Non-Invasive Prenatal Testing

Transcript Non-Invasive Prenatal Testing

THE VERIFI® PRENATAL TEST – MAKING A DIFFERENCE IN PATIENT SAFETY

L A W R E N C E D. P L A T T , M D P R O F O B G Y N U C L A S C H O O L O F M E D I C I N E P E R E S C E N T E R F O R P E A C E T E L AV I V Y A F O J U L Y 1 , 2 0 1 3

THE VERIFI® PRENATAL TEST: NIPT TECHNOLOGY OVERVIEW

Prenatal Prevalence of Chromosomal Abnormalities

Percent of Reported Chromosome Abnormalities 16 8 5 5 13 53

Major fetal aneuploidies T21 T18 T13 45,X Sex trisomy Other rare Data adapted from Wellesley, D, et al., Rare chromosome abnormalities, prevalence and prenatal diagnosis rates from population-based congenital anomaly registers in Europe.

Eur J of Hum Gen

, 11 January 2012.

PRENATAL SCREENING OPTIONS – RISK SCORE

Down Syndrome Testing with 5% Screen Positive Rate 1 st Trimester NT Ultrasound 1 st Trimester 2 nd Trimester 2 nd Trimester Integrated Screen Serum Integrated 1 st Trimester Blood Screen NT Ultrasound Triple Screen Quadruple Screen 1 st Trimester Blood Screen NT Ultrasound 2 nd Trimester Blood Screen 1 st Trimester Blood Screen 2 nd Trimester Blood Screen

Detection Rate (%) 64-70 82-87 69 81 94-96 85-88 ACOG Practice Bulletin No. 77, January 2007 .

CURRENT DIAGNOSTIC OPTIONS KARYOTYPE

Trimester - Test 1 st – CVS Sensitivity 99.25% 1 Specificity 98.65% 1 2 nd - Amniocentesis 99.4% 2 99.5% 2

Definitive answers, but are invasive and come with risk to the patient Most are unnecessary due to the high rate of false positives in screening**

Hahnemann JM, Vejerslev LO. Accuracy of cytogenetic findings on chorionic villus sampling (CVS)--diagnostic consequences of CVS mosaicism and non-mosaic discrepancy in centres contributing to EUCROMIC 1986-1992. Prenat Diagn. 1997 Sep;17(9):801-20.

Mid-trimester amniocentesis for prenatal diagnosis. Safety and accuracy. JAMA. 1976 Sep 27; 236(13): 1471-6.

SPECTRUM OF PRENATAL TESTING

SCREENING

Risk scores are generated and modified based on biochemical analysis and population statistics

Serum Screening Combined Serum Screens, NT, Ultra sound DIAGNOSTIC

Results are based entirely on genetic factors

NIPT CVS Amnio SCREENING

*Not meant to represent percentage of accuracy

DIAGNOSTIC

WHAT ARE THE GOALS OF NIPT?

Reduce exposure of fetus to risk Reduce false positives Testing that can easily be offered to all pregnant women Enable a high detection rate .

TWO SOURCES OF FETAL DNA IN MATERNAL BLOOD

•

Fetal cells

• 1 in a billion of total cell population • Require isolation via mechanical and/or biochemical means •

Cell-free DNA (cfDNA)

• Maternal blood contains both maternal and fetal cfDNA • 2 –20% of total cfDNA is fetal .

FETAL CELL-FREE DNA IN MATERNAL BLOOD

A Reliable Analyte During Pregnancy

• Released through apoptosis • Fetal cfDNA likely arises from cytotrophoblastic cells of placenta • Released into bloodstream as small DNA fragments (150-200bp) • Reliably detected after 7+ weeks gestation • Undetectable within hours postpartum .

DNA SEQUENCING USING CELL FREE DNA

Fetal DNA fragments in maternal blood.

Cell free DNA fragments are then sequenced.

Compare the individual sequenced chromosomes against a reference for analysis.

