The Fetal Medicine Foundation
Clinical application and evidence of cfDNA testing
María del Mar Gil
No conflict of interest to disclose
The Fetal Medicine Foundation
Maternal blood
Extracellular DNA in the blood of pregnant women [Article in Russian]
Kazakov I et al. Tsitologiia 1995 Presence of fetal DNA in
maternal plasma and serum Lo D et al. THE LANCET 1997
Cell-free fetal DNA in maternal blood
The Fetal Medicine Foundation
1 2 3 4 5 6 7 8 9 10 11 12 13 14
Cell-free fetal DNA in maternal blood
The Fetal Medicine Foundation
13 18 21
4 X Y
The cf DNA fragments are sequenced, their chromosome origin is established and the quantity of each chromosome is determined
There are many millions of cf DNA fragments in maternal plasma
Cell-free fetal DNA in maternal blood
The Fetal Medicine Foundation
In trisomy 21 cfDNA fragments from chromosome 21 are increased
13 18 21
4 X Y
Cell free DNA test
Screening for Down Syndrome
The Fetal Medicine Foundation
Chrom 21 100 units
Chrom 18 100 units
Chrom 13 100 units Chrom 21
105 units
Trisomy 21
Cell free DNA test
Screening for Down Syndrome
The Fetal Medicine Foundation
Trisomy 21 (n=8)
0 20 40 60 80 100
Risk for trisomy 21 (%)
0 20 40 60 80 100
Risk for trisomy 18 (%)
Trisomy 18 (n=2)
0 20 40 60 80 100
Risk for trisomy 21 (%)
0 20 40 60 80 100
Risk for trisomy 18 (%)
Euploid (n=1939)
0 20 40 60 80 100
Risk for trisomy 21 (%)
0 20 40 60 80 100
Risk for trisomy 18 (%)
(n=1939) (n=1937)
No result 5%
Nicolaides et al, Am J Obstet Gynecol 2012
Are the results from high-risk pregnancies applicable to routine screening?
Stored plasma (2 mL) routine combined screening at 11-13 w n=2,049
Cell free DNA test
Screening for Down Syndrome
The Fetal Medicine Foundation
Cell free DNA in maternal blood Screening for trisomies
Gil MM et al. Ultrasound Obstet Gynecol 2017; doi: uog.17484
Trisomy 21 n=1,963 Trisomy 18 n= 563 Trisomy 13 n= 119 New
Trisomy 21 n=1,051 Trisomy 18 n= 389 Trisomy 13 n= 139 Previous
Gil MM et al. Ultrasound Obstet Gynecol 2015;45:249.
The Fetal Medicine Foundation
Publication bias
0 50 100 150
Precision
-0.06 -0.03 0.00 0.03 0.06 0
500 1000 1500 2000 2500
Proportion
Precision
Trisomy 13
PrecisionPrecision
0 10 20 30
0 1000 2000 3000 4000
Proportion
-0.5 0.0 0.5 1.0 1.5 2.0
-0.050 -0.025 0.000 0.025 0.050 Proportion
1000 2000 3000 4000
0
Precision
0 20 40 60 80
Precision
0.4 0.7 1.0 1.3 1.6 Proportion
-0.050 -0.025 0.000 0.025 0.050 Proportion
Trisomy 18
0.5 0.8 1.1 1.4 1.7 Proportion
Trisomy 21
Proportion of studies with low, high or unclear risk (%)
QUADAS-2 Assessment
0% 20% 40% 60% 80% 100%
CONCERNS REGARDING APPLICABILITY
Index test
Reference standard
Patient selection
RISK OF BIAS
Patient selection Flow and timing
Index test
Reference standard
Cell free DNA test
Quality / Bias assessment
The Fetal Medicine Foundation
• Which conditions to screen for
• Interpretation of results
• Importance of fetal fraction
• Test failure
• Screening in twins
• Models of implementation
Cell free DNA test
Points of discussion
The Fetal Medicine Foundation
• Lethal Turners easily detectable by ultrasound
• Most cases are mild without intellectual disability
• 50% of sex chromosome aneuploidies are mosaics
• High incidence of maternal mosaicism
• Performance of screening is uncertain - Failure rate is higher than for T21
- Detection rate is lower (about 90%) than for T21 (>99%) - False +ve rate is higher (about 0.3%) than for T21 (<0.1%) - Positive predictive value much lower than for T21
• Management of positive result: need for amniocentesis
Cell free DNA test Which aneuploidies?
