Transcript Genetiikan teknologia muuttuu, muuttuuko diagnostiikka?

Suomen Perinatologinen Seura
04.10.2012
Towards genomic testing in antenatal care –
are we ready?
Kristiina Aittomäki
Director of the Department of Medical Genetics
Helsinki University Central Hospital/HUSLAB
The wish for a healthy child
Practically every couple has the wish for a healthy child.
This wish, however, will not be fulfilled in 2-3% of
families, where a new-born child is diagnosed with a
congenital malformation or disease.
The aim of prenatal diagnosis (PND) is to
 help families to have a healthy child
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Kristiina Aitomäki HUSLAB
04.10.2012
help prepare for the birth of a child that needs
special medical care
help psychological prepare for the birth of a child
with a handicap
enable for the couple to consider termination of the
pregnancy, if the fetus is affected
to provide reproductive autonomy to women
to make decisions about their pregnancy
based on medical information (as they do
by their social situation)
From chromosomes to genes to genomes
Chromosome microarray
analysis (CMA)
Kristiina Aitomäki HUSLAB
04.10.2012
What can CMA do for you?
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Identification of new microdeletion and
other syndromes not detectable in
karyotyping
More efficient diagnostic testing
particularly for learning disability and
congenital anomalies
Deletion
Duplication
Copy number variations (CNV)
Kristiina Aitomäki HUSLAB
04.10.2012
Blake et al.
Results after normal result on chromosome analysis
Sagoo et al. 2009
Girirajan et al NEJM September 2012
>32 000 patients, > 8000 controls
>2300 children with
CNV associated with
intellectual disability and
congenital anomalies
CMA vs. chromosome analysis
CMA will
 detect all unblanced chromosome aberrations detectable
with classical chromosome analysis
 detect much smaller unbalanced aberrations (deletions
or duplications) not detectable with chromosome
analysis
 give more information on identified chromosome
aberrations such as de novo translocations or marker
chromosomes
 will detect mosaicism with same level as karyotyping
Kristiina Aitomäki HUSLAB
04.10.2012
CMA vs. chromosome analysis
CMA will NOT
 detect balanced rearrengements
 does not give positional information
(translocation trisomy vs standard trisomy)
 detect triploidy (depending on the array)
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we still need classical chromosome analysis
Kristiina Aitomäki HUSLAB
04.10.2012
CMA
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detects small (and smaller and smaller) copy
number variations (CNV)
human genome includes two types of CNVs:
 harmful
 harmless, benign changes, with no health
consequences
 those contributing to phenotypes with other
genetic changes
presently we do not yet know all the CNVs in the
genome and their significance
Kristiina Aitomäki HUSLAB
04.10.2012
Establishing the pathogenecity of a de novo CNV
Extensive work-up for defining the clinical significance:
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Size of the CNV
Review of relevant databases
Review of literature
Has the CNV been previously identified in patients /
healthy controls
Is there a phenotype
What is the gene conent of the change
Deletions more often deleterious than duplications
Family history, variable penetrance and expressivity ...
Kristiina Aitomäki HUSLAB
04.10.2012
CMA results
Three categories of CMA results:
1. Normal
2. Abnormal
3. Variant on unknown significance (VOUS)
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In post natal testing we do not know, if this
finding will explain the disease in a child
In prenatal testing we do not know, if the
fetus/child will be healthy or affected
Kristiina Aitomäki HUSLAB
04.10.2012
CMA
CMA can also identify
 Incidental findings - assume deletions removing known
disease genes
 diagnosis of adult onset neurodegenerative
disorder in the child
 reveal the same diagnosis also in one of the
healthy parents
 diagnosis of cancer suceptibility in the child
 carriership of recessive disorders
 Non – paternity
 Relatedness of parents (incest)
Kristiina Aitomäki HUSLAB
04.10.2012
Example 1
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US finding: unilateral club foot
CMA: 1.6 Mb deletion in the area of known
microdeletion syndrome
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Found in patients with developmental delay
Familial and de novo cases
Cognitive ability normal to moderate mental
retardation
The change pathogenic, but the
phenotype unertain
Kristiina Aitomäki HUSLAB
04.10.2012
Example 2
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Previous child with devopmental delay with known
chromosome 21 trisomy
CVS: a deletion in chromosome 9
The databases of literature does not reveal any similar
cases
The change is de novo
Deleted region includes several known genes, three are
potentially disease-causing with a known function in
central nervous system
The change is a VOUS with unknown significance
Kristiina Aitomäki HUSLAB
04.10.2012
Example 2 b
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Previous child with devopmental delay with
known chromosome 21 trisomy
CVS: a deletion in chromosome 1
The databases and literature include many cases
found in control populations
No genes in the region
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A benign harmless CNV
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Kristiina Aitomäki HUSLAB
04.10.2012
CMA in PND
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Several studies performed
Difficult to compare results,
because
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Different platforms used
Heterogeneous patient series
Differing indications
Definition of abnormal findings (VOUS
included)
Definition of VOUS
Kristiina Aitomäki HUSLAB
04.10.2012