VERINATA’S MASSIVELY PARALLEL SEQUENCING (MPS)- A SUPERIOR APPROACH

MPS Provides Precise, Across the Genome Coverage Benefits

• Lowest Assay Failure Rates <1% • Ability to rapidly add new content to test menu. Verinata’s approach allows rapid evolution of product •22.8 Million reads

Targeted Sequencing is Limited to Few Chromosomes, Loci Drawbacks

DETECTION OF FETAL ANEUPLOIDY

MPS Enables Precise Molecular Counting Fetal cfDNA (20%) NOT TO SCALE Counting 10% more Chr21 cfDNA in T21 Maternal cfDNA Chromosomes: 1 2 VS …… 3 21 Trisomy 21

DUAL THRESHOLD CLASSIFICATION

Indicates Borderline Results

Trisomy Diploid

verifi ® prenatal test Dual Threshold

VS.

0.2 to 0.6 %

Single Threshold Method

PUBLICATIONS IN MOST PRESTIGIOUS JOURNALS IN FIELD

• Large-scale,

prospective

and

blinded

clinical trials • Only study in the industry that represents real-world clinical use • High-risk patient population • Singleton gestations analyzed • Over 60 U.S. centers enrolled .

VERIFI

PRENATAL TEST PERFORMANCE

Trisomy 21 Trisomy 18 Trisomy 13

Sensitivity

>99.9% 97.4% 87.5%

Sensitivity 95% CI

96.0 – 100.0

86.2 – 99.9

61.7 – 98.5

95% CI Specificity

99.8% 99.6% >99.9%

Specificity 95% CI

98.7 – 100.0

98.5 – 100.0

99.2 – 100.0

95% CI

Monosomy X XX 95.0% 97.6% 75.1 – 99.9

94.8 – 99.1

99.0% 99.2% 97.6 – 99.7

97.2 – 99.9

XY 99.1% 96.9 – 99.9

98.9% 96.9 – 99.8

XXX, XXY, XYY Limited data of these more rare aneuploidies preclude performance calculations.

Verinata Health, Inc. Data on file.

Original Publication: * Bianchi et al.

Obstetrics and Gynecology

, Vol 119, No. 5, May 2012

LARGE CLINICAL TRIALS

Source: ISPD Position Statement April 2013

SEX CHROMOSOME ANALYSIS

SEX CHROMOSOMES ANEUPLOIDY

WHY

?

CONSIDERATION OF NIPT FOR

CYSTIC HYGROMA

• Highly associated with common aneuploidies including monosomy X (Turner syndrome) that are associated with pregnancy loss and are medically significant at birth.

• Prevalence ~1:285 • To study, we examined performance of NIPT for patients with cystic hygroma in the MELISSA study Bianchi, et al,

Obstetrics and Gynecology

, Vol 121, No. 5, May 2013

Cystic hygroma

MPS OF MATERNAL PLASMA DNA IN CYSTIC HYGROMA

• Electronic clinical database of the MELISSA study was searched to identify women carrying singleton fetuses with cystic hygroma • 113 cases were identified—69 (61%) had chromosome abnormalities, but 4 had abnormalities other than T21, T18, T13, or monosomy X • Archived plasma samples were sequenced using updated chemistry • Samples were classified for aneuploidy status of chromosomes 21, 18, 13, and presence or absence of monosomy X , Vol 121, No. 5, May 2013 21

MPS and Fetal Nuchal Cystic Hygroma

Obstet Gynecol 2013;121:1057–62

CYSTIC HYGROMA: SEQUENCING RESULTS

•

113 cases

• 29/30 cases of T21 detected, 1 suspected • 20/21 cases of monosomy X detected • 10/10 cases of T18 detected • 2/4 cases of T13 detected, 1 suspected • None of the 44 euploid cases was called positive

CONCLUSIONS AND PRACTICE IMPLICATIONS

• Using sequencing of 4 chromosomes, 61/65 (94%) of aneuploid cases were detected and two more were suspected • Overall, 107/113 (95%) of cases were correctly classified • 4 cases were “other” and 2 aneuploidies were not detected • NIPT for aneuploidy can be considered as an immediate noninvasive point of care test at time of sonographic diagnosis of cystic hygroma.

• Allow management to move forward for women who decline, do not have access, or have a contraindication to an invasive procedure.

DISCORDANT RESULTS

Case

• Second Trimester Ultrasound Male Genitalia VERIFY …… XY • Amniocentesis ………46,XX WHAT NEXT???????????

