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!