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The largest one study so far N=5003 from one lab
2004-2011 (changing CMA platform over time)
Indications:
Known chromosome abnormality (648)
Chromosome abnormality in one of the parents (62)
Spontaneous abortion/foetus mortus (417)
US abnormality (2858)
Abnormal 1st or 2nd trimester screening (77)
Inherited disorder (non chromosomal) (487)
Advanced maternal age (417)
Parental concern (95) other (13)
Kristiina Aitomäki HUSLAB
04.10.2012
N=5003
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Overall detection rate 5.3%
5.5% (140/2533) with significant findings although normal karyotype
71% of significant CNVs < 10kb (unlikely detection with karyotyping)
Turnaround time mean 7.5 days (median 6 days)
Frequency of VOUS 4.2%, de novo 0.4%
Kristiina Aitomäki HUSLAB
04.10.2012
Prenatal chromosomal microarray analysis in a
diagnostic laboratory; experience with < 1000 cases
and review of literature
Breman et al. Prenatal diagnosis 2012
clinically significant CNVs 7.6% (85/1115)
 clinically significant CNVs 4.2% without
chromosomal indications
 frequency of VOUS 1.6%
Findings by incidation:
 Abnormal US
8.8%
 AMA
1.3%
 Serum screening 5.4%
 Parental concern
0
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Kristiina Aitomäki HUSLAB
04.10.2012
Non-targeted whole genome 250K SNP array analysis as
replacement for karyotyping in fetuses wth structural ultrasound
anomalies: evaluation of a one-year experience
Faas et al. Prenatal diagnosis 2012
Upon US detection of fetal anomalies couples were offered
counselling for alternative methods and a choice of
 Trisomy screening and CMA (QF/array) or
 Trisomy screenig and karyotyping (QF/karyo)
Results
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153/220, 70% chose QF/array (later <82%)
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35/153 an abnormal finding in QR-PCR
5/118 a microdeletion syndrome was identified
3/118 variant of uncertain significance
Inherited CNVs 11/118
homozygous stretches 3/67
67/220 30% chose QF/karyo
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23/67 an abnormal QF-PCR
3/67 abnormal karyotype
Kristiina Aitomäki HUSLAB
04.10.2012
Non-targeted whole genome 250K SNP array analysis as
replacement for karyotyping in fetuses wth structural ultrasound
anomalies: evaluation of a one-year experience
Faas et al. Prenatal diagnosis 2012
For recieving results,
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46% of couples chose to receive information of CNVs unrelated to
fetal US findings regardless of the availability of current treatment for
a late-onset disease
33% chose not to recieve such information
21% chose to recieve the information only when threre was either
screening or treatment available
in all but two cases both parents chose the same options
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Couples have different views to incidental findings
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Kristiina Aitomäki HUSLAB
04.10.2012
We now know
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CMA identifies more unbalanced
abnormalities than karyotyping in prenatal
and postnatal diagnostis
Pre and postnatal testing have differences
CMA gives important additional information
in many abnormalities found in karyotyping
CMA is less labour intensive and has a
better turnaround time
Kristiina Aitomäki HUSLAB
04.10.2012
CMA
will identify CNVs of unknown significance, presently
with 1.5 (-5%) frequency
 can produce incidental findings of late- onset
diseases
Both may cause sometimes long-lasting concern and
anxiety in parents
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Is this a reason not to do CMA?
No, because
 also in these cases you still have excluded a large
number of known abnormalities
 the uncertainty about the health of the fetus/child
remains, but on a higher level if no studies are done
Kristiina Aitomäki HUSLAB
04.10.2012
CMA
will identify CNVs of unknown significance
 can produce incidental findings of late-onset diseases
which may cause sometimes long-lasting concern and
anxiety in parents
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Is this a reason to withold information from parents
(in relevance to the aims of PND)?
Absolutely NO, because
 that would be dishonest and paternalistic
Kristiina Aitomäki HUSLAB
04.10.2012
Informed consent needed for CMA
Before prenatal CMA patients need
counselling for
 Possibility of identifying VOUS
 Possibility of incidental findings
Patients need to decide what information they
want to receive, particularly concerning
incidental findings
Kristiina Aitomäki HUSLAB
04.10.2012
In conclusion
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We should provide our patients with the benefits or
modern genetic technology in prenatal testing
We should provide patients/couples with adequate
choice and counselling
We need to educate professionals to provide the
counselling
We need to provide patients with all our best
information but also all the support they may need
Kristiina Aitomäki HUSLAB
04.10.2012
Towards genomic testing in
antenatal care – are we ready?
YES, we are!
Thank you!
Poikkeavan löydöksen selvittely
sikiötutkimuksissa
Lapsiveden soluissa havaittiin kromosomin
16 lyhyessä käsivarressa ylimääräistä
materiaalia, 46,XX,add(16)(p13)
Vanhempien kromosomitutkimuksen tulos oli normaali.
Trisomia 16p? Krittinen alue 16p13.1-13.3.
Oireet: mm. vaikea kehitysviivästymä, epilepsia, CHD,
raaja-anomalioita, persoonalliset ulkonäköpiirteet
Dignoosilla olisi tärkeä merkitys pariskunnalle,
joten päätettiin tehdä molekyylikaryotyypitys.
K. Aittomäki / Kirsi Jänkälä
aVGH tulos
Tutkimus tehtiin 244k sirulla.
Duplikoitunut 16p13.11p13.3
sikiöllä
Vanhemmat päätyivät
keskeytykseen.
Sikiöllä todettiin mm. VSD ja
muita
16p trisomiaan sopivia oireita.
Sikiö
Äiti
Isä
K. Aittomäki / Kirsi Jänkälä