Report on Prenatal Diagnostic Testing in Victoria in 2017.

Report on Prenatal Diagnostic Testing in Victoria in 2017 This report presents descriptive statistics on the uptake, indications for, and results of prenatal diagnostic procedures for fetal chromosome or DNA testing (PNDx) in the Australian state of Victoria during 2017. Victoria has approximately 80,000 confinements annually and in 2016 had a median maternal age of 31 years1.

The data are sourced from the Victorian Prenatal Diagnosis Database (VPDD). The VPDD contains all amniocentesis and chorionic villus (CVS) results from all cytogenetic laboratories in Victoria analysing prenatal diagnostic samples (the Victorian Clinical Genetics Service, Monash Medical Centre and Melbourne Pathology, and until 2015, Australian Clinical Labs, formerly Healthscope). This routine data collection began in 1976, and continues to operate annually on a state-wide basis. Only pregnancies of Victorian residents, tested at <25 weeksâ&#x20AC;&#x2122; gestation are included in this report. Repeat diagnostic tests on the same pregnancy and tests done on twin pregnancies (or other forms of multiple pregnancy) are combined into a single record per pregnancy.

Trends in the uptake of prenatal diagnostic procedures in Victoria.

Over the 42-year study period, 124,913 pregnancies underwent PNDx for fetal chromosome or DNA analysis prior to 25 weeks gestation.

Numbers have been declining for the last 20 years and in 2016, only 1468 women underwent PNDx, representing the lowest number recorded in 30 years and corresponding to 1.8% of all registered live births in Victoria (Figure 1). In 2017, numbers rose slightly, with 1643 (652 CVS and 989 amniocentesis) procedures recorded.

10.0% 9.0% 5000

8.0% 7.0%

4000

6.0% 3000

5.0% 4.0%

2000

3.0% 2.0%

1000

1.0% 0

0.0%

CVS

AMN

% Uptake

Figure 1: Number of prenatal diagnostic procedures by year and the annual percentage uptake in the Victorian population of pregnant women (1986-2016).

Alice Poulton, Lisa Hui and Jane Halliday, 2019

Percentage uptake in the Victorian population

Number of prenatal diagnostic procedures

6000

Indications for prenatal diagnosis Clinical indications for testing were obtained from requests forms completed by the referring clinician for G-banded karyotype, chromosomal microarray and single gene tests. More than one indication can be recorded, and there were subsequently 1739 indications recorded for 1643 tests in 2017 (Figure 2).

Ultrasound abnormalities

40.3%

Cell-free DNA screening

17.3%

First trimester combined screening

15.7%

Single gene test

10.2%

History of chromosomal abnormality

5.8%

Outside guidelines

3.4%

Second trimester screening

2.5%

High risk screen - not specified*

1.3%

Other inside guidelines

1.4%

Advanced maternal age**

1.0%

Failed/inconclusive NIPT

0.8%

No clinical notes

0.3% 0

100

200

300

400

500

600

700

Figure 2: Indications for prenatal diagnosis in 2017. * A high risk screening test result, where the type of screening was not recorded. ** Maternal age >36 years at estimated due date of delivery.

Trends in indications since 2000 are shown in Figure 3. Key points to note in relation to trends are as follows: ď&#x201A;ˇ

There has been a remarkable decline in prenatal diagnosis for advanced maternal age alone, and conversely a high uptake of prenatal screening among Victorian women.

ď&#x201A;ˇ

The finding of a fetal ultrasound abnormality has remained the most common indication for PNDx since 2015. These ultrasound indications include fetal structural abnormality, fetal death, abnormal amniotic fluid volume, and soft markers (e.g. thickened nuchal fold, hypoplastic nasal bone).

ď&#x201A;ˇ

PNDx performed for a high risk cell-free DNA screening result has continued to rise following its introduction in 2013. 2017 marks the first year where cell-free DNA screening has been the 2nd most frequent indication for testing, surpassing high risk first trimester combined screening. There was no Medicare rebate for a cell-free DNA screening test at the time of this report.

800

A single gene indication is given when a pregnancy has a known increased risk of a heritable condition, caused by a monogenic mutation. Historically, single gene tests have comprised 2-3% of all indications.

However, over the past 5 years this annual percentage and absolute numbers have risen. The 178 tests in 2017 was the highest annual number ever recorded. The scope of monogenic disorders for which prenatal diagnosis has been performed has also increased, rising from n=22 individual conditions in 1993, to n=58 in 2017. The recent growth in the number and percentage of pregnancies being tested for monogenic conditions in recent years has many potential contributing factors, including better identification of couples at risk, and the availability of self-funded reproductive carrier screening and clinical exome sequencing.

However, as the clinical details on the prenatal diagnostic referral rarely provide enough detail to analyse how genetic risk was first identified for that pregnancy, we are unable to ascertain the cause of this rise in testing

50%

40% Advanced maternal age

% of all prenatal diagnosis

ď&#x201A;ˇ

Second trimester screening

30%

Ultrasound abnormality Cell-free DNA screening

20%

First trimester screening 10%

Single gene disorder Previous chromosome abnormality

0%

Year

Figure 3: Indications for prenatal diagnosis 2000-2017 as a percentage of total tests.

