Update Screening performance

• T21, T18 and T13

• Combined test

• Quadruple test

NIPT • Current & proposed pathway

• Changes in choice behaviour

• Modelled performance

• Positive predictive values

• Changes to the cut-off

Twins • Vanishing twins

• Quad test twin factors

DQASS reports • Reporting T13/T18

• Changes to diagnostics

NIPT

Current policy

IPD

Combined test

Offer IPD

No further testing

Offer combined test

IPD

Combined test

Offer IPD or cf DNA No

further testing

cf DNA test

Offer IPD

Offer combined test

Choice

Screening result

Proposed policy

Choice

Screening result

Change

Existing Policy New Policy

Discussion: What changes to choice behaviour would we expect

Choice

Screening result

Change

Existing Policy New Policy

Choice behaviour

Current policy

Starting with 100,000 accepting testing here

• Assume a population of 100,000 screened at 12 weeks using the combined test

• Maternal age distribution of England and Wales 2011

• Expected number of trisomies at screening • Trisomy 21 271 • Trisomy 18 116 • Trisomy 13 37

Composition of screened population

Choice behaviour after a +ve result: modelled results

RiskP

r[A

ccept|R

isk]

0.0

0.2

0.4

0.6

0.8

1.0

1/150 1/50 1/20 1/10 1/5 1/2

Outcome N +ve N %

Normal 99,576 2,104 1,236 59

T21 271 234 137 59

T18 116 97 57 59

T13 37 27 16 59

100,000 2,462 1,446

Accept IPD

Age distribution of E&W 2011

Most of the previous work assumes that the proportions accepting IPD following a high risk results are independent of outcome. In practice the pregnancies with trisomies are the ones with higher risks so they choose IPD more often.

Choice behaviour after a +ve result: modelled results

Risk

Pr[

Accept|R

isk]

0.0

0.2

0.4

0.6

0.8

1.0

1/150 1/50 1/20 1/10 1/5 1/2

Outcome N +ve N %

Normal 99,576 2,104 1,143 54

T21 271 234 198 85

T18 116 97 84 86

T13 37 27 21 80

100,000 2,462 1,446 59

Accept IPD

Outcome N +ve N %

Normal 99,576 2,104 1,236 59

T21 271 234 137 59

T18 116 97 57 59

T13 37 27 16 59

100,000 2,462 1,446

Accept IPD

Choice depends on risk

Unrealistic assumptions

Realistic assumptions

Choice behaviour after a +ve result: modelled results

Risk

Pr[

Accept|R

isk]

0.0

0.2

0.4

0.6

0.8

1.0

1/150 1/50 1/20 1/10 1/5 1/2

Outcome N +ve N %

Normal 99,576 2,104 1,143 54

T21 271 234 198 85

T18 116 97 84 86

T13 37 27 21 80

100,000 2,462 1,446 59

Accept IPD

Outcome N +ve N %

Normal 99,576 2,104 1,236 59

T21 271 234 137 59

T18 116 97 57 59

T13 37 27 16 59

100,000 2,462 1,446

Accept IPD

Fewer IPDs in normal pregnancies

Unrealistic assumptions

Realistic assumptions

Choice behaviour dependent on risk: modelled results

Risk

Pr[

Accept|R

isk]

0.0

0.2

0.4

0.6

0.8

1.0

1/150 1/50 1/20 1/10 1/5 1/2

Outcome N +ve N %

Normal 99,576 2,104 1,143 54

T21 271 234 198 85

T18 116 97 84 86

T13 37 27 21 80

100,000 2,462 1,446 59

Accept IPD

Outcome N +ve N %

Normal 99,576 2,104 1,236 59

T21 271 234 137 59

T18 116 97 57 59

T13 37 27 16 59

100,000 2,462 1,446

Accept IPD

More women with affected pregnancies choose IPD

Unrealistic assumptions

Realistic assumptions

Choice behaviour new policy

IPD

Combined test

Offer IPD or cfDNA No further testing

cf DNA test

Offer IPD

Offer combined test

Risk

Pr[

Accept|R

isk]

0.0

0.2

0.4

0.6

0.8

1.0

1/150 1/50 1/20 1/10 1/5 1/2

IPD

IPD is chosen less often. cfDNA is chosen instead. Less harm.

Cf DNA instead

Choice behaviour new policy

IPD

Combined test

Offer IPD or cfDNA No further testing

cf DNA test

Offer IPD

Offer combined test

Risk

Pr[

Accept|R

isk]

0.0

0.2

0.4

0.6

0.8

1.0

1/150 1/50 1/20 1/10 1/5 1/2

No further testing

Cf DNA

IPD

Many choose cf DNA instead of nothing. More information.