Screening for sex chromosome aneuploidies
The Fetal Medicine Foundation
Microdeletions 1/ births >3Mb
22q11.2 deletion 2-4,000 85%
Angelman / Prader Willi
(15q11.2-q13 deletion) 20,000 70%
1p36 del 5,000 85%
Cri-du-chat (5p deletion) 50,000 99%
Maternal age (yrs) RiskT21
Di George - common features:
75% immune deficiencies 50% hypocalcemia
30% feeding problems 35% renal abnormalities 75% cardiac defects 95% intellectual deficits
25% schizophrenia in adulthood
- Detection rates *: 60-99%
- Total false positive rates: 1%
- Positive predictive value for 22q11.2 deletion: 5%
- Proportion of cfDNA panel of significant microdeletions: 10%
* quoted by companies, but do not include those of <3 Mb
Yaron Y et al. Current status of testing for microdeletion syndromes and rare autosomal trisomies using cell-free DNA technology. Obstet Gynecol 2015;126:1095 Wapner RJ et al. Expanding the scope of noninvasive prenatal testing: detection of fetal microdeletion syndromes. Am J Obstet Gynecol 2015;212:332.e1-9.
Cell free DNA test
Which aneuploidies?
The Fetal Medicine Foundation
Feta l frac tion ( % )
0 5 10 15 20 25 30 35 40
50 60 70 80 90 100 110 120
Maternal weight (kg)
Triploidy Diandric 4 Correct 4
Triploidy Digynic 4 ‘Low FF’ 3 Failed 1
Normal 48 Correct 44
Failed 4
0.5th centile
Nicolaides KH, Syngelaki A, Gil MM, Quezada MS, Zinevich Y. Prenatal detection of fetal triploidy
from cell-free DNA testing in maternal blood. Fetal Diagn Ther 2014; 35: 212-217.
Cell free DNA test
Which aneuploidies?
The Fetal Medicine Foundation
• Trisomy 21 YES
• Trisomies 18/13 Yes
• Sex chromosomes No
• Triploidy No
• Microdeletions Not yet
Cell free DNA test
Which aneuploidies?
The Fetal Medicine Foundation
100,000 pregnancies
Trisomy 21 N=200
99,705 normal
199
99.7% 0.04% 40
Detected
DR False positive
Trisomy 18 N=67 98.2% 66 0.05% 40
Trisomy 13 N=28 99.0% 27 0.04% 40
Cell free DNA test
Interpretation of results
292 / 295 120
The Fetal Medicine Foundation
Trisomy 21
• DR 99.7%
• FPR 0.05%
• LR +ve 2506
• 1/(LR -ve) 300
a priori risk Odds of being affected
cfDNA +ve cfDNA -ve
1:100,000 1 in 42 (2.4%) 1 in 30,000,000 1:10,000 1 in 6 (20.1%) 1 in 3,000,000 1:1,000 1 in 1.4 (71.5%) 1 in 300,000 1:500 1 in 1.2 (83.4%) 1 in 150,000 1:100 1 in 1.03 (93.2%) 1 in 30,000 1:10 1 in 1.004 (99.6%) 1 in 3,000
1:2 1 in 1.001 (99.9%) 1 in 600
Cell free DNA test
Interpretation of results
The Fetal Medicine Foundation
Fetal fraction
