Non-Invasive Prenatal Testing (NIPT)

Developed by Dr. June Carroll, Ms. Shawna Morrison and Dr. Judith Allanson

Last updated April 2015

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 non-invasive prenatal testing (NIPT)

– Discuss and address patient concerns regarding NIPT– Find high quality genomics educational resources

appropriate for primary care

Typical Prenatal Testing Algorithm

Offer PN screening to all pregnant womenOffer PN screening to all pregnant women

18-20 week fetal morphology scan18-20 week fetal morphology scan

FTS/IPS/SIPSFTS/IPS/SIPS NIPT for AMA and for women willing to payNIPT for AMA and for women willing to pay Family historyFamily history Ethnicity-based

screeningEthnicity-based

screening

If positive

*for ethnicity-based screening, if both members of the couple are carriers of the same condition

If negative or decline

Refer to GeneticsRefer to Genetics

If indicated (e.g. fetal anomalies )

Additional Testinge.g. Chromosomal

microarray

Prenatal Testing Algorithm for Women at Increased Risk

IndicationAdvanced maternal age, multiple soft markers on ultrasound, ultrasound

anomaly, positive prenatal screen, etc.

IndicationAdvanced maternal age, multiple soft markers on ultrasound, ultrasound

anomaly, positive prenatal screen, etc.

Genetic counselling with testing optionsGenetic counselling with testing options

No further testingNo further testing Screening Teste.g. NIPT

QF-PCRDetects common aneuploidies: Down syndrome, Trisomy 18, Trisomy 13 and sex chromosome aneuploidies

QF-PCRDetects common aneuploidies: Down syndrome, Trisomy 18, Trisomy 13 and sex chromosome aneuploidies

KaryotypeKaryotype

No further testingNo further testing

If positiveIf negative

Depending on indication:•No further testing•Consider additional testing

If negativeIf positive

Invasive Testing(diagnostic)

Invasive Testing(diagnostic)

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 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?

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)

• NIPT measures circulating cell-free DNA (cfDNA) from placenta present in maternal blood

• ‘fetal’ cfDNA 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)• Prior U/S preferable– viability, accurate GA, exclude

multiples

What is Non-Invasive Prenatal Testing?

How does non-invasive prenatal testing compare to traditional prenatal screening for Down syndrome?

Screening test Test info Detection rate / Sensitivity for T211

False Positive Rate for T211

Positive predictive value for T212,3

FTS MA, NT, PAPP-A, beta-hCG

80-85% 3-9%

~4%

IPS MA, NT, PAPP-A, AFP, uE3, hCG

85-90% 2-4%

Quad/MSS MA, AFP, uE3, total hCG, inhibin

75-85% 5-10%

SIPS MA, PAPP-A, AFP, beta-hCG/total hCG, uE3, inhibin

80-90% 2-7%

NIPT

+/-MA, cfDNA

>99%

0.1-0.2%

~80.9% for all populations (high and low risk women)

1 Prenatal Screening Ontario2 Bianchi et al 2014 N Engl J Med 370:93 Norton et al 2015 N Engl J Med Apr 1 [Epub ahead of print]

Non-Invasive Prenatal Testing (NIPT) Landscape

• Increasing demand from women • Increasing uptake in most (urban) centres• 3 separate companies, 3 separate

technologies• Costs between $795 and $1200• 8-10 days for result

Recommendations

• Offer to all women:– Prenatal screening using either FTS, IPS or MSS (SIPS or

Quad)– Fetal morphology scan at about 18-20 weeks gestation

• Consider NIPT as an option for women who have a high risk for having a baby with an aneuploidy

Consider offering Non-Invasive Prenatal Testing (NIPT) 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 a 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].* Are 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.