TEST PERFORMANCE IN “ REAL WORLD POPULATION”

May 2013

Initial clinical laboratory experience in noninvasive prenatal testing for fetal aneuploidy from maternal plasma DNA samples Tracy Futch1, John Spinosa2,3, Sucheta Bhatt1, Eileen De Feo2, Richard P. Rava4 and Amy J. Sehnert5* DOI: 10.1002/pd.4123

•

5, 974 patients

•

Positive Predictive value of 99.8%

•

Negative Predictive Value of 99.92%

•

Turn around time 5.1 days

•

Assay failure rate of 0.7%

Quantity Not Sufficient Cancelled by Phs/Pat Sample received beyond stability Gestational Age less than 10 Weeks Sample Improperly Labeled Test Valid for Singletons Only Interfering Substances (too much cfDNA) Duplicate Specimen Improper sample type NY State Permit Denied Internal Processing Error Unable to isolate sufficient cfDNA Sample integrity compromised Sample lost or destroyed during shipping Expired Tube Red text indicates a technical test failure 0.53% 0.23% 0.22% 0.15% 0.13% 0.09% 0.08% 0.04% 0.03% 0.03% 0.01% 0.01% 0.01% 0.01% 0.01% © 2013 Verinata. Content is proprietary and confidential.

Test Cancellations: Rolling 6 month window, ending May 2013 1,46% 98,4% 0,10% Total Samples Reported Administrative Cancellations Technical Test Failures

KEY DIFFERENTIATORS – CLINICAL TEST

• • • Low assay failure rate and need for re-draw (<1%) Low TAT (Average TAT 4 days, 95% 8 days) Sample requirement – 1 tube (7-10 mL) maternal blood only Weeks Matter! • • • Broadest validated test menu including sex chromosomes Accept samples from ART pregnancies including egg donors Result type – Clear and descriptive for physicians • • Non risk score Independent of other pre-test factors (i.e., gestational age, maternal age) © 2013 Verinata. Content is proprietary and confidential.

NIPT TEST COMPARISON

Result Types Assay Failure Rate Sample verifi® Verinata

• Aneuploidy Detected • Aneuploidy Suspected • No Aneuploidy Detected

<0.7% 1 tube

blood maternal

Egg Donors Test Menu Published Clinical Validation Harmony Ariosa Risk score

incorporating maternal, gestational age 4.6 – 4.9%

MaterniT21 Sequenom

• Positive • Negative 1%

NIPT Natera Risk score

incorporating maternal, gestational age 5.9 – 12.6% Yes (with data) T21, T18, T13 Optional sex chromosome aneuploidies (Published data) Large-scale, blinded clinical validation 2 tubes maternal blood 2 tubes maternal blood No Yes T21, T18, T13 Y chromosome (optional)(not published) Large-scale, blinded clinical validation T21, T18, T13 Mandatory sex chromosome aneuploidies (not published) Large-scale, blinded clinical validation 2-4 tubes maternal blood (best with paternal sample) No T21, T18, T13 Sex chromosome aneuploidies (only MX published) Small, blinded clinical validation

NIPT IS A GAME CHANGER

EFFECT OF NIPT ON INVASIVE TESTING: EVMS

100 90 80 70 60 50 40 30 20 10 0 2004 2006 2008 2010 2012 CVS

INVASIVE PROCEDURE UPDATE BY MONTH

(7/2010 THROUGH 3/2013)

IMPACT OF INVASIVE TESTING IN PATIENTS WITH A POSITIVE FIRST OR SECOND TRIMESTER SCREEN

NIPT RESULTS FROM CFFM 6/1/2010 THROUGH 3/31/2013 POSITIVE FIRST AND SECOND TRIMESTER SCREEN

• Total patients seen 6/1/2010 – 3/31/2013: 808 • Total procedures performed 6/1/2010 – 3/31/2013: • Total singleton, non-ONTD patients seen: • Total singleton, non-ONTD procedures performed: 539 728 500 Total patients seen Total singleton, non-ONTD, patients seen Total procedures performed Total singleton, non-ONTD procedures performed

6/2010 – 10/2011 10/2011 – 3/2013

362 446 323 405 283 262 256 238 .

