Download NIPT

Aneuploidy screening in pregnancy - modern
approaches
Prof. Lina Basel
Director, The Raphael
Recanati Genetics Institute,
Beilinson hospital, Rabin
Medical Center
Schneider Children’s Medical
Center of Israel
Tel Aviv University
Rabin Medical Center/Schneider Children’s Medical Center of Israel
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Pediatric genetics
Adult genetics
Prenatal counseling
Oncogenetics
Genetic screening
Molecular lab
Cytogenetic lab including
chromosomal microarray
 PGD
Types of genetic disorders
Our genome
Chapter:
Chromosomal
Karyotype
Sentence:
Microdeletions/
microduplications
Chromosomal
microarray
Letter:
Single gene
mutations
Gene sequencing
Role of ObGyn in providing the screening program
Before and during pregnancy:
genetic counseling, population
genetic screening
During pregnancy:
fetal US, aneuploidy screening
After pregnancy:
diagnostic tests
Before and during pregnancy: genetic counseling
Before pregnancy
During pregnancy
Family history of genetic
disease, ID, autism,
recurrent pregnancy loss,
infertility, premature
ovarian failure
Abnormal biochemical
screening/NIPT/invasive
testing result
Fetal abnormalities on the US
Before and during pregnancy: genetic carrier screening
 Gene is known in about 3000 diseases
 Carrier tests for prospective parents are recommended for a
small number of selected diseases
 Common mistake: there is no history of genetic disease in
my family, therefore I am not at risk…
Before pregnancy: genetic carrier screening
Frequent diseases?
SMA, Fragile X, CF,
other
All diseases?
Recent advances in DNA sequencing led for identifying carriers of
known mutations that cause more than 400 recessive genetic
diseases
Attitude of different populations in Israel towards prenatal
testing
 Prenatal testing by CVS or amniocentesis;
preimplantation genetic diagnosis (pregnancy
interruption possible up to birth, even at 40 weeks of
pregnancy)
 Preimplantation genetic diagnosis (pregnancy
interruption possible up to 40 days only – no prenatal
testing possible)
 Prenatal testing by CVS or amniocentesis;
preimplantation genetic diagnosis (pregnancy
interruption possible up to 120 days of pregnancy)
Types of genetic screening tests
Recommended to everyone
Recommended by ethnicity
 Cystic Fibrosis (CF)
 Spinal muscular
atrophy
 Fragile X Syndrome
 Canavan
 Fanconi Anemia
 Familial Dysautonomia
 Mucolipidosis type 4
 Bloom Syndrome
In Israel – prenatal genetic screening possible due
to a large number of founder mutations
Covered by Health
Insurance and
Ministry of Health
http://server.goldenhelix.org/israeli/
Carrier burden of 448 pediatric diseases
22% of literature-cited disease mutations
were common SNPs or misannotated
Average carrier burden of severe childhood diseases 2.8
Next-generation carrier screening
In Israel 1:200 couples
both carriers of the
same disease
Disorder and gene
Carrier frequency
Bloom syndrome, BLM
1 in 946 (3/2838)
Canavan disease, ASPA
1 in 189 (16/3017)
Cystic fibrosis, CFTR
1 in 30 (333/10085)
Dihydrolipoamide
dehydrogenase deficiency, DLD
1 in 525 (4/2101)
Familial dysautonomia, IKBKAP
1 in 301 (10/3009)
Familial hyperinsulinism, ABCC8
