Non-Invasive Prenatal Testing (NIPT)

Developed by Dr. Judith Allanson, Ms. Shawna Morrison and Dr. June Carroll Last updated November 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 regarding 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 scree

ningEthnicity-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 )

AMA – Advanced Maternal Age, ≥40y@EDB

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 ~3-10% 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 T211,4

False Positive Rate for T211,4

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%

~80.9% for all populations (high and low risk women)1 Prenatal Screening Ontario

2 Bianchi et al 2014 N Engl J Med 370:93 Norton et al 2015 N Engl J Med 372:174 Gil et al 2015 Ultrasound Obstet Gynecol 45

Aneuploidy Detection Rate

False Positive Rate

Trisomy 18 96.3% 0.13%Trisomy 13 91.0% 0.13%Monosomy X (Turner syndrome) 90.3% 0.14%

Other sex chromosome aneuploidies

93.0% 0.14%

How does non-invasive prenatal testing perform for other common aneuploidies?

Gil et al 2015 Ultrasound Obstet Gynecol 45

Non-Invasive Prenatal Testing (NIPT) Landscape

• Offered at genetics centres all over Canada– To all vs. high risk varies

• Increasing demand and uptake by women• 3 separate companies, 3 separate

technologies (available in Canada)• Costs about 500$• 8-10 days for result

Recommendations

• Offer to all women:– Conventional 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

Women who have a high risk for having a baby with an aneuploidy

Are of advanced maternal age, defined as 40 years of age or older at estimated date of birth

Have an abnormal multiple marker screen i.e. FTS/IPS/MSS

Have had a previous pregnancy or child with aneuploidy

In consultation with genetics or maternal-fetal-medicine, consider NIPT for women where:

Fetal nuchal translucency (NT) measures 3.5mm or greater

Fetal congenital anomalies on ultrasound are highly suggestive of trisomy 13, 18 or 21

Soft markers on ultrasound are highly suggestive of aneuploidy [Refer to SOGC guidelines, 2005].

There is a risk of carrying a male fetus with an X-linked condition (NIPT would be used for sex determination)

Women who have a high risk for having a baby with an aneuploidy

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

• Labs that report the chance of aneuploidy commonly use “>99%” as indicative of high risk and “<1/10,000” as indicative of low risk, intermediate results are also occasionally reported

Non-Invasive Prenatal Testing (NIPT) results

• 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

Negative result: Low risk

Non-Invasive Prenatal Testing (NIPT) results

• Genetic counselling• Confirmation by diagnostic testing• Consider the positive predictive value (PPV)– www.perinatalquality.org/Vendors/NSGC/NIPT/

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

Positive result: High risk

NIPT and PPVwww.perinatalquality.org/Vendors/NSGC/NIPT/

NIPT and PPVwww.perinatalquality.org/Vendors/NSGC/NIPT/

• Possible explanation for a false positive result• Present in 1-2% of first trimester placentas

Confined Placental Mosaicism

Benefits of Non-Invasive Prenatal Testing (NIPT)

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

• Increased access• 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

• Possibility of no result (~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 (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– www.GeneticsEducation.ca has more information, links to

companies and sample completed forms

• Refer for genetic counselling when appropriate

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

Harmony Prenatal Test™ by Ariosa Diagnostics through Dynacare

Panorama™ by Natera through Lifelabs Genetics

Verifi® Prenatal Test by Verinata through Mount Sinai Services Inc. and Medcan Clinic in Toronto

Ordering Non-Invasive Prenatal Testing (NIPT)

Expansion of non-invasive prenatal testing

• In October 2013 one company expanded their NIPT test menu to include screening for microdeletion syndromes (e.g. 22q deletion/DiGeorge) and trisomies associated with early pregnancy loss (e.g. trisomy 16) and in spring 2014 others followed suit

22q.org – Teddy Bohan, 3y

Expansion of non-invasive prenatal testing

• Clinically relevant microdeletions and duplications occur in 1-1.7% of all structurally normal pregnancies

• Incidence is independent of maternal age• Cumulatively these disorders are common– The combined at-birth incidence of the 5 commonly

offered microdeletion syndromes is approximately 1 in 1,000

• Less women are expected to have invasive procedures and be offered microarray, so these conditions should be added to NIPT

Arguments for NIPT with microdeletions nowArguments for NIPT with microdeletions now

Microdeletion syndrome

Incidence (at birth)Clinical features

Babies born with this syndrome often have:

22q11.2 deletion syndrome/ DiGeorge

1 in 4,000-2,000heart defects, immune system problems, and mild-to moderate intellectual disability. They may also have kidney problems, feeding problems, and/or seizures.

1p36 deletion syndrome

1 in 10,000-5,000weak muscle tone, heart and other birth defects, intellectual disabilities, and behavior problems. About half will have seizures.

Angelman syndrome 1 in 12,000

delayed milestones (like sitting, crawling and walking), seizures, and problems with balance and walking. They also have severe intellectual disability and most do not develop speech.

Prader-Willi syndrome

1 in 25,000- 10,000

low muscle tone and problems with feeding and gaining weight. They also have intellectual disability. As children and adults, they have rapid weight gain and often develop obesity related medical problems.

Cri-du-chat syndrome (5p-)

1 in 50,000- 20,000

low birth weight, small head size, and decreased muscle tone. Feeding and breathing difficulties are also common. They have moderate-to-severe intellectual disability.

Expansion of non-invasive prenatal testing

• There are no published clinical validation studies, only proof of concept• There are no guidelines – not considered standard of care• Because these are low-prevalence disorders, false positive results are

inevitable and the positive predictive value will be low– Undermine benefit of NIPT reducing the number of women undergoing invasive

testing– Uncertainty about the prenatal prevalence

• Informed consent– Familiarity with rare conditions– Familiarity with testing limitations

• E.g. 22q - 85% of individuals with 22qdeletion will have typical full deletion screened for by NIPT while 15% will have ‘nested’ deletions within the region; ~ 65-70% of Angelman syndrome is caused by (maternal) deletions at 15q11.2 screened for by NIPT while others will have various other genetic mechanisms

• Provinces are not currently funding

Arguments against NIPT with microdeletions nowArguments against NIPT with microdeletions now

How does NIPT perform with microdeletions?

• Yes– She is at high risk to have a baby with aneuploidy

• May be eligible for provincial funding where applicable

• 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

Back to case 1: IPS positive, 17W GA Is NIPT a good option?

Back to case 2: 40yo G1 Is NIPT a good option?

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

EDB) is an appropriate indication for NIPT– Covered by some provincial health plans– Better screen than IPS– Earlier result – Decreased chance with NIPT that patient would

receive screen positive result

Back to case 3: NT 4.4mm, low risk NIPT 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, diagnostic testing should follow a positive result

• Not an all purpose genetic test, only gives info on specific chromosomes, and so not indicated in all circumstances

Resources

• See www.geneticseducation.ca for more details and how to connect to your local genetics centre and the GECKO on the run resource for more information

• For a recent review on NIPT see Cuckle H, Benn P, Pergament E. Cell-free DNA screening for fetal aneuploidy as a clinical service. Clin Biochem 2015; [Epub ahead of print]