NIPT STATUS AND DECLINING INVASIVE TESTING

CHANGING TRENDS IN PRENATAL DIAGNOSIS THE PLATT EXPERIENCE

Amnio CVS Total

2010 (%)

8.0

4.0

12.0

2011 (%)

6.0

3.9

9.9

2012 (%)

4.2

3.0

7.2

2013 (%)

Next slide Next slide

CHANGING TRENDS IN PRENATAL DIAGNOSIS THE PLATT EXPERIENCE JANUARY THROUGH MAY BY YEAR

Amnio CVS Total

2010 (%)

7.5

4.4

11.9

2011 (%)

7.5

2012 (%)

5.3

4.6

12.1

3.5

8.8

2013 (%)

2.7

3.4

6.1

UPTAKE OF NIPT IN WOMEN FOLLOWING POSITIVE ANEUPLOIDY SCREENING CHETTY S, GARABEDIAN MJ, NORTON ME. PRENAT DIAGN 2013; 33: 542-546

• • Norton et al observed an increased uptake of NIPT following abnormal 1 st ∆ screening compared with abnormal 2 nd ∆ screening (56% vs 37%) This study revealed that women with a positive aneuploidy screening result are influenced by NIPT for their follow-up testing • When the procedure-associated risk is eliminated, women may be less likely to decline testing

CALIFORNIA PDC EXPERIENCE WITH NIPT

Data for patients with initial PDC visit (January – 2013) March # of pts offered NIPT at PDC

# of PNS screen positive pts offered/requested NIPT PNS screen positive patients accepting NIPT PNS screen positive patients declining NIPT

# of patients offered/requesting NIPT for other indications (i.e., maternal age, US abnormality, US marker, etc.)

Pts with other indications accepting NIPT Pts with other indications declining NIPT

# of patients coming to PDC with prior NIPT results through OB TOTAL PATIENTS HAVING NIPT PERFORMED Totals

3,400 1,063 454 609 2337 661 1676 147 1,262

CALIFORNIA PDC EXPERIENCE WITH NIPT

Data for patients with initial PDC visit (January – 2013) March Total # of NIPT positive results

Number of NIPT positive patients having diagnostic procedures: T21 confirmed by CVS/amnio/other T18 confirmed by CVS/amnio/other T13 confirmed by CVS/amnio/other 45,X/other confirmed by CVS/amino/other Normal karyotype (false positive) confirmed by CVS/amnio/other

SUB-TOTAL OF NIPT POSITIVE RESULTS W/ DIAGNOSIS Totals

53 29 16 3 3 2 5 29

OFFICIAL SOCIETY STATEMENTS

The National Society of Genetic Counselors (NSGC) currently supports Noninvasive Prenatal Testing/Noninvasive Prenatal Diagnosis (NIPT/NIPD) as an option for patients whose pregnancies are considered to be at an increased risk for certain chromosome abnormalities. NSGC urges that NIPT/NIPD only be offered in the context of informed consent, education, and counseling by a qualified provider, such as a certified genetic counselor. Patients whose NIPT/NIPD results are abnormal, or who have other factors suggestive of a chromosome abnormality, should receive genetic counseling and be given the option of standard confirmatory diagnostic testing

• •

cfDNA should not be part of routine prenatal lab assessment, but should be an informed patient choice after pretest counseling cfDNA should not be offered to low-risk women or women with multiple gestations – not yet sufficiently evaluate d

• Negative cfDNA test result does not ensure an unaffected pregnancy • Patient with a positive test should be referred for genetic counseling and offered

invasive PND for confirmation

• cfDNA does not replace the accuracy and diagnostic precision of PND w/ CVS or

amnio

•

Reliable cfDNA screening methods have only been reported for trisomy 21 and 18. cfDNA screening results have been reported for trisomy 13 but the numbers are not large and efficacy appears to be less than for trisomies 21 and 18. cfDNA screening results have also been reported for sex chromosome aneuploidy and the efficacy is unacceptably low.

•

There are insufficient data available to judge whether any specific cfDNA screening method is most effective.

•

The tests should not be considered to be fully diagnostic and therefore are not a replacement for amniocentesis and CVS.

•

Analytic validity trials have been mostly focused on patients who are at high risk. Efficacy in low risk populations has not yet been fully demonstrated .