cfDNA test Likelihood ratio FPR (%) DR (%) +ve -ve
4% 0.1 62.1 620 3
5% 0.1 87.4 870 8
6% 0.1 97.6 980 42
7% 0.1 99.8 990 410
8% 0.1 100 1,000 7,350
9% 0.1 100 1,000 >10,000
≥10% 0.1 100 1,000 >10,000
All 0.1 99.0 990 100
Wright D, Wright A, Nicolaides KH: A unified approach to risk assessment for fetal aneuploidies. Ultrasound Obstet Gynecol 2015; 45: 48-54 Fetal fraction
Chromosome 21 Z-score
-3 0 3 6 9 12 15 18 21
0 5 10 15 20 25 30 35
FF 8%
FF 2%
24
Cell free DNA test
Importance of fetal fraction
The Fetal Medicine Foundation
Management of failed result
In cases of failed result women should be offered diagnostic testing because of an increased risk of aneuploidy Septiembre 2015
Cell free DNA test
Test failure
The Fetal Medicine Foundation
Singleton pregnancies (n=10,698)
25
20
15
10
5
0 Normal
n=10,472
T21 n=160
T18 n=50
T13 n=16
Fetal fraction (%)
Failed result:
Normal 304
(2.9%)
Trisomy 21 3 (1.9%) Trisomy 18 4 (8.0%) Trisomy 13 1 (6.2%)
Revello R,Sarno L, Ispas A, Akolekar R, Nicolaides KH. Cell-free DNA testing for trisomies: management of failed result. Ultrasound Obstet Gynecol 2016; 47: 698-704.
Combined risk >1 in 5 Ultrasound defects Normal
placenta Small placenta
Cell free DNA test
Test failure
The Fetal Medicine Foundation
DC twins:
-The placental products of the normal fetus may mask the abnormality of the co-twin.
-Measure fetal fraction in both.
• The test is not offered by all companies
• Only some companies measure fetal fraction
Screening in twins
Cell free DNA test
The Fetal Medicine Foundation
0
Cel l- free DN A fail ure ra te (% )
100 90 80 70 60 50 40 30 20 10
Maternal body mass index (kg/m
2) 15 20 25 30 35 40 45 50 55 60
IVF
High failure rate in twins, compared to singletons (9% vs. 3%) mainly because many twins are IVF conceptions (56% in twins vs. 10% in singletons)
BMI (kg/m2)
Rate of failure of cell free DNA testing (%)
Singleton pregnancy Twin pregnancy
Spontaneous
IVF
SpontaneousIVF
20 0.6 4 1 6
25 1.4 9 2 12
30 3 17 5 24
35 7 32 10 41
40 14 51 19 61
45 26 70 35 77
50 44 84 54 88
Harmony test in 10,698 singletons and 438 twins Significant predictors of fetal fraction & cfDNA test failure: increasing BMI, IVF conception and twins
Failure in singletons and twins
Sarno L, Revello R,Hanson E, Akolekar R,Nicolaides KH. Prospective screening for trisomies by cell-free DNA testing of maternal blood in first trimester twin pregnancies. Ultrasound Obstet Gynecol 2016; 47: 705-11.
