Non-Invasive Prenatal Testing

Developed by Dr. June Carroll, Ms. Shawna Morrison and Dr. Judith AllansonSpecial thanks to the Children’s Hospital of Eastern Ontario’s Prenatal Genetics Team

Last updated April 2014

Disclaimer

• This presentation is for educational purposes only and should not be used as a substitute for clinical judgement. GEC-KO aims to aid the practicing clinician by providing informed opinions regarding genetic services that have been developed in a rigorous and evidence-based manner. Physicians must use their own clinical judgement in addition to published articles and the information presented herein. GEC-KO assumes no responsibility or liability resulting from the use of information contained herein.

Objectives• Following this session the learner will be able to:

― Refer to their local genetics centre and/or order genetic testing appropriately for prenatal screening

― Discuss and address patient concerns regarding prenatal screening

― Facilitate patient informed decision making regarding prenatal screening options

― Find high quality genomics educational resources appropriate for primary care

Case 1

A 32 year old woman has had a positive Integrated Prenatal Screening Test (IPS) result for Down syndrome. She is about 17 weeks gestation.

― Is NIPT a good option?

Case 2

A 40 year old G1 woman is about 9 weeks gestation. She is in your office to discuss prenatal testing options in this pregnancy conceived by IVF.

―Is NIPT a good option?

Case 3

• A 36 year old G1P0 woman is very anxious about Down syndrome in this pregnancy because she had a second cousin with Down syndrome who passed away as a child.― Is NIPT a good option?

Case 4

• A 29 year old patient had a nuchal translucency (NT) of 4.4mm at 12+5 weeks gestation

• You offered NIPT and she accepted• NIPT results were normal. She is now 14+2

weeks gestation

• What are the next steps?

Prenatal Screening tests for:DS, T18, T13 and ONTD

Screening Test Markers Trimester Term Risk Cut Off

DR (%) FPR(%)

FTS

NT, PAPP-A, f-BhCG/total hCG , MA

1st

1/350

85*

5.4*

IPS NT, PAPP-A, AFP, uE3, f-BhCG / total hCG, MA

1st & 2nd 1/200 85.5** 2.5**

Quadruple Screen

AFP, uE3, total hCG, MA

2nd 1/200 82.5* 5.6*

Serum Integrated Screen

PAPP-A, f-BhCG / total hCG, AFP, uE3, inhibinA, MA

1st & 2nd 1/200 Insufficient data 3.3%†

*Estimation based on data from NYGH and MSH screening laboratories. Note there is not complete ascertainment of false negatives

** Estimation based on data from NYGH (Jan 2003-Jun 2011)

† Total positive rate for SIPS from all Ontario labs. This is an estimate for the FPR given the small volume of uptake on this particular screen test.

NIPT Cell free DNA 1st or 2nd n/a >99% <0.1%

What is Non-Invasive Prenatal Testing?• Screening test to prenatally detect Down

syndrome and other aneuploidies (extra or missing chromosomes)― trisomy 21, 18, 13― trisomy of sex chromosomes (XXX, XXY, XYY) ― Turner syndrome (monosomy X)― triploidy (extra copy of all chromosomes)

Non-Invasive Prenatal Testing (NIPT)• NIPT measures circulating cell-free DNA (cfDNA) from

placenta present in maternal blood • Comprises ~10% of DNA in maternal blood• Increases with gestational age• Companies offering NIPT use various technologies to

analyze cfDNA and determine chromosome quantities• Performed on maternal blood sample• As early as 9 weeks gestation (company specific)• Dating U/S – viability, accurate GA, exclude multiples

How good is Non-Invasive Prenatal Testing?

• Moving target• Currently literature is primarily from companies or those

holding patents

*ASHG Oct 2013 platform presentation – data from BGI China; 63,543 pregnancies

Overall ranges

T21 T18 T13

Specificity (%) 99-100 99-100 99-100

Sensitivity (%) 98-100 97-100 79-100

Positive Predictive Value [PPV] (%)

90-95* 84* 52*

Negative Predictive Value [NPV] (%)

99.9 99 100

• Studies emerging in low-risk population• Performance of NIPT in a general obstetrical

population ―False Positive Rate (FPR) for T21 and T18 combined was

0.5% vs 4.2% for standard screening ―Positive Predictive Value (PPV) was significantly higher

than that for standard screening, for both trisomy 21 (45.5% vs. 4.2%) and trisomy 18 (40.0% vs. 8.3%)

Bianchi et al, NEJM 2014; 370:9

What is the evidence for Non-Invasive Prenatal Testing (NIPT)?

What is the evidence for Non-Invasive Prenatal Testing (NIPT)?