•

There is insufficient information to know how well the test will perform in multiple gestation pregnancies

ISPD Position Statement April 2013

•

In a proportion of cases there is insufficient fetal cfDNA in the maternal plasma specimen or there is test failure for other reasons.

•

Specific independently developed laboratory minimum standards, quality control, proficiency testing and inspection requirements have not yet been developed for this testing.

•

It has not been demonstrated that the test can be provided in a cost-effective, timely, and equitable manner to total populations

ISPD Position Statement April 2013

FUTURE HORIZONS

• Large studies in low-risk populations • Studies in multiple gestations • Detection of sub-chromosomal abnormalities • cfDNA and pregnancy complications • Treatment of genetic syndromes (Downs)

CELL-FREE FETAL DNA IN MULTIPLES

Presented at SMFM, Feb. 2013

Study Objective

: Effects of Multiple Gestation on Aneuploidy Detection and the Relative Cell-free Fetal DNA (cffDNA) per Fetus About.com

RESULTS: FF/FETUS DISTRIBUTION FOR TWIN AND SINGLETON PREGNANCIES

0,3 0,25 0,2 0,15 0,1 0,05 0 0 0,05 0,1 0,15 0,2 Fetal Fraction per Fetus 0,25

0,3 0,35 Twins Singletons

RESULTS: CALCULATED

S FOR TWINS

Chorionicity

Dichorionic (n=19) (Both male) Dichorionic ([n=26) (different genders) Monochorionic (n=3)

Singleton (n=160) Karyotype

46,XY/46,XY 47,XY+21/46,XY 46,XY/46,XX 46,XY/46,XY 47, XY+18/47,XY+18

46,XY Total FF

0.124

0.082

FF/Fetus

0.062

0.041

0.068

0.113

0.073

0.126

0.068

0.057

0.037

0.126

RESULTS: DEEPER SEQUENCING (16 TWINS)

NCVs for Trisomy 21 and 18 Increase with Deeper Sequencing

• Sequencing with more sequence tags/sample (180M versus 25M) reduces the standard deviation of the measurement and increases the NCV • The measurement leads to more confidence at the same

CONCLUSIONS FROM THE STUDY

• Autosomal Aneuploidies in 2 Twin Cases Here Were Correctly Classified • However,

Deeper Sequencing

is Required to Classify Samples from Multiple Gestations with High Confidence due to the Lower Fetal Fraction per Fetus • The Deeper Sequencing Approach Provides a “Safety Net”, Thereby Reducing the Potential Number of False Negative Cases © 2013 Verinata. Content is proprietary and confidential.

The performance of screening for trisomy 21 and trisomy 18 by NIPT using chromosome-selective sequencing in a routine population is as effective as previously reported in high-risk groups with DR 99% and FPR 1%.

Am J Obstet Gynecol 2012;207:374.e1-6.

On the basis of existing data, NIPT can potentially be used in universal screening for trisomies 21 and 18 in all singleton pregnancies and the main limiting factor for such widespread application of the test at present is the associated cost.

Am J Obstet Gynecol 2012;207:374.e1-6.

CHROMOSOMAL MICROARRAY FOR PND

N Engl J Med 2012; 367 (23): 2175-84

NON-INVASIVE SUBCHROMOSOMAL ANALYSIS Noninvasive Detection of Fetal Subchromosome Abnormalities via Deep Sequencing of Maternal Plasma Anupama Srinivasan

1 ,

Diana W. Bianchi

2 ,

Hui Huang

1 ,

Amy J. Sehnert

Richard P. Rava

and

The American Journal of Human Genetics, Volume 92, Issue 2, 167-176, 10 Jan 2013

CFDNA AND DETECTION OF 22Q11

Clin chem. 2012; 58:1148-51

This work shows that in nonmosaic cases, it is possible to obtain a fetal molecular karyotype by MPS of maternal plasma cfDNA that is equivalent to a chromosome microarray and in some cases is better than a metaphase karyotype Am J Hum Genet 2013;92:167-76

Exciting Time

•Advancement in ultrasound technology

•Early & accurate diagnosis of fetal congenital abnormalities

•NIPT on cfDNA in maternal plasma

•Early screening of fetal karyotypic abnormalities

Expand access for fetal intervention

How does Verifi® make pregnancy safer?