Cell free DNA test
The Fetal Medicine Foundation
Stored samples from pregnancies with known outcome
Canick et al: Prenat Diagn 2012; 32: 730
Gil et al: Fetal Diagn Ther 2014; 35 : 204
Gromminger et al: J Clin Med 2014; 3: 679
Fosler et al: Ultrasound Obstet Gynecol 2016;doi10.1002/uog
Trisomy 21: DR 23/24 (96%)
Trisomy 13: DR 2/2 (100%) FPR: 0/321 (0%)
Prospective studies with complete outcome Trisomy 21: DR 28/28 (100%)
Trisomy 18: DR 4/6 (67%)
FPR: 1/1098 (0.2%)
Lau et al: J Matern Fetal Neonatal Med 2013; 26: 434
Huang et al: Prenat Diagn 2014; 34: 335
Benachi et al: Obstet Gynecol 2015; 125: 1330
Papageorghiou et al: Ultrasound Obstet Gynecol 2016; 47: 188 Sarno et al: Ultrasound Obstet Gynecol 2016; 47: 705
Tan et al: Prenat Diagn 2016; 36: 672
Le Conte et al; Ultrasound Obstet Gynecol 2017; 10.1002/uog
Trisomy 13: DR 0/1 (0%) Trisomy 18: DR 1/1 (100%)
Validation / implementation in twins
Cell free DNA test
The Fetal Medicine Foundation
Cut off
FPR (%)
DR T21 (%) 100 2.2 87.0 200 3.9 90.4 300 5.4 92.1 400 6.7 93.2 500 7.9 94.0 1000 13.0 96.1 1500 17.2 97.0 2000 20.8 97.6 2500 23.9 98.0 3000 26.6 98.3 3500 29.0 98.5 4000 31.3 98.7 5000 35.2 98.9 6000 38.7 99.1
Combined screening at 11-13 wks (age, fetal NT, serum ß-hCG & PAPP-A)
High risk
>1:10
Low risk
<1:1000
Invasive test
Intermediate risk
Nothing else cfDNA test
+ve -ve
T 21 73%
T 18 91%
T 13 85%
Turner 94%
Triploidy 86%
Other 32%
Normal 0.8%
All 1.4%
Santorum M, Wright D, Syngelaki A, Karagioti N,Nicolaides KH. Accuracy of first trimester combined test in screening for trisomies 21, 18 and 13. Ultrasound Obstet Gynecol 2016; doi 10.1002/uog.17283
Nicolaides KH, Syngelaki A, Poon LC, Gil MM, Wright D. First-trimester contingent screening for trisomies 21, 18 and 13 by biomarkers and maternal blood cell-free DNA testing. 2014; 35: 185-92.
Model of clinical implementation
Cell free DNA test
The Fetal Medicine Foundation
• Which conditions to screen for: T21 and perhaps 18 / 13
• Interpretation of results: Modify prior risk with +ve and –ve LRs
• Importance of fetal fraction: Depends on the company
• Test failure: Does not increase the risk for trisomy 21
• Screening in twins: Need for more data on accuracy
• Models of implementation: Intermediate risk from combined test
Cell free DNA test
Conclusions
Thank you
The Fetal Medicine Foundation
María del Mar Gil
mgil@torrejonsalud.com
The Fetal Medicine Foundation
15 20 25 30 35 40 45 50
Maternal age (yrs)
10,000 1,000 100 10 1
Risk 1 in:
30% of fetuses with trisomy 21 in women >35 yrs
Detection rate for FPR 5%
0 10 20 30 40 50 60 70 80 90 100
%
Maternal age
Screening for Down syndrome
1970’s
The Fetal Medicine Foundation
Screening for Down syndrome
1980’s & 1990’s 2 nd trimester biochemical testing
Cuckle et al., 2005: Meta-analysis
hCG AFP 0
10 20 30 40 50 60 70 80 90
100 Detection rate for FPR 5%
56%
ß-hCG AFP 61%
hCG AFP E3 60%
ß-hCG AFP
E3 65%
hCG AFP E3
I
A67%
ß-hCG AFP
E3 I
A71%
Age 30%
%
Merkatz IR, Nitowsky HM, Macri JN, Johnson WE. Association between low maternal serum alpha-fetoprotein and fetal chromosomal abnormalities. Am J Obstet Gynecol 1984;
148: 886–894.
Wald NJ, Cuckle HS, Densem JW, Nanchahal K, Royston P, Chard T, Haddow JE, Knight GJ, Palomaki GE, Canick JA. Maternal serum screening for Down's syndrome in early pregnancy. BMJ 1988; 297:883-7.
Cuckle HS, Holding S, Jones R, Wallace EM, Groome NP. Maternal serum dimeric inhibin A in second-trimester Down's syndrome pregnancies. Prenat Diagn 1995; 15:385-6.