Consider offering Non-Invasive Prenatal Testing (NIPT) for women who:

Non-Invasive Prenatal Testing (NIPT) results

• Results will be reported in various ways and may be worded as: – positive or negative – aneuploidy detected, no aneuploidy detected or

aneuploidy suspected/borderline value – high risk or low risk

Non-Invasive Prenatal Testing (NIPT) results

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

– As per SOGC guidelines, MS-AFP should only be offered to pregnant women with a pre-pregnant body mass index ≥ 35 kg/m2 or when geographical or clinical access factors limit timely and good quality ultrasound screening

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

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%)– 1/2- 2/3 can be successfully resolved with redraw at later gestation

• False positives and false negatives • Twins and IVF pregnancies

Non-Invasive Prenatal Testing: Discordant results

Wang et al 2014 Genet in Med 17(3)Cheung et al 2015 N Engl J Med [Epub ahead of print]

Condition OverallTrue Positive

Overall False Positive

Down syndrome 91-93% 6-9%

Trisomy 18 60-77% 23-47%

Trisomy 13 44-54% 46-56%

Sex chromosome abnormality (varies with type e.g. Monosomy X, XXY, XYY)

38-88% 12-100%

Limitations of Non-Invasive Prenatal Testing: Biological factors

• Vanishing twin• Fetal fraction (ff)• Mosaicism

• Fetal fraction (ff)– Is the amount of fetal cfDNA divided by total

(maternal and fetal) cfDNA– Low ff result in test failures (<4%)– Is affected by:

• Maternal BMI • Gestational age• Multiple gestations

– Higher overall ff, but lower per fetus, risk of false negative

• Mosaicism – High level of mosaicism vs low level mosaicism

Limitations of Non-Invasive Prenatal Testing: Biological factors

• Confined placental mosaicism – Present in 1-2% of first trimester placentas

Limitations of Non-Invasive Prenatal Testing: Biological factors

Limitations of Non-Invasive Prenatal Testing: Control and Standards

• Takoudes and Hamar (2014) made headlines when blood samples from 2 non-pregnant women were sent to 5 American commercial labs offering NIPT– 3/5 labs reported normal result (no aneuploidy)– 2/5 labs unable to report due to low fetal fraction

Non-Invasive Prenatal Testing (NIPT) and counselling

• Pre- and post-test counselling is important– Invasive testing following positive results– Conditions tested for in addition to T21– Incidental findings

• Consult genetics if unsure– Geneticseducation.ca has more information, links to companies and

sample completed forms

• Refer for genetic counselling when appropriate• Company websites:

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

– Panorama™ by Natera through Lifelabs/CML– Verifi® Prenatal Test by Verinata through Mount Sinai Services Inc. or

Medcan Clinic

• www.geneticseducation.ca • Educational Resources > GECKO on the run > NIPT

Ordering Non-Invasive Prenatal Testing (NIPT) in Ontario

Expansion of non-invasive prenatal testing• In October 2013 one company expanded their NIPT test to

include screening for microdeletion syndromes (e.g. 22q deletion/DiGeorge and trisomies 16 and 22), and in spring 2014 others followed suit

• Rationale: – Cumulatively common disorders

• The combined at-birth incidence of the 5 commonly offered microdeletion syndromes is approximately 1 in 1,000

– Incidence is independent of maternal age• Appear to have high sensitivity BUT no clinical validation

studies, no guidelines, rare conditions decrease PPV and increase FPR

• No MOHLTC approval

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:– In the event of an abnormal result, is termination of

pregnancy an option for the couple? – More rapid result from amniocentesis, consider GA

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

– What is her IPS risk? • 1 in 2 versus 1 in 120

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 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

Non-Invasive Prenatal Testing Pearls

• Consider offering NIPT to high risk women• Consider NIPT as a screen of higher sensitivity

than current screening if your patient is willing to pay for the test

• Not a diagnostic test• Not an all purpose genetic test, only gives info

on specific chromosomes, and so not indicated in all circumstances

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 the basis for recommending invasive testing when non-invasive PN screening is available

• Prenatal testing menu continues to evolve and expand with new screening and diagnostic tests

• More, complex options may add to patient’s decisional conflict

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

Resources• NIPT GECKO on the run• GEC-KO website: Genetics Education

• www.geneticseducation.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.

• Recent Reviews:– Cuckle H, Benn P, Pergament E. Cell-free DNA screening for fetal

aneuploidy as a clinical service Clin Biochem. 2015; [Epub ahead of print]

– Bianchi D and Wilkins-Haug L. Integration of non-invasive DNA testing for aneuploidy into prenatal care: What has happened since the rubber met the road? Clin Chem 2014; 60:1