• There are various chromosomal microarray (CMA) platforms,
increasingly a single nucleotide polymorphism (SNP) based
approached is being used
• SNPs, pronounced ‘snips’, are the most common type of
genetic variation
• Each SNP represents a difference in a single DNA building
block, a nucleotide (guanine, cytosine , adenine, thymine)
• An individual inherits one SNP from their mother and one SNP
from their father, these can be the same (homozygous) or
different (heterozygous) 
• An individual can be one of three possibilities at each SNP
– AA e.g. A/T and A/T TAC AGA CCA
– BB e.g. C/G and C/G
TAC AGA
ACT CCA
Maternal allele
– AB e.g. A/T and C/G Paternal allele
ACC
Single Nucleotide Polymorphism Array

Licence for use of figures:

https://creativecommons.org/licenses/by/3.0/
 Prenatal Chromosomal Microarray
• Canadian College of Medical Geneticists (CCMG) states
(2009):

• Chromosomal microarray (CMA) may be an

appropriate investigative measure in cases with fetal
structural abnormalities detected on ultrasound or fetal
MRI

• CMA is generally not recommended in pregnancies at increased

risk for a numerical chromosomal abnormality (aneuploidy) e.g.
advanced maternal age, positive maternal serum screen
What do the genetic test results mean?

1. Normal
2. Pathogenic
3. Variant of Uncertain Significance (VUS)
4. Incidental Finding
 What do the genetic test results mean?
Normal: No clinically significant copy number changes were
identified in the DNA of this specimen in the areas tested

Excludes a micro-deletion/micro-duplication (CNV) within the

limits of resolution of the test (typically very high)

Limitations: CMA is not able to detect balanced genomic

rearrangements, low levels of mosaicism, and mutations within
single genes

Next Steps: Referral for genetic consultation should be

considered, depending on the initial reason for the invasive
prenatal testing – additional testing may be indicated
 What do the genetic test results mean?
Pathogenic: A copy number variant known to be associated with
an abnormal phenotype
Provides insight to the genomic etiology of ultrasound findings
and may assist in counselling about prenatal and postnatal
outcomes and management options
Limitations: Not all pathogenic findings are associated with a
severe clinical presentation, and the clinical presentation can be
extremely variable. Uncertainty often remains and may cause
anxiety for a pregnant couple.

Next Steps: Genetic counselling is recommended to review

significance , provide information, resources and support and if
indicated discuss further testing/change in medical
management (e.g. fetal echocardiogram) and parental testing
 VUS identified in fetus 
Test parents

Neither parent has One parent has

the VUS identified in
same CMA result as
the pregnancy (both
have a normal result) child

Finding in the fetus is

pathogenic, and the Finding in the
Barring non-paternity,
parent displays reduced fetus is a
the finding in fetus is normal familial
penetrance (not everyone
new, de novo, and likely variant and not
with the CNV will have
pathogenic pathogenic
symptoms), variable
expressivity (individuals
with this CNV have varied
presentation)
 What do the genetic test results mean?
Variant of Uncertain Significance (VUS): This is a genomic
variant that has not yet been categorized as benign or
pathogenic, either because too few cases have been reported in
the literature or the affected gene’s content and/or function are
not yet understood
Next Steps:
•Parental testing: Parental status can help determine
whether or not the CNV is familial, and less likely to be
pathogenic, or de novo (new in the affected individual) and
more likely pathogenic
•Refer for genetic counselling

Occurs in about 1% of pregnancies

 What do the genetic test results mean?
Incidental Finding (IF): Genetic variant(s) – either benign or
pathogenic - identified by a genetic test that is unrelated to the
primary indication for testing
An IF may signify:
• Presence of late-onset disorder with result having clinical
utility e.g. hereditary cancer syndrome
• Presence of late-onset disease without therapeutic
possibilities e.g. Alzheimer disease risk
• Carrier status for autosomal recessive or X-linked diseases
e.g. cystic fibrosis (CF), Duchenne Muscular Dystrophy (DMD)
• Parental consanguinity

Next Steps: Genetic counselling is recommended

Rare (1/1,500). Depends on a patient’s motivation for testing

 Benefits of Chromosomal Microarray
• Normal result can provide reassurance
• Increased diagnostic yield over traditional karyotype
– A pathogenic copy number variant (CNV) will be identified
in more than 6% of pregnancies following a normal
karyotype
• Potentially valuable information for parents making
reproductive decisions, and may have significant
value in the future management of the child
 • A systematic review of the literature was conducted to
calculate the utility of prenatal microarrays in the presence of
a normal conventional karyotype.
12,362 cases from all PN ascertainment groups1
i.e. abnormal u/s, AMA, prenatal screening, parental anxiety