NIPT

MAKING PRENATAL DIAGNOSIS SAFER

1. NIPT broadens the available prenatal testing options for women

•

2. NIPT offers an alternative to invasive diagnostic testing for women with screen positive fetuses

•

With high sensitivity and specificity for T18 and T21 (T13 performance somewhat poorer comparatively)

NIPT

MAKING PRENATAL DIAGNOSIS SAFER

3. NIPT offers reassurance to those women for whom invasive diagnostic testing was not an acceptable option 4. NIPT removes the risk of procedure-related risks and women may be less likely to decline testing

הדות

THANK YOU

1 ST TRIMESTER CONTINGENT SCREENING FOR T21 BY BIOMARKERS AND MATERNAL BLOOD CELL-FREE DNA TESTING NICOLAIDES KH, ET AL. ULTRASOUND OBSTET GYNECOL 2013; DOI: 10.1002/UOG.12511 (AHEAD OF PUBLICATION)

• Objective of study is to define cut-offs w/DRs and FPRs in T21 screening using maternal age and combinations of 1 st ∆ biomarkers to determine which women should undergo contingent maternal blood cell-free DNA (cfDNA) testing • March 2006 through May 2012, prospective analysis using biomarkers (NT, DV-PIV at 11+0 to 13+6 weeks, and ß-hCG, PAPP-A, PIGF, and AFP at 8+0 to 13+6 weeks

• • Contingent screening offers 98% DR of T21 fetuses; overall invasive testing rate <0.5% can be potentially achieved through cfDNA testing to • 36% combined test alone • • 21% using combined test + PIGF and AFP 11% using combined test + PIGF, AFP and DV-PIV Conclusion: • Effective 1 st trimester screening for T21 with DR of 98% and invasive testing rate <05% can be potentially achieved by contingent screening incorporating biomarkers and cfDNA.

POTENTIAL REASONS FOR DISCORDANT RESULTS

Technology

• • MPS counting statistics follow a normal distribution Classification cut-off sets likely false positive rate • 3 standard deviations above mean cut-off yields 0.13% FP • 4 standard deviations above mean cut-off yields 0.003% FP

Biology

• • • • Placental mosaicism reflected in cfDNA (similar to CVS) Vanishing twin may be reflected in cfDNA Maternal Fetal fraction

DISCORDANT RESULTS

Case Discussion

• Maternal aneuploidy • • • NIPT: Detected XXX CVS: 46,XX Maternal karyotype: Mosaic 46,XX[44]/45,X[5]/47,XXX[1] • Co-twin demise • • • NIPT: Detected 13 Amnio: normal karyotype Co-twin demise reported in first trimester • Low fetal fraction • False negative T21

DISCORDANT RESULTS

Case Discussion

• Confined placental mosaicism • • • • NIPT: Detected 13 CVS FISH: mosaicism for trisomy 13 Cultured CVS: normal karyotype Amnio (FISH and cultured cells): normal karyotype • Maternal malignancy • • • NIPT: Double detected 13 and 18 (confirmed on repeat testing) Amnio: normal karyotype Patient diagnosed with cancer postpartum

DISCORDANT RESULTS

Case Discussion

SUMMARY VERIFI® TEST

• • • Low assay failure rate and need for re-draw (<1%) Lowest TAT in industry (Average TAT 4 days, 95% 8 days) Sample requirement – 1 tube (7-10 mL) maternal blood only Weeks Matter! • • • Broadest validated test menu including sex chromosomes Accept samples from ART pregnancies including egg donors Result type – Clear and descriptive for physicians • • Non risk score Independent of other pre-test factors (i.e., gestational age, maternal age) © 2013 Verinata. Content is proprietary and confidential.

APPENDIX

Product Profile Chromosomes Analyzed Blood draw requirement Patient Eligibility Sample collection Turn-around time Clinical Support Cancellation Rate

21, 18, 13, and (Optional) X and Y 1 blood tube (7-10mL) Validated in high risk pregnancies Singletons at ≥10 weeks gestation On-site collection kits, ambient shipping Average of 4 days with 95% within 8 days In-house genetic counselors for consultation with healthcare providers <1% (0.14% current rate) 77

VERIFI

PRENATAL TEST

Test Report

• Red alert at top to highlight abnormal results • Abnormal results are highlighted in red • Comments included to provide additional guidance • Test claims restated as reference

VERIFI

PRENATAL TEST LIMITATIONS

Test designed to detect full chromosomal aneuploidies, and has been validated for chromosomes 21, 18, 13, X and Y.