1 in 263 (8/2105)
Fanconi anemia group C, FANCC
1 in 482 (6/2890)
Glycogen storage disease, type
1A, G6PC
1 in 263 (8/2102)
Maple syrup urine disease, type
A, BCKDHA
1 in 2110 (1/2110)
Maple syrup urine disease, type
B, BCKDHB
1 in 352 (6/2110)
Mucolipidosis, type IV, MCOLN1
1 in 722 (4/2890)
Niemann-Pick disease, type AB,
SMPD1
1 in 578 (5/2889)
Tay-Sachs disease, HEXA
1 in 93 (36/3336)
Usher syndrome, type 1F,
PCDH15
1 in 700 (3/2101)
Usher syndrome, type III, CLRN1
1 in 526 (4/2103)
During pregnancy: aneuploidy screening
Test
NT
Parameters
NT
GA (w)
Detection rate
10-14
67%
1st Trimester
NT, free bHCG,
PAPP-A
10-14
83%
2nd Trimester
AFP, HCG, uE3
16-22
70%
Quadritest
AFP, HCG , uE3,
Inhibin-A
16-22
85%
Integrated
1+2 trimester
10-14/16-22
93%
During Pregnancy: Aneuploidy Screening Tests
 High AFP: neural tube defects,
congenital nephrotic syndrome,
skin diseases
 Low uE3: ichthyosis, Smith-LemliOpitz syndrome, adrenal axis
disorders
Twin pregnancy: NT only
IVF: as spontaneous pregnancy
Amniocenthesis:
Ist trimested DS risk
>1:200
IInd trimested DS risk
>1:380
During pregnancy: fetal US
Relative risk for DS – integrated with biochemical screening
14-15 wk, 21-24 wk
Hyperechogenic bowel – X6
Short femur – X2
Lt echogenic intracardiac focus - X1.5
Pyelectasis – X1
Single umbilical artery (SUA) – X1
Chorioid plexus cyst (CPC) - X1
Indications for invasive fetal testing
Abnormal biochemical
serum screening/NIPT
“Soft signs” on the fetal
ultrasound- 2 soft signs
or combined risk >1:380
Fetal malformations
on the ultrasound
Parents carriers of genetic
disease/affected
Invasive prenatal testing
Chorionic villus
sampling (CVS) – 10-13
wk
Amniocentesis starting from 16 wks
Cordocentesis starting from 18 wk
CVS – 1% confined placental mosaicism
Fetal loss: CVS and Amniocentesis: 0.11%
Prenatal invasive testing: chromosomal aberrations
 Karyotype
 FISH or QPCR for
aneuploidy:
chromosomes 21, 18, 13,
X, Y – 24-48 hours
 Chromosomal microarray
Karyotype vs chromosomal microarray (CMA)
FISH: specific locus (22q11)
CMA: all chromosomes
Chromosomal microarray
Trisomy 21
Chromosomal microarray
Current indications for prenatal CMA
 U/S – Major fetal malformations
 Abnormal de-novo karyotype abnormality
(translocation/marker)
 Inherited microdeletion/microduplication
 U/S – Minor malformations???
 Low risk pregnancy???
Chromosomal microarray: limitations
Databases: normal and abnormal CNVs
Classification of CNVs
Benign
Pathogenic
Uncertain
Clinical
Significance
Likely
Benign
NOS
Likely
Pathogenic
PREGNANCIES – LOW
RISK
PREGNANCIES HIGH
RISK – abnormal U/S
1% PATHOGENIC
7% PATHOGENIC
1% NOS
2% NOS
CMA example
CMA example
To test or not to test?
CMA in prenatal diagnosis
Why to test for Down syndrome by amniocenthesis (1:380 risk)
if every woman has a risk of 1:100-200 for microdeletion or
microduplication syndrome in the fetus?
Microdeletion/microduplication = frequently intellectual
disability
Both karyotyping and CMA do
not discover monogenic
disorders
Non-Invasive Prenatal Testing (NIPT)
Cell free fetal
(placental) DNA
• High risk populations?
• Low risk populations?
Comparison of commercially-available NIPTs
Curr Genet Med Rep.
2013; 1: 113–121.