The Fetal Medicine Foundation
Crown-rump length (mm) 45 55 65 75 85 NT (mm)
0 2 4 6 8
Trisomy 21
0 4 8 n
Serum PAPP-A (M0M) 0 0.5 1.0 1.5
Euploid Trisomy 21 0
10 20 n
Serum free ß-hCG (MoM) 0 1.0 2.0 3.0 4.0 5.0
Euploid
Trisomy 21
Detection rate for FPR 5%
0 10 20 30 40 50 60 70 80 90
100 T21
Age
NT, hCG/PAPP-A T18/13
%
1990’s and beyond
•
Nicolaides KH, Azar GB, Byrne D, Mansur CA, Marks K. Nuchal translucency: ultrasound screening for chromosomal defects in the first trimester of pregnancy. BMJ 1992;304:867
•
Snijders RJ, Noble P, Sebire N, Souka A, Nicolaides KH. UK multicentre project on assessment of risk of trisomy 21 by maternal age and fetal nuchal-translucency thickness at 10-14 weeks of gestation. Lancet 1998; 352:343•
Spencer K, Souter V, Tul N, Snijders R, Nicolaides KH. A screening program for trisomy 21 at 10-14 weeks using fetal nuchal translucency, maternal serum free beta-human chorionic gonadotropin and pregnancy-associated plasma protein-A. Ultrasound Obstet Gynecol 1999; 13:231.•
Kagan KO, Wright D, Valencia C, Maiz N, Nicolaides KH. Screening for trisomies 21, 18 and 13 by maternal age, fetal nuchal translucency, fetal heart rate, free ß-hCG and pregnancy-associated plasma protein-A. Hum Reprod 2008; 23:1968-75.Screening for Down syndrome
1 st trimester combined test
The Fetal Medicine Foundation
DR for FPR 3%
0 10 20 30 40 50 60 70 80 90
100
97%
%
Screening for Down syndrome 1 st trimester combined test PLUS
11 12 13 14 Gestation (wks)
0.6 Trisomy 21
0.0 0.5 1.0 1.5 2.0
Maternal serum PLGF (MoMs)
2000-10
•
Cicero S, Curcio P, Papageorghiou A, Sonek J, Nicolaides K. Absence of nasal bone in fetuses with trisomy 21 at 11-14 weeks of gestation: an observational study. Lancet 2001;358:1665-1667.•
Kagan KO, Cicero S, Staboulidou I, Wright D, Nicolaides KH. Fetal nasal bone in screening for trisomies 21, 18 and 13 and Turner syndrome at 11-13 weeks of gestation. Ultrasound Obstet Gynecol 2009; 33:259-64.•
Kagan KO, Valencia C, Livanos P, Wright D, Nicolaides KH. Tricuspid regurgitation in screening for trisomies 21, 18 and 13 and Turner syndrome at 11 + 0 to 13 + 6 weeks of gestation. Ultrasound Obstet Gynecol 2009; 33:18-22.•
Maiz N, Valencia C, Kagan KO, Wright D, Nicolaides KH. Ductus venosus Doppler in screening for trisomies 21, 18 and 13 and Turner syndrome at 11-13 weeks of gestation. Ultrasound Obstet Gynecol 2009; 33:512-7.The Fetal Medicine Foundation
Prospective validation of 1
sttrimester combined screening for trisomy 21 (n=108,982); FPR 5.3%
Dete c tion ra te a t ris k c ut -of f 1 i n 1 0 0 (% )
T18 T13
T 21 45,XO Triploidy
0 10 20 30 40 50 60 70 80 90 100
96% 93%
92% 98% 97%
Other 46%?