2.4% had a clinically

significant CNV
(295/12,362)
3,090 Abnormal
ultrasound 1 6.5% had clinically
significant
significant CNV (201/3,090)
(201/3,090)

Variant of
Unknown
significance 4,164 other 1.1% had clinically
(VUS) are found indications1 significant CNV (44/4,164)
in about 1% of
cases2,3

5,108 AMA1 1.0% had clinically

[1] Callaway et al 2013 Prenat Diagn
[2] Shaffer et al 2012 Prenat Diagn significant CNV (50/51,08)
[3] Wapner et al 2012 NEJM
 Back to case 1
• 29-year-old G1P0 woman, in good health
• 19 week fetal morphology ultrasound showed ventricular
septal defect (VSD), polyhydramnios and suspected cleft lip
and palate
• Patient was seen in Genetics and offered amniocentesis with
QF-PCR to rule out common aneuploidies (Down syndrome,
trisomy 18, trisomy 13 and sex chromosome differences)
• QF-PCR showed normal male
• Chromosomal microarray was offered and the results showed
a 2.54-Mb deletion within 22q11.2
• The patient is now about 23weeks gestation
 22q11.2 deletion syndrome
• Caused by a sub-microscopic deletion on
chromosome 22
– 85% of individuals will have the typical deletion
size and about 15% will have smaller atypical
deletions within the critical region
• About 93% of affected individuals have a de
novo deletion of 22q11.2 and about 7% have
inherited the deletion from a parent

McDonald-McGinn, 2015
 22q11.2 deletion syndrome
• Multi-system disorder with variable expressivity
– Clinical presentation will vary between affected individuals even within the
same family (variable expressivity)

• Features include:

McDonald-McGinn, 2015
 Back to case 2
• 42-year-old G3P2 woman
• No significant family history or history of
prenatal exposure
• Integrated Prenatal Screening (IPS) was
positive
– 1 in 100 versus her age-related risk to have a baby
with Down syndrome of about 1 in 61
 Back to case 2
• Patient chose amniocentesis
• QF-PCR showed normal female
• This genetics centre has implemented a new
algorithm for all prenatal invasive testing so that
all normal QF-PCR samples are then sent for
chromosomal microarray testing
• Chromosomal microarray results showed a
pathogenic deletion that includes the BRCA1
gene
 Back to case 2
• This incidental finding has diagnosed the fetus with
an adult-onset hereditary cancer predisposition
syndrome
• Consider:
– Was disclosure of incidental results, including adult onset
conditions, part of the pre-test counselling and consent?
– Implications for autonomy and insurance discrimination
for the fetus
– Implications if either parent carries this deletion and is at
increased risk for cancer
 Prenatal Microarray
• Chromosomal microarray (CMA) has a greater
yield than traditional karyotype, particularly in
high risk pregnancies
• There is variability in practice with regards to
who will be offered prenatal CMA
• Consent, pre- and post- test counselling is
complicated
 Resources
• Visit www.geneticseducation.ca to connect to your local genetics centre and
for the GECKO on the run resource
• You may also wish to consult your local maternal-fetal medicine (MFM)
specialist or high risk obstetrician/gynaecologist depending on the reason
CMA has being considered
• If there are terms that require further elaboration please visit the GECKO
Glossary in Educational Resources
• Unique – Disorder Guides 
– Unique has been collecting information about specific chromosome disorders in
their offline database for nearly 30 years and produces family-friendly,
medically-verified, disorder-specific information guides.
• Orphanet
– A reference portal for information on rare diseases and orphan drugs, for all
audiences 
How to explain genetic testing to
patients
 Library analogy for explaining genetic
testing
• Clinical examination =
• Observing the outside
of building
– Number of windows
– Doors
– Roof
– Height of the windows

Wikimedia
 Library analogy for explaining genetic
testing
• Karyotype =
• Standing in one spot in the
library and looking at the
number of rows (46 rows, 2
row 1s, 2 row 2, etc… the
location of the rows, large
extra or missing pieces

Wikimedia
 Library analogy for explaining genetic
testing
• Microarray =
• Walking through the library
and seeing if there are
extra or missing shelves
• A shelf may be thought of
as a collection of books or
genes, that are closely
located and extra or
missing shelves would be
called microduplication or
microdeletions

Flikr.com
 Library analogy for explaining genetic
testing
• Sequencing
– Next-gen sequencing, Sanger
sequencing

=
• Reading through the books
word by word, letter by
letter to detect small
changes: substitutions,
extra or missing words

Wikimedia.org
www.2dayfm.com.au