Modelling

Numbers based on a population of 100,000 accepting screening

IPD

Combined test

Offer IPD or cfDNA No further testing

cf DNA test

Offer IPD

Offer combined test

Starting with 100,000 accepting testing here

Offer choice of cfDNA or IPD: modelled results

Outcome N +ve N %

Normal 99,576 2,104 1,143 54

T21 271 234 198 85

T18 116 97 84 86

T13 37 27 21 80

100,000 2,462 1,446 59

Accept IPD

Outcome N +ve N % N % N %

Normal 99,576 2,104 702 33 1,355 64 2,057 98

T21 271 234 170 73 58 25 228 98

T18 116 97 74 76 21 21 95 98

T13 37 27 18 66 9 32 26 98

100,000 2,462 964 39 1,443 59 2,407 98

Accept IPD Accept cfDNA Accept IPD or cfDNA

Offer IPD only (Current)

Offer choice of cfDNA or IPD

Offer choice of cfDNA or IPD: modelled results

Outcome N +ve N %

Normal 99,576 2,104 1,143 54

T21 271 234 198 85

T18 116 97 84 86

T13 37 27 21 80

100,000 2,462 1,446 59

Accept IPD

Outcome N +ve N % N % N %

Normal 99,576 2,104 702 33 1,355 64 2,057 98

T21 271 234 170 73 58 25 228 98

T18 116 97 74 76 21 21 95 98

T13 37 27 18 66 9 32 26 98

100,000 2,462 964 39 1,443 59 2,407 98

Accept IPD Accept cfDNA Accept IPD or cfDNA

Offer IPD only (Current)

Offer choice of cfDNA or IPD

Fewer IPDs in unaffected pregnancies

Offer choice of cfDNA or IPD: modelled results

Outcome N +ve N %

Normal 99,576 2,104 1,143 54

T21 271 234 198 85

T18 116 97 84 86

T13 37 27 21 80

100,000 2,462 1,446 59

Accept IPD

Outcome N +ve N % N % N %

Normal 99,576 2,104 702 33 1,355 64 2,057 98

T21 271 234 170 73 58 25 228 98

T18 116 97 74 76 21 21 95 98

T13 37 27 18 66 9 32 26 98

100,000 2,462 964 39 1,443 59 2,407 98

Accept IPD Accept cfDNA Accept IPD or cfDNA

More information about trisomies

Offer IPD only (Current)

Offer choice of cfDNA or IPD

Positive predictive values

Prevalence 0.3% FPR = 0.2% DR = 100%

Screened population of 1,000 Screen positives

Positive predictive values

PPV = 3/5 = 60%

Practical Session: PPV of NIPT in the high risk group

• The prevalence of trisomies in the combined tests with risks if 1 in 150 or higher is estimated to be 7.5%

• Assume that the FPR of cfDNA is 0.2% and its DR is 99%

• What is the PPV of cf DNA?

Prevalence 7.5% FPR = 0.2% DR = 99%

Combined/Quadruple test risk ≥ 1 in 150

Practical Session: PPV of NIPT in the high risk group

PPV = 0.075×0.99/(0.075×0.99 + 0.925×0.002) = 0.976

FPR = 0.2% DR = 99%

NIPT Positive

Positive predictive values of cf DNA tests

For cfDNA test assume FPR = 0.2% DR = 99%

In the general population (E&W 2011)

In 20 year olds

In 40 year olds

In women who screen positive

In women with risks of 1 in 5

In women with risks of 1 in 150

Independent of other factors

PPV = 60%

PPV = 33%

PPV = 88%

PPV = 98%

PPV = 99%

PPV = 77%

Cf DNA testing fetal fraction

• Performance of cf DNA depends on fetal fraction

• There are differences amongst providers about the use of fetal fraction

• Some providers report inconclusive or failed test results in cases where the fetal fraction is too low (e.g. below 4%)

Sparks AB, Struble CA, Wang ET, et al. Noninvasive prenatal

detection and selective analysis of cell-free DNA obtained from

maternal blood:

evaluation for trisomy 21 and trisomy 18. Am J Obstet Gynecol

2012;206:319.e1-9.