Screening for Down syndrome 1 st trimester combined test
A beneficial side-effect of screening for trisomy 21 is detection of many other aneuploidies
Santorum M, Wright D, Syngelaki A, Karagioti N,Nicolaides KH. Accuracy of first trimester combined test in screening for trisomies 21, 18 and 13. Ultrasound Obstet Gynecol 2016; doi 10.1002/uog.17283
The Fetal Medicine Foundation
Holoprosencephaly, Exomphalos, Megacystis, NT >3.5 mm
Screen +ve rate 1.1%
This group contained 57% of all aneuploidies
Trisomy 21 53%
Trisomy 18 72%
Trisomy 13 88%
Triploidy 34%
Monosomy X 94%
Other 23%
50% T21 80% T13 20% all 45% T18
1 st trimester combined test – validation n = 108,982
Syngelaki A,Guerra L, Ceccacci I,Efeturk T,Nicolaides KH. Impact of holoprosencephaly, exomphalos, megacystis and high NT in first trimester screening for chromosomal abnormalities. Ultrasound Obstet Gynecol 2016; doi 10.1002/uog.17283
The Fetal Medicine Foundation
Screen positive rate
T ris omy 1 8 dete c tion % (n)
0 10 20 30 40 50 60 70 80 90 100 0
10 20 30 40 50 60 70 80 90 100
1 in 10 1 in 100 1 in 1000 (DR 99%)
T ris omy 1 3 dete c tion % (n)
0 10 20 30 40 50 60 70 80 90 100 0
10 20 30 40 50 60 70 80 90 100
1 in 10 1 in 100 1 in 1000 (DR 96%)
FHR
T ris omy 2 1 dete c tion % (n )
0 10 20 30 40 50 60 70 80 90 100 0
10 20 30 40 50 60 70 80 90 100
1 in 1000 (DR 98%)
1 in 100
1 in 10
1 st trimester combined test
Prospective validation n=108,982
Santorum M, Wright D, Syngelaki A, Karagioti N,Nicolaides KH. Accuracy of first trimester combined test in screening for trisomies 21, 18 and 13. Ultrasound Obstet Gynecol 2016; doi 10.1002/uog.17283
The Fetal Medicine Foundation
100,000 pregnancies
Trisomy 21 N=200 99,800 normal
Serum biochemistry at 16 wks 70% 140 5% 4990
Combined test at 12 wks 90% 180 3% 2994
Cell-free DNA >99% 199 0.04% 40
Maternal age 30% 60 5% 4990
METHOD OF SCREENING DR Detected False positive
Cell-free DNA in maternal blood
Screening for Down syndrome
The Fetal Medicine Foundation
Source:
MEDLINE, EMBASE
Key words:
Non invasive/Non-invasive/Noninvasive prenatal detection/diagnosis, Cell free DNA prenatal
Inclusion criteria:
• Peer-reviewed
• Year of publication >2011
• Language English
• Follow-up rate >85%
• Analysis performed blindly
Exclusion criteria:
• Proof of concept articles
• Case-control studies
Bivariate analysis performed to calculate random-effect estimate of pooled weighted for:
• Singletons: Trisomies 21, 18 and 13
Univariate analysis performed to calculate random-effect estimate of pooled weighted for:
• Singletons: Monosomy X and SCA; Twins: Trisomy 21
Records screened n = 3,353
Included in systematic review n = 35
Non-relevant articles n = 2,001
Proof of concept articles n = 29
Records identified n = 7,759
Duplicates n= 4,406
Case-control studies n = 35
Conference abstracts n = 1,070
Review / opinion articles n = 154
Outcome in < 85% cases n = 29
Cell free DNA test
Systematic review 31/12/16
The Fetal Medicine Foundation
Cell free DNA test
Importance of fetal fraction
Company Result
A No aneuploidy, female fetus B No aneuploidy, female fetus C No aneuploidy, female fetus
FF on request: 4.3% and 3.9%
D No result due to FF of 0.6%
E No result due to low FF
Takoudes T, Hamar B. Performance of non-invasive prenatal testing when fetal cell-free DNA is absent. Ultrasound Obstet Gynecol 2015; 45: 112.