1. 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

2. 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

3. Types of genetic disorders
Our genome
Chapter:
Chromosomal
Karyotype
Sentence:
Microdeletions/
microduplications
Chromosomal
microarray
Letter:
Single gene mutations
Gene sequencing

4. 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

5. 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
Rare Diseases Meeting 2011

6. 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…
Rare Diseases Meeting 2011

7. 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
Rare Diseases Meeting 2011

8. 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)
Rare Diseases Meeting 2011

9. Types of genetic screening tests
Recommended to everyone
Cystic Fibrosis (CF)
Spinal muscular atrophy
Fragile X Syndrome
Canavan
Fanconi Anemia
Familial Dysautonomia
Mucolipidosis type 4
Bloom Syndrome
Recommended by ethnicity
Covered by Health Insurance and Ministry of Health
In Israel – prenatal genetic screening possible due to a large number of founder mutations

10.
Rare Diseases Meeting 2011

11. 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
Rare Diseases Meeting 2011

12. Next-generation carrier screening
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)
In Israel 1:200 couples both carriers of the same disease
Rare Diseases Meeting 2011

13. During pregnancy: aneuploidy screening
Test
Parameters
GA (w)
Detection rate NT
10-14
67%
1st Trimester
NT, free bHCG, PAPP-A
83%
2nd Trimester
AFP, HCG, uE3
16-22
70%
Quadritest
AFP, HCG , uE3, Inhibin-A
85%
Integrated
1+2 trimester
10-14/16-22
93%

14. During Pregnancy: Aneuploidy Screening Tests
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 >1:200
IInd trimested DS risk >1:380
Twin pregnancy: NT only
IVF: as spontaneous pregnancy

15. During pregnancy: fetal US
Relative risk for DS – integrated with biochemical screening
14-15 wk, 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

16. 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

17. Invasive prenatal testing
Chorionic villus sampling (CVS) – wk
Amniocentesis - starting from 16 wks
Cordocentesis - starting from 18 wk
CVS – 1% confined placental mosaicism
Fetal loss: CVS and Amniocentesis: 0.11%

18. Prenatal invasive testing: chromosomal aberrations
Karyotype
FISH or QPCR for aneuploidy: chromosomes 21, 18, 13, X, Y – hours
Chromosomal microarray

19. Karyotype vs chromosomal microarray (CMA)
FISH: specific locus (22q11)
CMA: all chromosomes

20. Chromosomal microarray
Trisomy 21

21. Chromosomal microarray

22. 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???

23. Chromosomal microarray: limitations

24. Databases: normal and abnormal CNVs

25. Classification of CNVs Clinical Significance
Benign
Pathogenic
Uncertain
Clinical Significance
Known syndrome
Polymorphism
Likely Pathogenic
Likely Benign
NOS

26. 1% PATHOGENIC 7% PATHOGENIC 1% NOS 2% NOS
PREGNANCIES – LOW RISK
PREGNANCIES HIGH RISK – abnormal U/S
1% PATHOGENIC
1% NOS
7% PATHOGENIC
2% NOS

27. CMA example

28. CMA example

29. To test or not to test?

31. CMA in prenatal diagnosis
Why to test for Down syndrome by amniocenthesis (1:380 risk) if every woman has a risk of 1: for microdeletion or microduplication syndrome in the fetus?
Microdeletion/microduplication = frequently intellectual disability
Both karyotyping and CMA do not discover monogenic disorders

32. Non-Invasive Prenatal Testing (NIPT)
Cell free fetal (placental) DNA
High risk populations?
Low risk populations?

33. Comparison of commercially-available NIPTs
Curr Genet Med Rep.
2013; 1: 113–121.

34. 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
The ACOG and the SMFM do not currently recommend NIPT as a first screening test in low-risk or multiple pregnancies

35. Comparison of NIPTs Sequenom Materni21 Verinata Verifi Ariosa Harmony
Natera
Panorama
BGI
NIFTY
Method used
NGS of all chromosomes
NGS of relevant chromosomes only
SNP-based
Chromosomes
21, 18, 13, X & Y
triploidy
Multi-fetal gestations
Yes
Yes + vanishing twin
Egg donor/
surrogate No

36. NIPT contraindications
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

37. 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

38. NIPT reliability

39. NIPT reliability

40. 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

41. Microdeletion syndromes/other chromosomes detected by NIPT
High false positive rate

42. 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

43. The future: monogenic disorders detection by NIPT

44. 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)

45. 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

46. 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

47. Preimplantation genetic diagnosis (PGD)

48. Types of PGD Cytogenetic Single gene Aneuploidy Autosomal Dominant
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)

49. Preimplantation genetic screening
5 or 24 chromosome PGS: FISH or karyomapping

50. Partially penetrant CNVs
Ethical considerations
When is a disorder “serious” enough to warrant prenatal diagnosis + termination of pregnancy? Or PGD?
Hearing loss
Gaucher
HNPCC
Partially penetrant CNVs

51. Thank you!