NIPT indications according to the American College of
Obstetricians and Gynecologists
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A woman aged 35 years or older at delivery
Biochemical screening test result shows and increased risk
for aneuploidy
A woman has a history of pregnancy with fetal trisomy
An ultrasound shows a fetal abnormality that could be
caused by aneuploidy
Parental balanced robertsonian translocation involving 13
and 21
The ACOG and the SMFM do not currently recommend NIPT as a
first screening test in low-risk or multiple pregnancies
Comparison of NIPTs
Sequenom
Materni21
Natera
Panorama
BGI
NIFTY
NGS of
relevant
chromosomes
only
Chromosom 21, 18, 13, X 21, 18, 13, 21, 18, 13, X &
es
&Y
X&Y
Y
Multi-fetal Yes
Yes
Yes
gestations
SNP-based
NGS of all
chromos
omes
Egg donor/ Yes
surrogate
No
Method
used
Verinata
Verifi
Ariosa
Harmony
NGS of all
NGS of all
chromosom chromoso
es
mes
Yes
Yes
21, 18, 13, X & Y 21, 18,
triploidy
13, X & Y
Yes + vanishing Yes
twin
Yes
NIPT results
 Normal result: no specific follow up necessary, unless ultrasound
examination of the fetus reveals anomalies
 Test failure: in up to 3% pregnancies not enough fetal DNA
 Abnormal NIPT result: amniocentesis or chorion biopsy
NIPT contraindications
NIPT is NOT the test of choice when there is :
• Fetal anomalies (excluding soft signs) on ultrasound
• A triplet pregnancy
• Known genetic anomalies that cannot be diagnosed by NIPT
NIPT reliability
 Phenotype for sex aneuploidies is highly variable
 Mosaicism in the fetus is a problem
 Mosaicism in the mother is a problem
 NIPT for sex aneuploidies is less accurate
NIPT reliability
NIPT reliability
NIPT disadvantages
 50% of cytogenetic abnormalities will not be detected.
<35 years or >35 years: 75 and 43% of cytogenetic abnormalities will be missed.
 NIPT is not able to distinguish specific forms of aneuploidy (extra chromosome,
Robertsonian translocation or high-level mosaicism (recurrence risk
counseling)
 Most microdeletions/microduplications will not be detected
 NIPT does not screen for open neural tube defects
 NIPT does not replace fetal US examination (NT, congenital anomalies)
 NIPT has no role in predicting late-pregnancy complications
Microdeletion syndromes/other chromosomes detected
by NIPT
High false positive rate
The future: Microdeletion syndromes detected by NIPT
 Sensitivity 94%
 False-positive rate of 3.8% would potentially limit the clinical utility as a
stand-alone screening test
 Of 55 false-positive samples, 35 were caused by deletions/duplications present
in maternal DNA
The future: monogenic disorders detection by NIPT
Detection of monogenic disorders in the fetus
Known family history/carrier couple
In CVS/amniocytes
Identify the disease first (through affected family
member or genetic screening)
Fetal Exome Sequencing
 Congenital abnormalities (e.g.
omphalocele and complex cardiac
disease) can be associated with
chromosomal aneuploidy or related to a
single-gene disorder
 Knowing the cause of a congenital
structural anomaly can aid in making a
more accurate diagnosis and provides
information about prognosis and
recurrence risks for parents
Fetal Exome Sequencing
 Exome sequencing on 30 non-aneuploid fetuses with structural
abnormalities first identified by prenatal US
 Monogenic cause identified in 10% - diagnostic yield comparable
to microarray testing
Preimplantation genetic diagnosis (PGD)
Types of PGD
Cytogenetic
Single gene
• Aneuploidy
• Balanced translocation carriers
• Inherited CNV syndromes
• Autosomal Dominant
• Autosomal recessive
• X – linked disorders
Sex selection
HLA - typing
• Medical indication
• Non- medical indication
• Isolated
• With Mendelian disease
Adult onset diseases
• Cancer susceptibility mutation carriers
• Full penetrate adult onset (including non-disclosure)
Preimplantation genetic screening
5 or 24 chromosome
PGS: FISH or
karyomapping
Ethical considerations
• When is a disorder “serious” enough
to warrant prenatal diagnosis +
termination of pregnancy? Or PGD?
Hearing loss
Gaucher
Partially penetrant CNVs
HNPCC
Thank you!