• 7 studies of “high risk” women • High risk:

―Screen (IPS, FTS) positive ―AMA (≥35 yrs)―Ultrasound findings suggestive of aneuploidy―Previous pregnancy with aneuploidy

• By far most accurate performance for T21/18

Benn et al, Ultras Obstet Gynecol 2013, 42: 15-33

What is the evidence for Non-Invasive Prenatal Testing (NIPT)?

What do the experts say?

• Society of Obstetricians & Gynecologists of Canada 2013― Non-invasive prenatal testing using massive

parallel sequencing of cell-free DNA to test for trisomies 21, 18, and 13 should be an option available to women at increased risk in lieu of amniocentesis. Pre-test counselling of these women should include a discussion of the limitations of non-invasive prenatal testing.

Genetics Ctte Technical Update JOGC: Feb 2013

What do the experts say?

• Society of Obstetricians & Gynecologists of Canada 2013― No irrevocable obstetrical decision should be

made in pregnancies with a positive non-invasive prenatal testing result without confirmatory invasive diagnostic testing.

Genetics Ctte Technical Update JOGC: Feb 2013

Recommendations• Offer all women:

― Prenatal screening using either FTS, IPS or MSS (SIPS or Quad)

― Fetal morphology scan at 18-20 weeks’ gestation

Consider discussing Non-Invasive Prenatal Testing (NIPT) as an option for women who:

Are of advanced maternal age , defined as 40 years of age or older at estimated date of birthHave an abnormal multiple marker screen i.e. FTS/IPS/MSSHave fetal nuchal translucency (NT) measurement of 3.5mm or greater Have had a previous pregnancy or child with aneuploidy

Have other high risk factors:Fetal congenital anomalies on ultrasound highly suggestive of trisomy 13, 18 or 21*Soft markers on ultrasound which are highly suggestive of aneuploidy [Refer to SOGC guidelines, 2005].* At risk of carrying a male fetus with an X-linked condition (NIPT would be used for sex determination)*

In Ontario, MOHLTC funding applications for the indications above marked by an asterisk (*) must be submitted by a geneticist or maternal fetal medicine (MFM) specialist. In other provinces circumstances may be different. Consult your local genetics centre or MFM specialist.

Non-Invasive Prenatal Testing (NIPT) results

• Results will be reported differently and may be worded as: ― positive or negative ― aneuploidy detected, no aneuploidy detected or

aneuploidy suspected/borderline value ― high risk or low risk

• If the result is negative, this is reassuring • Your patient should still be offered:

― MS-AFP between 15 and 20+6/7 weeks to screen for open neural tube defect, as NIPT does not screen for this physical anomaly

― fetal morphology scan at 18-20 weeks’ gestation― referral for genetic and/or maternal fetal medicine

consultation, which may be indicated for additional counselling and testing, depending on the reason your patient qualified for NIPT (e.g. increased NT, other soft markers, congenital anomalies)

Non-Invasive Prenatal Testing (NIPT) results

• If the result is positive: ― Genetic counselling― Confirmation by diagnostic testing

No irrevocable obstetrical decisions should be made in pregnancies with abnormal NIPT results without confirmatory invasive testing (CVS or amniocentesis) - SOGC

Non-Invasive Prenatal Testing (NIPT) results

Benefits of Non-Invasive Prenatal Testing (NIPT)

• Fewer women having diagnostic tests with associated risk of pregnancy loss

• Early test result (drawn at ≥ 9-10 weeks at earliest)

• No risk of miscarriage• Detects the most common chromosomal

aneuploidies • Higher detection rates and lower false positive

rates than IPS or MSS

Limitations of Non-Invasive Prenatal Testing (NIPT)

• NIPT cannot:― Detect chromosome differences other than aneuploidy of

chromosomes 13, 18, 21, X and Y• some companies are now adding screening for other trisomies and certain

microdeletion syndromes ― Completely rule out aneuploidy― Detect single gene conditions― Detect congenital anomalies

• Failed results― 6.1% untested for insufficient sample quality― 2% no result after testing (rarely happens with conventional screening)

• cfDNA decreases with increased maternal BMI, twin pregnancies and where trisomy 18 and 13 are present

• Limited data on performance in IVF pregnancies

• False positives (and negatives) are possible―Confined placental mosaicism

Limitations of Non-Invasive Prenatal Testing: Confined placental mosaicism

Non-Invasive Prenatal Testing (NIPT) Landscape

• Increasing demand from women • Increasing uptake in most (urban) centres• 3 separate companies, 3 separate technologies• Has NIPT become “standard of care”? • Costs between $795 and $1200• 8-10 days for result

Where does Non-Invasive Prenatal Testing (NIPT) fit with respect to the 11 to 14 wk scan?

