Danish experiences with Chromosomal Micro-Array (CMA) in a prenatal setting

Ida Vogel MD, PhD, Clinical Genetics, Aarhus University Hospital Denmark idavogel@rm.dk

Since 2004-

All Danish women are offered: •  combined First Trimester Screening (93%)

•  Double test (PAPP-A/fβhCG) •  NT scan •  Age

•  Anomaly scan (96%)

Post- and prenatal Downs syndrom diagnoses

0

20

40

60

80

100

120

140

2000 2002 2004 2006 2008 2010

Postnatal Prænatal Data from DCCR

Abortions in Denmark •  Large increase (>100%) in late abortions after new

screening criteria in 2004

Mette Svane Bech, Jette Sørensen and Olav Bjørn Petersen

90

166

4 0 25

265

7 0 0

50

100

150

200

250

300

Lethal Severe Moderate minor

No.

of c

ases

Severity

Severity of structural anomalies after TOP. N=557, 2007-2014

<17 weeks of gestation ≥17 weeks of gestation

Saltved et al. BJOG, 2006 Jun;113(6):664-74

Neonatal death due to chromosomal/fetal anomalies

0

50

100

150

200

250

2000 2002 2004 2006 2008 2010

No/year

SST: Dødsårsagsregistret 2000-2011

Prenatal screening tools

Assay Chromosome diseases

Screen og diagnostic test

Risk of miscarriage

NIPT T21, T18, T13 +sex Screen - QFPCR/MLPA T21, T18, T13 +sex Diagnostic 0.22%* cFTS >>10 Screen - Chromosome analyses

10-100 Diagnostic 0.22%*

Chromosomal Micro Array

>1000 Diagnostic 0.22%*

*Akolekar et al, UOG 2015; 45:16-26

Chromosomal microarray CMA

Patient DNA

Control DNA

Rat

io

Position on Sequence

Hybridize

Quantitate

Detection Rate (DR): CMA: 10% (CI 8-12%) Chromosomal analyses 3%

Consensus 2010

CMA in pregnancy – 2010

Additional Detection Rate by CMA • All indications +3,6% • Structural malformation +5,2%

2013 Meta-analyses N=12,362 DR CMA after normal karyotype

– All indications +2.4 % – Abnormal UL +6.5 %

January 2013

National guideline (DSOG, DSMG) • CMA is first tier analysis in pregnancy for:

– Malformations – NT >= 3,5mm – Small biometries in 2nd-3rd trimester –  Intra-Uterine Death

13

Aarhus, 1036 prenatal cases

1. Aneuploidy (13, 18, 21, X, Y) 2.0 %

2. Pathogenic variation (CNV) 7.9 %

3. Variation of Unknown Significance (VUS) 1.2 %

Clinical significant finding (1+2+3) 11.1 %

More than karyotype (2+3) 9.1 %

4. Familiar variation (CNV) 3.2 %

5. Incidental finding (STS, DMD) 0.7 % Turn Around Time <7 working days

15

Acta Obstet Gynecol Scand. 2013 Jul;92(7):762-8

Case Indication (14+1): malformed upper extremities, micrognathia, small head

0.4 Mb deletion, chromosome 1, de novo SF3B4: Nager acrofacial dysostosis (OMIM #154400) Malformation of the craniofacial skeleton and the limbs

Nager syndrome (acrofacial dysostosis)

17

Case

•  Facial cleft w 19 •  No other malformations. •  Tertiary scan by fetal

medicin expert •  aCGH result after 4 days is normal

•  MAJORITY of cases (85%)

”In the absence of associated anomalies, chromosomal defects were found prenatally in CLP (3.9%)” Maarse W et al. J Med Genet. 2012.