Possibility test results might not reflect the chromosomes of the fetus, but may reflect chromosomal changes to the placenta or of the mother.

Does not eliminate the possibility of other chromosomal abnormalities, birth defects, or other genetic disorders.

Not currently for use in multiple gestations.

VERIFI

PRENATAL TEST DISCLAIMERS

If definitive diagnosis desired, invasive procedures are suggested to confirm detected and suspected (borderline) results.

Test results should always be used in the context of all available clinical findings.

How the test is used is at the discretion of the healthcare provider.

FOLLOW-UP AND OUTCOMES

• All “Detected” and “Suspected” results are called out to a client by a Genetic Counselor • Outbound Calls • • • Collect relevant pre-test indication when calling result Indicate interest to collect follow-up information if/when available Call (or fax request) for follow-up at or near due date • Inbound Calls • • Record information that is called from sites If discordance, file complaint and follow internal process

VERIFI

TEST ADVANTAGES

• Non-invasive reassurance, available as early 10 weeks • Not affected by maternal factors (like serum screen) • Can be used in IVF and with egg-donor pregnancies • Higher sensitivity and specificity compared to analyte screen • Low (<1%) false positive rate • Very low false negative rate • TAT: Average of 4 days with 95% within 8 days • Failure rate of <1%

CASE EXAMPLES

CASE 1

Primary Screen for High Risk Patients

• Patient Profile: 33 year old woman at 10 weeks gestation with a history of a prior miscarriage affected with Down syndrome • Genetic Counseling: • Screening • • • • CVS/amniocentesis verifi ® prenatal test Ultrasound Too early for conventional serum screening and detailed ultrasound and concerned about undergoing CVS/amniocentesis due to procedural loss rate • verifi ® prenatal test Results (

option of sex chromosome analysis elected

): • Chromosome 21 – aneuploidy detected • • • Chromosome 18 Chromosome 13 – no aneuploidy detected – no aneuploidy detected Sex chromosomes – no aneuploidy detected (XY)

CASE 1

Counseling considerations

• verifi ® prenatal test – chromosome 21 aneuploidy detected • Received results prior to 12 weeks gestation

Suggestive of trisomy 21 in fetus

Patient now has information earlier in pregnancy and has more time to make informed decisions regarding testing options and pregnancy management.

CASE 2

Secondary Screen for Screen Positive Patients

• Patient Profile: 40 year old woman with 1 in 32 risk for Down syndrome on serum screening.

• Genetic Counseling: • • • amniocentesis verifi ® prenatal test ultrasound • verifi ® prenatal test Results: • • • Chromosome 21 – no aneuploidy detected Chromosome 18 – no aneuploidy detected Chromosome 13 – no aneuploidy detected

CASE 2

Counseling Considerations

• Serum screen -

screen positive

for Down syndrome (1 in 32) • Serum screening can have screen/false positive rate (FPR) in women 40+ of 20% (NOTE: FPR dependent upon type of screening utilized) • verifi ® prenatal test – 18 and 13

no aneuploidy detected

for chromosomes 21, • Normal ultrasound - reassuring but need to discuss limitations Patient comfortable declining amniocentesis and avoids risk of procedural loss

CASE 3

High Risk Patient Considering CVS/Amniocentesis

• • • Patient Profile: 38 year old woman with history of infertility who conceived via in vitro fertilization (IVF).

Genetic Counseling: • • • • Screening • Declined serum screening due to sub-optimal detection rates for trisomies CVS/Amniocentesis • Considering invasive testing but fearful of procedural loss verifi ® prenatal test Ultrasound verifi ® prenatal test Results (

option of sex chromosome analysis elected

): • Chromosome 21 – no aneuploidy detected • • • Chromosome 18 Chromosome 13 – no aneuploidy detected – no aneuploidy detected Sex chromosomes – no aneuploidy detected (XX)

CASE 3

Counseling Considerations

• verifi ® prenatal test – no aneuploidy detected • Normal ultrasound - reassuring but need to discuss limitations Patient comfortable declining invasive testing due to NIPT results and normal ultrasound. Procedural risks avoided.

