Prof. Lina Basel
Director, The Raphael Recanati Genetics Institute,
Beilinson hospital, Rabin Medical Center
Schneider Children’s Medical Center of Israel
Tel Aviv University
Prof. Lina Basel
Director, The Raphael Recanati Genetics Institute,
Beilinson hospital, Rabin Medical Center
Schneider Children’s Medical Center of Israel
Tel Aviv University
Aneuploidy screening in pregnancy - modern approaches
Rabin Medical Center/Schneider Children’s Medical Center of Israel
Pediatric genetics Adult genetics Prenatal counseling Oncogenetics Genetic screening Molecular lab Cytogenetic lab including
chromosomal microarray PGD
Types of genetic disorders
Chapter:Chromosomal
Karyotype
Sentence:Microdeletions/
microduplicationsChromosomal
microarray
Our genome
Letter:Single gene mutations
Gene sequencing
Before and during pregnancy:genetic counseling, population
genetic screening
During pregnancy:fetal US, aneuploidy screening
After pregnancy:diagnostic tests
Role of ObGyn in providing the screening program
Family history of genetic disease, ID, autism,
recurrent pregnancy loss, infertility, premature
ovarian failure
Abnormal biochemical screening/NIPT/invasive
testing resultFetal abnormalities on the US
Before pregnancy During pregnancy
Before and during pregnancy: genetic counseling
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 and during 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
Before pregnancy: genetic carrier screening
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)
Recommended to everyoneRecommended to everyone
Recommended by ethnicityRecommended by ethnicity
In Israel – prenatal genetic screening possible due to a large number of founder mutations
Covered by Health Insurance and Ministry of Health
Cystic Fibrosis (CF) Spinal muscular
atrophy Fragile X Syndrome Canavan Fanconi Anemia Familial Dysautonomia Mucolipidosis type 4 Bloom Syndrome
Cystic Fibrosis (CF) Spinal muscular
atrophy Fragile X Syndrome Canavan Fanconi Anemia Familial Dysautonomia Mucolipidosis type 4 Bloom Syndrome
http://server.goldenhelix.org/israeli/
Carrier burden of 448 pediatric diseases
Average carrier burden of severe childhood diseases 2.8
22% of literature-cited disease mutations were common SNPs or misannotated
Next-generation carrier screening
In Israel 1:200 couples both carriers of the
same disease
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)
TestTest ParametersParameters GA (w)GA (w) Detection rateDetection rate
NT NT 10-14 67%
1st Trimester NT, free bHCG, PAPP-A
10-14 83%
2nd Trimester AFP, HCG, uE3 16-22 70%
QuadritestAFP, HCG , uE3,
Inhibin-A16-22 85%
Integrated 1+2 trimester 10-14/16-22 93%
During pregnancy: aneuploidy screening
High AFP: neural tube defects, congenital nephrotic syndrome, skin diseases
Low uE3: ichthyosis, Smith-Lemli-Opitz syndrome, adrenal axis disorders
High AFP: neural tube defects, congenital nephrotic syndrome, skin diseases
Low uE3: ichthyosis, Smith-Lemli-Opitz syndrome, adrenal axis disorders
Amniocenthesis:Ist trimested DS risk
>1:200IInd trimested DS risk
>1:380
Amniocenthesis:Ist trimested DS risk
>1:200IInd trimested DS risk
>1:380Twin pregnancy: NT only
IVF: as spontaneous pregnancy
During Pregnancy: Aneuploidy Screening Tests
Hyperechogenic bowel – X6Short femur – X2Lt echogenic intracardiac focus - X1.5Pyelectasis – X1Single umbilical artery (SUA) – X1Chorioid plexus cyst (CPC) - X1
Hyperechogenic bowel – X6Short femur – X2Lt echogenic intracardiac focus - X1.5Pyelectasis – X1Single umbilical artery (SUA) – X1Chorioid plexus cyst (CPC) - X1
During pregnancy: fetal US
Relative risk for DS – integrated with biochemical screening
14-15 wk, 21-24 wk
Indications for invasive fetal testing
Abnormal biochemical serum screening/NIPT
Fetal malformations on the ultrasound
“Soft signs” on the fetal ultrasound- 2 soft signs
or combined risk >1:380
Parents carriers of genetic disease/affected
Chorionic villus sampling (CVS) – 10-13 wk
Amniocentesis - starting from 16 wks
Cordocentesis - starting from 18 wk
Invasive prenatal testing
Fetal loss: CVS and Amniocentesis: 0.11%
CVS – 1% confined placental mosaicism
Karyotype
FISH or QPCR for aneuploidy: chromosomes 21, 18, 13, X, Y – 24-48 hours
Chromosomal microarray
Karyotype
FISH or QPCR for aneuploidy: chromosomes 21, 18, 13, X, Y – 24-48 hours
Chromosomal microarray
Prenatal invasive testing: chromosomal aberrations
Karyotype vs chromosomal microarray (CMA)
FISH: specific locus (22q11)CMA: all chromosomes
Trisomy 21
Chromosomal microarray
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
BenignBenign PathogenicPathogenic
UncertainClinical
Significance
UncertainClinical
Significance
Classification of CNVs
Likely Pathogenic
Likely PathogenicNOSNOS
Likely BenignLikely
Benign
PREGNANCIES – LOW RISK
1% PATHOGENIC
1% NOS
PREGNANCIES HIGH RISK – abnormal U/S
7% PATHOGENIC
2% NOS
CMA example
CMA example
To test or not to test?To test or not to test?
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
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
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
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
Sequenom Materni21
Verinata Verifi
Ariosa Harmony
NateraPanorama
BGINIFTY
Method used
NGS of all chromosomes
NGS of all chromosomes
NGS of relevant chromosomes only
SNP-based NGS of all chromosomes
Chromosomes
21, 18, 13, X & Y
21, 18, 13, X & Y
21, 18, 13, X & Y
21, 18, 13, X & Y triploidy
21, 18, 13, X & Y
Multi-fetal gestations
Yes Yes Yes Yes + vanishing twin
Yes
Egg donor/surrogate
Yes Yes Yes No Yes
Comparison of NIPTs
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 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 contraindications
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
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
NIPT disadvantages
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
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
Fetal Exome Sequencing
Preimplantation genetic diagnosis (PGD)
Cytogenetic
• Aneuploidy• Balanced translocation carriers• Inherited CNV syndromes
• Aneuploidy• Balanced translocation carriers• Inherited CNV syndromes
Single gene
• Autosomal Dominant• Autosomal recessive• X – linked disorders
• Autosomal Dominant• Autosomal recessive• X – linked disorders
Sex selection
• Medical indication • Non- medical indication• Medical indication • Non- medical indication
HLA - typing
• Isolated• With Mendelian disease• Isolated• With Mendelian disease
Adult onset diseases
• Cancer susceptibility mutation carriers • Full penetrate adult onset (including non-disclosure)• Cancer susceptibility mutation carriers • Full penetrate adult onset (including non-disclosure)
Types of PGD
Preimplantation genetic screening
5 or 24 chromosome PGS: FISH or karyomapping
HNPCCGaucherHearing loss
Partially penetrant CNVs
Ethical considerations
• When is a disorder “serious” enough to warrant prenatal diagnosis + termination of pregnancy? Or PGD?
Thank you!