2. Non-invasive Prenatal Testing
Kuwait Medical Association Updates in Medicine
Obstetrics and Gynecology
Non-invasive Prenatal Testing
March 18th 2016
Dr. Shakir Bahzad, MD, FRCPC
Kuwait Medical Genetics Center
Kuwait Cancer Control Center

3. Disclosure:
Nothing to disclose.

4. Outlines: What is Non-Invasive Prenatal Screening (NIPS)?
To use or not to use NIPS? That is the question!

5. NIPS = Non-Invasive Prenatal Screening
Part 1:
NIPS = Non-Invasive Prenatal Screening
NIPT = Non-Invasive Prenatal Testing
NIPD = Non-Invasive Prenatal Diagnosis (please don’t use this one!)
“ … is a screening test that utilizes bioinformatic algorithms and next generation sequencing of fragments of cfDNA in maternal serum to determine the probability of certain chromosome conditions in a pregnancy.”
Not to be confused with “Preimplantation Genetic Screening” (PGS)!

7. All individuals have their own cell-free DNA in their blood stream
All individuals have their own cell-free DNA in their blood stream. During pregnancy, cell-free DNA from the placenta (predominantly trophoblast cells) also enters the maternal blood stream and mixes with maternal cell-free DNA. The DNA of the trophoblast cells usually reflects the chromosomal make-up of the fetus.

8. Pre- and post-test genetics counseling.
10-11 weeks of gestation
U/S (singleton)
High risk women only
Looking for Fetal aneuploidy (T21, T18, T13, X and Y aneuploidy)

9. BambniTest
Harmony
informaSeq
MaterniT21 PLUS
NIFTY
Panorama
PrenaTest
verifi
VisibiliT
iGeneScreen
Counsyl
Others

10. SNPs: Single Nucleotide Polymorphism

11. Schematic illustration of the procedural framework for using massively parallel genomic sequencing for the noninvasive prenatal detection of fetal chromosomal aneuploidy.
Schematic illustration of the procedural framework for using massively parallel genomic sequencing for the noninvasive prenatal detection of fetal chromosomal aneuploidy. Fetal DNA (thick red fragments) circulates in maternal plasma as a minor population among a high background of maternal DNA (black fragments). A sample containing a representative profile of DNA molecules in maternal plasma is obtained. In this study, one end of each plasma DNA molecule was sequenced for 36 bp using the Solexa sequencing-by-synthesis approach. The chromosomal origin of each 36-bp sequence was identified through mapping to the human reference genome by bioinformatics analysis. The number of unique (U0–1–0–0, see text) sequences mapped to each chromosome was counted and then expressed as a percentage of all unique sequences generated for the sample, termed % chrN for chromosome N. Z-scores for each chromosome and each test sample were calculated using the formula shown. The z-score of a potentially aneuploid chromosome is expected to be higher for pregnancies with an aneuploid fetus (cases E–H shown in green) than for those with a euploid fetus (cases A–D shown in blue).
Rossa W. K. Chiu et al. PNAS 2008;105:
©2008 by National Academy of Sciences

14. Biochemical Screening
Part 2: How good is NIPS?
Biochemical Screening

15. NIPS

16. In reality …..

17. Wang et al. Genet Med 2005;17:234

19. ACOG states that DNA-based screening tests may be performed only on women who are at increased risk of having a fetus with aneuploidy. Among the indications listed for women considered to be at increase risk are:

20. Pre-test counseling for cfDNA should include: - All genetic screening is optional and may be declined. - cfDNA appears to be the most accurate screening test for trisomy False positive and false negative results do occur with cfDNA Patients who desire definitive information about chromosome conditions in their pregnancy should be offered the option of amniocentesis or CVS. - Confirmatory diagnostic testing is recommended for abnormal cfDNA results. - A negative cfDNA result indicates a decreased risk and does not definitively rule out chromosome conditions. - cfDNA screening may not yield a result (inconclusive), which may indicate an increased risk for a chromosome condition. - cfDNA does not evaluate for all chromosome conditions. - Limitations of the test are explained.

21. General limitations from ACOG:

23. False Negative NIPS:
Too little fetal DNA (usually reported as failed)
Mosaicism confined to the fetus.
False positive NIPS:
- Placental mosaicism
- Vanishing twin
- Maternal sex chromosome abnormality
- Neoplasia – apoptosis of cancer cells, aneuploidy common

28. Post-test Counseling:
- If a positive NIPT result:
- Remember False Positives occur
- What is the PPV for this patient?
- Refer for genetic counseling
- Always offer invasive testing for confirmation
- If parents decline invasive testing, postnatal confirmation should be completed
- If a Negative NIPT result:
- Remember False Negatives occur – especially in higher risk pregnancies
- Always offer invasive testing if parents want to “know for sure”

29. Take-home Message!

30. Norton ME, et al. NEJM, epub 4/1/15

31. Norton ME, et al. NEJM, epub 4/1/15