Canick, Palomaki Prenatal Diagnosis 2013, 33, 667–674

DNA testing and estimated fetal fraction

Fetal fractions in high risk pregnancies

• For larger fetal fractions (10%+) cf DNA dominates other markers and is close to diagnostic

• For lower fetal fractions performance deteriorates

• Pregnancies with very high combined test risks for T13/T18 would be predicted to have low fetal fractions because of reduced PAPP-A and hCG β

Number of second stage tests 000's

Tri

so

my 2

1 p

reg

nan

cie

s c

overe

d %

(n

)

0 10 20 30 40 50 60 70 80 90 100

0

10

20

30

40

50

60

70

80

90

100

(0)

(27)

(54)

(81)

(108)

(136)

(163)

(190)

(217)

(244)

(271)

10

150

500

10002000

Trisomy 21

Proposed policy

What if we change the cut-off

Trisomy 18

Number of second stage tests 000's

Tri

so

my 1

8 p

reg

nan

cie

s c

overe

d %

(n

)

0 10 20 30 40 50 60 70 80 90 100

0

10

20

30

40

50

60

70

80

90

100

(0)

(12)

(23)

(35)

(46)

(58)

(70)

(81)

(93)

(104)

(116)

10

150

5001000

2000

Proposed policy

Trisomy 13

Number of second stage tests 000's

Tri

so

my 1

3 p

reg

nan

cie

s c

overe

d %

(n

)

0 10 20 30 40 50 60 70 80 90 100

0

10

20

30

40

50

60

70

80

90

100

(0)

(4)

(7)

(11)

(15)

(18)

(22)

(26)

(30)

(33)

(37)

10

150

500

1000

2000

Proposed policy

Screening performance

Performance of combined testing

• Predictive models

• Newcastle study

• FMF Validation study

Modelled

Age T21 T18 T13

20 0.9% 76% 70% 58%

25 1.0% 77% 70% 59%

30 1.3% 80% 71% 62%

35 2.6% 85% 84% 68%

40 8.2% 92% 91% 80%

45 24.0% 97% 97% 91%

All 2.2% 86% 84% 72%

Detection RatesFPR

Newcastle

T21 T18 T13

All ages 2.30% 84% 97% 82%

(n =10,000) (n=238) (n=72) (n=28)

Detection RatesFPR

Performance of combined testing: current policy

Term risk for T21 Term risk for T18 or T13 Risk cut-off 1 in 150 Age distribution of E&W 2011

Performance of combined testing: validation

FMF Screening cohort - crude rates; separate term risks for T21 and (T13 or T18) compared to the same risk cut-off

Risk

≥ T 21 T 18 T 13 T21+T18+T13 Turner Triploidy Other Normal All pregnancies

432 166 56 654 63 35 118 108,112 108,982

1 in 2 199 107 19 325 25 22 10 93 475

46.1 (41.3, 50.9) 64.5 (56.7, 71.7) 33.9 (21.8, 47.8) 49.7 (45.8, 53.6) 39.7 (27.6, 52.8) 62.9 (44.9, 78.5) 8.5 (4.1, 15) 0.1 (0.1, 0.1) 0.4 (0.4, 0.5)

1 in 5 270 129 28 427 43 27 18 269 784

62.5 (57.7, 67.1) 77.7 (70.6, 83.8) 50 (36.3, 63.7) 65.3 (61.5, 68.9) 68.3 (55.3, 79.4) 77.1 (59.9, 89.6) 15.3 (9.3, 23) 0.2 (0.2, 0.3) 0.7 (0.7, 0.8)

1 in 10 308 140 35 483 51 29 27 506 1,096

71.3 (66.8, 75.5) 84.3 (77.9, 89.5) 62.5 (48.5, 75.1) 73.9 (70.3, 77.2) 81 (69.1, 89.8) 82.9 (66.4, 93.4) 22.9 (15.7, 31.5) 0.5 (0.4, 0.5) 1 (0.9, 1.1)

1 in 25 346 148 40 534 59 30 43 1,093 1,759

80.1 (76, 83.8) 89.2 (83.4, 93.4) 71.4 (57.8, 82.7) 81.7 (78.5, 84.5) 93.7 (84.5, 98.2) 85.7 (69.7, 95.2) 36.4 (27.8, 45.8) 1 (1, 1.1) 1.6 (1.5, 1.7)

1 in 50 364 153 43 560 60 32 57 1,866 2,575

84.3 (80.5, 87.6) 92.2 (87, 95.8) 76.8 (63.6, 87) 85.6 (82.7, 88.2) 95.2 (86.7, 99) 91.4 (76.9, 98.2) 48.3 (39, 57.7) 1.7 (1.6, 1.8) 2.4 (2.3, 2.5)

1 in 100 383 154 45 582 62 33 61 3,227 3,965

88.7 (85.3, 91.5) 92.8 (87.7, 96.2) 80.4 (67.6, 89.8) 89 (86.3, 91.3) 98.4 (91.5, 99.96) 94.3 (80.8, 99.3) 51.7 (42.3, 61) 3 (2.9, 3.1) 3.6 (3.5, 3.8)