NIH Study. 1,082 fetuses with malformations, 2032 without. (CNV=Pathogenic and VUS) •  Heart: DR 16% •  Face: DR 15% •  Kidney DR 12% •  One talipes DR 7%

•  Leung (Danish cohort) DR +8.3% •  Donelly (US cohort) DR +5% •  Huang ( Kings college Cohort) DR +1.4% •  Lund (Danish cohort): DR +12.8%

Low risk

•  Fiorentino: DR +0.6% •  Oneda: DR +1.6% •  Warpner: DR +1.7% •  Shaffer: DR +0.3% •  DR of CMA is a little better than chromosome analyses

also in low risk pregnancies

Carey: finds mosaicism > 9% Fiorentini: finds mosaicism >10% Hall: finds mosaicism >10-13% = chromosome analyses of 10 metaphases Risk of CPM? •  1.8% CVS •  0.46 % AM

Do we wish to know? False positive?

32 years, GA 19 +2, 2 healthy children UL: IUGR

Trisomi 2 mosaicisme TAT: 4 days

Case

”Gold standard” chromosomal analyses

Case NT 7.5mm Risk T21 1:39

Uncultured CVS:

Cultured CVS:

26

Wobbly legs when conselling in difficult CMA cases (VUS)?

27

•  Based on surveys completed by 193 prenatal genetic counselors, we found that when there is an uncertain CMA result, only 59% would be comfortable providing genetic counseling and only 43% would be comfortable helping a patient make a decision about pregnancy termination.

•  Being less comfortable was associated with seeing fewer patients having prenatal CMA testing.

Blog By Dr Cohen after Warpner et al. N Engl J Med 2012; 367;23:2175-2183

”One can only imagine the anxiety we would cause in our patients undergoing relatively routine testing when we informed them that their baby has a chromosomal abnormality, but it may or may not be normal. I can just hear myself telling a healthy 37 year old woman, “Your guess is as good as mine!”

Stina Lou, PhD 2014, AU, Denmark Title: Exploring how clinicians, pregnant women, and their partners manage and negotiate a high risk screening result for chromosomal abnormality in the fetus

Conclusions: •  Informed choice is insufficient •  Care is necessary •  Worry can be managed •  Anxiety decrease

Stina continued

•  Sharing uncertainty democratizes the relationship between patient and doctor

Is this the key to how we manage variants of uncertain significance?

Case GA 12+6 NT 3.8 mm

1.3 Mb duplication 1q21. Paternally inheritet Variant of unknown significance Penetrance incomplete (17%?). Increased risk of low IQ, autism, ADHD, dysmorphia. After counselling they decided to continue the pregnancy – as they knew about the problems of this family before-hand

!

Multi Disciplinary set-up AUH •  Weekly conferences fetal medicine experts + clinical

geneticists •  Joint patient counselling •  Fetal patologist •  Pediatricians •  Antropologists, •  Counsellors, religious heads •  Stepwise approach into changes •  Our next step: CMA for risk >1:300 from 01.09.15

AUH Conclusions on CMA •  CMA finds aneuploidy, microdeletions and

microduplications. •  Detection rate for CMA>>>> chromosome analysis >> NIPT •  CMA is THE analysis of choice for high risk individuals •  Few incidental findings •  Meaningful and manageable •  Much shorter turn around time (<7 days, median 4 days) •  Experience helps! Centralize to large tertiary centers

•  MUCH more important to implement CMA than NIPT - NOW

Dr Cohens blog revisited It is easy to see that this is the beginning of a revolution in Medicine. It is likely that within a few years, we will combine NIPT with gene-sequencing to cause an explosion in the world of prenatal diagnosis. Here will lie the potential to prevent more disease than vaccination and even the possibility of extending the average human life span. These are exciting times and maternal-fetal medicine specialists would do well to hear the drums and to start expanding their training in and knowledge of human genetics in anticipation of this great medical revolution. Comment on Warpner. N Engl J Med 2012; 367;23:2175-2183

Thanks! •  Else Marie Vestergaard, Rikke

Christensen, Dept Clinical genetics, AUH

•  Olav Bjørn Petersen, Departments of OBGYN, AUH+ Fetal medicine experts in region

•  Mette Svane Bech, Medical student

•  Helle Hørby, priest •  Mette Ramsing, pathology

•  Stina Lou Fleron, and Morten Deleuran Therkildsen, antropologists,

•  Center of rare Diseases, AUH •  Jon Hyett, Sydney •  Cardiologists •  Pediatricians •  And more…