CASE 4

Patients Who Have Abnormal Ultrasound Findings

• Patient Profile: 41 year old woman at 34 weeks gestation diagnosed with ultrasound findings of large echogenic kidneys and ventricular septal defect • Negative integrated screen (1/800 DS; 1/5000 T18; negative ONTD) • Genetic Counseling: • • • Ultrasound findings suspicious for trisomy 13 Amniocentesis • Patient declined as she would not alter course of pregnancy verifi ® prenatal test • verifi ® • prenatal test Results: Chromosome 21 – no aneuploidy detected • • Chromosome 18 – no aneuploidy detected Chromosome 13 –

aneuploidy detected

CASE 4

Counseling Considerations

• verifi ® prenatal test – chromosome 13 aneuploidy detected • Consistent with ultrasound findings

Suggestive of trisomy 13 in fetus

Patient continues to decline amniocentesis but now pregnancy management decisions can be made regarding delivery.

POTENTIAL FUTURE DIRECTIONS

Testing in low risk population Other whole autosomes Further testing in multiple gestations Sub chromosomal abnormalities

Further study of mosaicism

NON-INVASIVE SUBCHROMOSOMAL ANALYSIS Noninvasive Detection of Fetal Subchromosome Abnormalities via Deep Sequencing of Maternal Plasma Anupama Srinivasan

1 ,

Diana W. Bianchi

2 ,

Hui Huang

1 ,

Amy J. Sehnert

Richard P. Rava

and

The American Journal of Human Genetics, Volume 92, Issue 2, 167-176, 10 Jan 2013

SUB-CHROMOSOME PUBLICATION

Proof-of-Principle Study in AJHG

• Purpose of the Study: • To determine sequencing analysis necessary to detect fetal subchromosomal abnormalities from a maternal blood sample • Blinded Analysis of 11 Samples from MELISSA • 10 cases with subchromosomal abnormalities • Duplications, deletions, derivative chromosomes, mosaic cases • Trisomy 20 was used as a control

RESULTS

All Subchromosomal Abnormalities Detected in Non-Mosaic Samples

• 7 Non-Mosaic Samples: All Subchromosomal Abnormalities Detected.

• For karyotypes with unknown genetic material, deep MPS identified both translocation breakpoint as well as chromosomal origin of unknown material • Detected microdeletion as small as 300kb • 4 Mosaic Samples: Subchromosomal Abnormalities not Detected.

• Non-detection due to lack of sequence in human genome, or post-zygotic error

SUBCHROMOSOME ANALYSIS

Example

• Sample from the study • Multiple sub chromosome abnormalities detected in one sample • Laboratory personnel were blinded to karyotype

RESULTS

Abnormalities Detected by Deep MPS Concordant with Karyotype

• Abnormalities as small as 300kb detected • Precise location of abnormalities concordant with karyotype

RESULTS

Additional Abnormalities Detected by Deep MPS

• Deep MPS provided additional detection of abnormalities

NOT

identified by karyotype • Provides additional information not seen on karyotype • All abnormalities < 1 Mb

SUBCHROMOSOME ANALYSIS

Proof-of-Principle Study Recently Published in AJHG

• Study Shows the Ability of Deep MPS Technology to Detect Fetal Subchromosomal Abnormalities Non Invasively • Deep MPS Can Provide Greater Resolution and Can Detect Fetal Subchromosomal Abnormalities at a Resolution of 100kb Across the Genome • Given the Cost of the Method, a Deep MPS Test for Sub Chromosome Abnormalities

Could Be Available in the Near Future…

NIPT STATUS AND INVASIVE PROCEDURE UPTAKE

INVASIVE PROCEDURE UPDATE BY MONTH

(7/2010 THROUGH 3/2013)

THE VERIFI® PRENATAL TEST – MAKING A DIFFERENCE IN PATIENT SAFETY

L AW R E N C E D. P L A T T, M D T E L AV I V J U L Y 2 , 2 0 1 3