• 11 to 14 week scan has value to pregnancy care― Raised NT may suggest other chromosomal, genetic

and structural disorders― Accurate dating/establishment of live fetus― Multiples/chorionicity affects management― Detects structural abnormalities

Non-Invasive Prenatal Testing (NIPT) and counselling

• Pre- and post-test counselling is important• Consult genetics if unsure• Refer for genetic counselling when appropriate• Company websites:

―Harmony Prenatal Test™ by Ariosa Diagnostics through Gamma-Dynacare

―Panorama™ by Natera through Lifelabs―Verifi® Prenatal Test by Verinata

• In Ontario, to order NIPT, first determine your patient’s funding eligibility by looking at the MOHLTC checklist, then:

• Complete the checklist and pages 2 and 4 of the MOHLTC out-of-country testing prior approval form

• Download and complete the requisition from the NIPT company of your and your patient’s choice

― Selection may be based on the patient’s personal research and preference, your experience with a particular company, ease of access to a blood draw location

• Send all three completed forms to the fax number 613 536-3181 or 1 866 221-3536 and be sure to indicate the patient is pregnant so approval can be prioritized accordingly

• Once approval has been received, give the patient the approval letter and the NIPT requisition and she can then have her blood drawn

Ordering Non-Invasive Prenatal Testing (NIPT)

Case 1

A 36 year old woman has had a positive Integrated Prenatal Screening Test (IPS) result for Down syndrome. She is about 17 weeks gestation. ― Is NIPT a good option?

• Yes―She is eligible for NIPT with MOH funding

• But consider:―More rapid result from amniocentesis ―What is her IPS risk?

• 1 in 2 versus 1 in 120 ―She is at 17 weeks gestational age

• If NIPT is positive, guidelines recommend confirmatory diagnostic testing by amniocentesis – delays timing for diagnosis

―In the event of an abnormal result, is termination of pregnancy an option for the couple?

Case 2

A 40 year old G1 woman is about 9 weeks gestation. She is in your office to discuss prenatal testing options in this pregnancy conceived by IVF.

―Is NIPT a good option?

• Yes― Advanced maternal age (greater than 40 years at

EDB) is an appropriate indication for NIPT― Covered by MOH funding― Better screen than IPS― Earlier result ― Decreased chance with NIPT that patient would

receive screen positive result

Case 3

• A 36 year old G1P0 woman is very anxious about Down syndrome in this pregnancy because she had a second cousin with Down syndrome who passed away as a child.― Is NIPT a good option?

Case 3• She does not meet MOH criteria for

coverage of NIPT• You can reassure her that having a second

cousin with Down syndrome does not increase her risk to have an affected child

• If she is very anxious, you can proceed with NIPT and she can pay out of pocket

• If the patient herself had a previous affected pregnancy then she would be eligible for MOH funded NIPT

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Case 4

• A 29 year old patient had an NT of 4.4mm at 12+5 weeks gestation

• You offered NIPT and she accepted• NIPT results were normal. She is now 14+2

weeks gestation

• What are the next steps?

• Genetic counselling is recommended • Patient likely to be offered:

― Chromosomal microarray― Genetic testing for other single gene conditions― Level II ultrasound― Fetal echocardiogram

Prenatal Screening Summary• Offer all pregnant women, regardless of age:

― PN screening for fetal aneuploidy (trisomy 13, 18, 21) through FTS, IPS, SIPS or Quad screening

― Second trimester ultrasound for dating, assessment of fetal anatomy and detection of multiples

• Maternal age should not be used as a basis for recommending invasive testing when non-invasive PN screening is available

• Non-Invasive Prenatal Testing (NIPT)― Consider offering NIPT to high risk women― Consider NIPT as a screen of higher sensitivity if your patient is willing to

pay for the test― Best for Down syndrome (trisomy 21) (but can be wrong!)

• so far, others not as good (T13 and sex chromosomes)― Effectively sampling the placenta (not fetal cells directly)― It is not a diagnostic test― Not an all purpose genetic test, only gives info on specific chromosomes,

and so not indicated in all circumstances

Don’t forget

• Take a family history to identify familial and/or ethnicity-specific disorders and screen accordingly

• Consider consanguinity and screen and test accordingly

• Refer or consult genetics when in doubt

Useful Genetics Resources• GEC-KO website: Genetics Education

www.geneticseducation.ca • NIPT fact sheets:

― http://www.mountsinai.on.ca/care/family-medicine-genetics-program/prenatal

• Prenatal Screening Ontario Website― http://www.prenatalscreeningontario.ca/

• Society of Obstetricians and Gynaecologists of Canada (SOGC) national clinical guidelines in prenatal genetics visit http://sogc.org/clinical-practice-guidelines/ and scroll down to Genetics.