1 in 150 395 154 48 597 62 34 61 4,407 5,161

91.4 (88.4, 93.9) 92.8 (87.7, 96.2) 85.7 (73.8, 93.6) 91.3 (88.9, 93.3) 98.4 (91.5, 99.96) 97.1 (85.1, 99.9) 51.7 (42.3, 61) 4.1 (4, 4.2) 4.7 (4.6, 4.9)

1 in 200 401 155 49 605 62 34 63 5,523 6,287

92.8 (90, 95.1) 93.4 (88.5, 96.6) 87.5 (75.9, 94.8) 92.5 (90.2, 94.4) 98.4 (91.5, 99.96) 97.1 (85.1, 99.9) 53.4 (44, 62.6) 5.1 (5, 5.2) 5.8 (5.6, 5.9)

1 in 300 407 156 49 612 62 34 65 7,548 8,321

94.2 (91.6, 96.2) 94 (89.2, 97.1) 87.5 (75.9, 94.8) 93.6 (91.4, 95.3) 98.4 (91.5, 99.96) 97.1 (85.1, 99.9) 55.1 (45.7, 64.3) 7 (6.8, 7.1) 7.6 (7.5, 7.8)

1 in 500 413 160 51 624 62 34 71 10,898 11,689

95.6 (93.2, 97.3) 96.4 (92.3, 98.7) 91.1 (80.4, 97) 95.4 (93.5, 96.9) 98.4 (91.5, 99.96) 97.1 (85.1, 99.9) 60.2 (50.7, 69.1) 10.1 (9.9, 10.3) 10.7 (10.5, 10.9)

1 in 1,000 422 162 53 637 63 34 81 17,457 18,272

97.7 (95.8, 98.9) 97.6 (93.9, 99.3) 94.6 (85.1, 98.9) 97.4 (95.9, 98.5) 100 (94.3, 100) 97.1 (85.1, 99.9) 68.6 (59.5, 76.9) 16.1 (15.9, 16.4) 16.8 (16.5, 17)

Abnormal Karyotype

Performance of quadruple testing

Term risk for T21 Risk cut-off 1 in 150 Age distribution of E&W 2011

Age FPR T21 T18 T13

20 1.2% 64% 1% 12%

25 1.3% 66% 2% 13%

30 2.0% 71% 2% 16%

35 4.7% 80% 4% 23%

40 13.1% 91% 10% 37%

45 32.2% 97% 24% 56%

All 3.3% 82% 8% 29%

Detection Rates

Discussion: Vanishing Twins

Prevalence 21-30% (Sampson & de Crespigny, 1992)

First trimester vanishing twins

All Vanishing Twins Empty Twin Sac Singleton Controls

n 193 76 1,361

Free ß-hCG Median MoM 1.024 0.968 0.983

PAPP-A Median MoM 1.317 1.04 0.964

Sampson A, de Crespigny LC. Vanishing twins: the frequency of spontaneous fetal reduction of a twin pregnancy. Ultrasound Obstet

Gynecol. 1992 Mar 1. 2(2):107-9.

Suppose risks are calculated without any adjustments for twins.

What might be expected to happen to the risks of trisomies in a vanishing twin?

Is the biochemistry useful?

If so, how should the biochemistry be interpreted?

Data from Spencer.

Second trimester twin effects

1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4

Cycle 18

Cycle 19

Pooled

Second trimester twin effect: AFP

MoM

Spencer 2005 – Multiple Pregnancy: Epidemiology, Gestation & Perinatal Outcome (Blickstein & Keith eds.)

Spencer, 2005

1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4

Cycle 18

Cycle 19

Pooled

Second trimester twin effect: hCG

MoM

1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4

Cycle 18

Cycle 19

Pooled

Second trimester twin effect: hCG β

MoM

1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4

Cycle 18

Cycle 19

Pooled

Second trimester twin effect: uE3

MoM

MoM

1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4

Cycle 18

Cycle 19

Pooled

Second trimester twin effect: Inhibin

MoM

DQASS Reports: Reference distribution

DQASS Reports: Trisomies 18 and 13

Reporting

Laboratory reports

• Choice of test (Table/Bar Chart/Pie Chart)

• Screen positive rate overall (+ve = Any risk ≥ 1 in 150)

Cycle reports • SPRs by choice of test and overall

DQASS Reports: MoM diagnostics

Spot the difference

Robust DQASS diagnostics Geometric Mean Sample Median Trimmed geometric mean

Discussion

• The current diagnostics (geometric means) are affected by outliers and skewness

• The difference between DQASS diagnostics and the sample medians has been a source of considerable discussion with some laboratories

• We need to use mean log MoMs (i.e. geometric means) for CUSUM charts and flags

• Should we start using trimmed MoM diagnostics?