Chromosomal analysis uptake and results Use of chromosomal microarray (CMA) for the diagnostic assessment of fetal samples is now standard practice in Victoria. Research indicating the improved diagnostic yield of CMA over conventional karyotype, for fetuses with structural abnormalities, has contributed to the increased utilisation of CMA from 2012. In Victoria, CMA is now used for >85% of prenatal diagnosis, irrespective of indication (Figure 4).

No. Fetal samples analysed

4000 3500 3000 2500 2000

Karyotype

1500

Microarray

1000 500 0 2011

2012

2013

2014

2015

2016

2017

Year

Figure 4: Number of prenatal samples analysed using karyotype and CMA (2011-2017).

In 2017, 394 (24%) of CMA and karyotype analyses detected a major abnormality (aneuploidy, unbalanced rearrangements, pathogenic copy number variants (CNVs), polyploidy, level III mosaics and uniparental disomy).

(Figure 5). Of these abnormal results, 39 were pathogenic CNVs. In 2017, the number of variants of unknown or uncertain significance detected by CMA was 96 (5.7%).

35.0% 30.0% 25.0% 20.0% 15.0% 10.0%

Abnormal result

Total abnormalities including variants of unknown/uncertain significance

5.0% 0.0%

Figure 5: Percentage of abnormal results from all prenatal diagnostic tests by year (1996-2017).

Prenatal frequency of chromosome abnormalities There were 80,934 registered live births recorded in 2017, including infants from multiple pregnancies. The prenatal prevalence of trisomy 21 as a proportion of all births in 2017 was 1 in 426. The prevalence of trisomy 18, trisomy 13 and total sex chromosome abnormalities were 1 in 1471, 4496 and 1527 respectively. Overall, 1 in 205 fetuses (394/80934) were diagnosed by CVS or amniocentesis with a major chromosome abnormality in 2017.

450 400 350 300 250 200 150 100 50 0

Trisomy 21

Other major chromosome abnormality

Figure 6: Annual number of chromosomal abnormalities (1996-2017).

The number of major chromosome abnormalities detected annually has remained relatively consistent over the past 5 years, despite the decline in overall PNDx numbers (Table 1). There has been a slight increase in sex chromosome abnormalities identified prenatally, possibly though cell-free DNA testing programs Table 1: Karyotype and microarray outcomes of all prenatal diagnostic tests done 2014-2017 for pregnancies under 25 weeks of gestational age.

Karyotype/microarray result

Normal/benign variant Major chromosome abnormalities Trisomy 21 Trisomy 18 Trisomy 13 Other autosomal aneuploidy, polyploidy Pathogenic copy number variation Other abnormalities** Variant of unknown/uncertain significance

2014

2015

2016

2017

n=2046 1548 369 176 49 21 22 39 62 108

n=1957 1427 394 204 42 15 21 39 73 126

n=1468 1037 363 183 44 25 9 29 73 68

N=1643* 1152 394 190 55 18 14 44 73 93

*1 test did not have clinical notes attached. **Including sex chromosome abnormalities, level III mosaics, and uniparental disomy.

In 2017, only 4 diagnostic tests were performed for each diagnosis of a major chromosome abnormality. This demonstrates the continued improvement of diagnostic yield over the past 4 decades2.

Table 2: Number of tests performed per diagnosis in 10 year increments from 1976.

Year Procedures performed per diagnosis

1976 100

1986 25

1996 24

2006 13

2017 4

Trisomy 21 remains the most common chromosomal abnormality detected (n=190), and continues to comprise approximately half (48%) of all major chromosomal abnormalities (Figure 7).Other common abnormalities included trisomy 18 (n=55), pathogenic CNVs (n=39), Klinefelter syndrome (n=21) and monosomy X (n=20).

Uncertain/unknown array Trisomy 21

Normal/not clinically significant

Abnormal array or karyotype

Trisomy 18 Trisomy 13 Other autosomal aneuploidy and polyploidy Other abnormality*

Figure 7: Pie chart of major karyotype and microarray outcomes of all prenatal diagnostic tests done in 2016 for pregnancies under 25 weeks gestational age. * Including sex chromosome abnormalities, level III mosaics, uniparental disomy and pathogenic CNVs.

Acknowledgements We thank the contributors to the Victorian Prenatal Diagnosis Database - the Victoria Clinical Genetics Services, Monash Medical Centre and Melbourne Pathology. In particular, we acknowledge the following people for their cooperation in sending the data used to compose this report, and clarifying data where necessary: Lucy Gugasyan, Abhijit Kulkarni, Fiona Norris, Ralph Oertel and Mark Pertile.

Ethics approval number Human Research Ethics Committee (HREC) approval for the prenatal diagnosis data collection and associated research was obtained from the Royal Childrenâ&#x20AC;&#x2122;s Hospital HREC on 17 January 2012 (Ref. No. 31135A) and Monash Health HREC on 18 April 2012 (Ref. No. 2012).

References 1.

Australian Bureau of Statistics. Births, Australia, 2016 Canberra, Australia: Australian Government; 2017.

2.

Hui L, Muggli E, Halliday J. Population-based trends in prenatal screening and diagnosis for aneuploidy: a

retrospective analysis of 38 years of state-wide data. . British Journal of Obstetrics and Gynaecology 2016;123:90-7.