NIPT: State of the Art in 2020 - (Non Invasive Prenatal Testing) - Maternity & Midwifery Forum

NIPT:
 (Non Invasive Prenatal Testing)

State of the Art in 2020
          Dr Marc NOUCHY
             MD Geneticist
  Department of Genetics, Lyon - France

INTRODUCTION

History:
● Discovery of circulating foetal DNA by Lo in 1997, coupled with NGS techniques

● Why?
    ● Reduce invasive testing
    ● Decrease in the numbers of foetal loss (risk estimated at 1%).

Cell Free Fœtal DNA
in maternal blood

Circulating free DNA (cfDNA)
                               in maternal blood

Maternal blood = Maternal DNA + Foetal DNA
● 2-20% of cfDNA is foetal

Foetal cfDNA originates from trophoblasts
from the placenta

Released into maternal blood in the form
of small DNA fragments (150-200bp)

Detectable from Week 7 of pregnancy

Not detectable in maternal blood after birth
                                                        Maternal DNA
Totally non-invasive for the foetus                     Foetal DNA

Applications: screening vs diagnosis

Diagnosis (DNA sequences not present in the mother)
● Determination of foetal sex
● RHD genotyping
● Achondroplasia

Screening (Quantitative change in circulating DNA)
● NIPT

Technical aspects

Available commercial NIPT testing

USA
 ● Harmony Test (Ariosa - Roche)
 ● MaterniT21 Plus Test (Sequenom)
 ● Verifi Test (Verinata - Illumina)
 ● Panorama Test (Natera)
Europe
 ● Prena test-Life Codexx
 ● IONA test-Premaitha Health
 ● Vanadis- Perkin Elmer
 ● Ninalia Eurofins Biomnis
China
 ● Nifty test- BGI

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Technological approaches

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Comparison of different NIPT ‘s

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NIPT IN « ATYPICAL PREGNANCIES »

Ninalia NIPT can be offered in case of:

● Twin pregnancy

● Pregnancy vanishing twin

● Egg donor pregnancy

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Different options of Ninalia NIPT
       (GWS:March 2020)

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Technical overview (Veriseq°Ilumina)

Process steps :

Maternal blood    Extraction of both maternal and fetal circulating        Library prep / quantification / Pooling   NGS
                                       DNA

                                                                      Illumina Server

                                                Chromosome 21 NCV
        Final result
      CE-IVD software

                                                                                        Target           Reference
                                                                                     chromosome         chromosome
                                       Normalized Chromosome Value (NCV)                Alignement and sequene analysis

Performance and
limits of NIPT

Test performances depending
                     on aneuploidies

Gil et coll. Ultrasound Obstet.Gynecol (2017), Poon
Ultrasound Obstet.Gynecol (2016):

●T21: DR 99,7% PPV 99%

●T18: DR 98,2% PPV 64-77%

●T13: DR 99%      PPV 44-59%

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Limits of the test

False positives
● Vanishing twin
● Confined placental mosaicism (CPM)
● Maternal CNV (e.g., chr 18)
● Maternal mosaicism and neoplasm

False negatives
● Foetoplacental discrepancy
● Low levels of foetal DNA (< 1.4-2.7%)
● Triploidy

Fetal fraction of cfDNA is often considered
 as the main limitation to get a NIPT result.

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NIPT:
guidelines for use

ACMG GUIDELINES FOR NIPT

Allow parents to select diagnostic or screening approach for the detection of
fetal aneuploidies and/or genomic changes consistent with their personal goals and
preferences.
Inform parents that diagnostic testing (CVS or amniocentesis) is an option for
detection of chromosome abnormalities.

Inform all pregnant women that NIPS is the most sensitive screening option for
traditionally screened aneuploidies

Referring patients to a trained genetics professional when an increased risk of
aneuploidy is reported after NIPS.
Offering diagnostic testing when a positive screening test result is reported

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GUIDELINES ACMG (SCA)

    Inform all pregnant women, as part of pretest counseling for NIPS, of the
availability of the expanded use of screening for sex chromosome
aneuploidies.

Inform patients about the causes and increased possibilities of false-positive
results for sex chromosome aneuploidies as part of pretest counseling and
screening for these conditions.

Patients should also be informed of the potential for results of conditions that, once
confirmed, may have a variable prognosis (e.g., Turner syndrome) before
consenting to screening for sex chromosome aneuploidies.

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Recommendations and Guidelines
Women who have a no call test result from a cell free DNA screening should:
● receive further genetic counseling
● be offered comprehensive ultrasound evaluation and diagnostic testing

Cell free DNA screenings do not provide information regarding the potential for
open neural tube defects
● women shoud be offered assessment for fetal defects with ultrasonography, maternal
  serum alpha-fetoprotein screening, or both

Cell free DNA screening for microdeletions has not been validated clinically and is
not routinely recommended

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Eurofins Biomnis follows
         the ACOG and SMFM recommendations

  NIPT

Warning sign(s) on ultrasound
NT ≥ 3.5 mm                             INVASIVE
                                       PROCEDURE

                                                 Foetal
                                  Array CGH   karyotyping

In routine practice
at Eurofins Biomnis

Data Eurofins Biomnis

                                    ! TRISOMY 21
                                -     925 positive screening
                                -      3 mosaic trisomies
                                -        8 false positive
                                -       4 false negative

                                                                      TRISOMY 18
    91282 tests                                                  - 169 positive screening
     oct 2014-oct 2019                                               - 7 false positive
(dont 45600 Jan-Oct 2019)

                                              ! TRISOMY 13
                                              ! - 96 positive screening
                                                - 6 false^positive

                                          !          No call rate = 1,15%
                                          !          (4,3 % at 1st attempt)

How to proceed upon receipt of the results

b

Practical details

NIPT REQUEST FORM

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INFORMATION FORM

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BLOOD SAMPLING CONDITIONS

   Sample type: 1 x 10 ml tube of whole blood
   Temperature: Room temperature
   Method: NGS
   TAT: 8 working days
   Sample must be delivered to Eurofins Biomnis Ireland on the same day that
   the blood has been drawn*. You can bring the specimen to our laboratory yourself, or
   please call our Logistics Team on freephone: 1800 252 967 to arrange collection point, free of
   charge. Samples can be collected nationwide.
*To ensure sample viability for lab processing, we accept NIPT samples only on Monday,
   Tuesday and Wednesday.
   Please follow the sampling protocol provided with our NIPT kit. All NIPT requests
   must be accompanied by our patient consent and information form which you will receive
   together with the test kit.

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PRICE AND ADDITIONAL INFORMATIONS

NINALIA TEST 299 EUROS (Harmony test >400 Euros)

Information available on Eurofins Biomnis Ireland website:

                       www.eurofins.ie/biomnis

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Outlook and
conclusions

Conclusion

Detection of circulating foetal DNA in conjunction with NGS

The best screening method in terms of sensitivity and specificity
Non-invasive

Low failure rate
Mostly used for detection of trisomies 13, 18, 21, and sex chromosome aneuploidy

New screening possibilities (detection of Rare Autosomal Trisomies, duplications or
deletions above 7 Mb) (March 2020)

THANK YOU
FOR LISTENING

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