Towards genomic testing in antenatal care – are we ready?

1. Suomen Perinatologinen Seura 04.10.2012 Towards genomic testing in antenatal care – are we ready? Kristiina Aittomäki Director of the Department of Medical Genetics Helsinki University Central Hospital/HUSLAB

2. The wish for a healthy child Practically every couple has the wish for a healthy child. This wish, however, will not be fulfilled in 2-3% of families, where a new-born child is diagnosed with a congenital malformation or disease. The aim of prenatal diagnosis (PND) is to • help families to have a healthy child • help prepare for the birth of a child that needs special medical care • help psychological prepare for the birth of a child with a handicap • enable for the couple to consider termination of the pregnancy, if the fetus is affected • to provide reproductive autonomy to women to make decisions about their pregnancy based on medical information (as they do by their social situation) Kristiina Aitomäki HUSLAB 04.10.2012

3. From chromosomes to genes to genomes Chromosome microarray analysis (CMA) Kristiina Aitomäki HUSLAB 04.10.2012

4. What can CMA do for you? • Identification of new microdeletion and other syndromes not detectable in karyotyping • More efficient diagnostic testing particularly for learning disability and congenital anomalies Deletion Duplication Copy number variations (CNV) Kristiina Aitomäki HUSLAB 04.10.2012

5. Blake et al.

6. Results after normal result on chromosome analysis Sagoo et al. 2009

7. Girirajan et al NEJM September 2012 >32 000 patients, > 8000 controls >2300 children with CNV associated with intellectual disability and congenital anomalies

8. CMA vs. chromosome analysis CMA will • detect all unblanced chromosome aberrations detectable with classical chromosome analysis • detect much smaller unbalanced aberrations (deletions or duplications) not detectable with chromosome analysis • give more information on identified chromosome aberrations such as de novo translocations or marker chromosomes • will detect mosaicism with same level as karyotyping Kristiina Aitomäki HUSLAB 04.10.2012

9. CMA vs. chromosome analysis CMA will NOT • detect balanced rearrengements • does not give positional information (translocation trisomy vs standard trisomy) • detect triploidy (depending on the array) • we still need classical chromosome analysis Kristiina Aitomäki HUSLAB 04.10.2012

10. CMA • detects small (and smaller and smaller) copy number variations (CNV) • human genome includes two types of CNVs: • harmful • harmless, benign changes, with no health consequences • those contributing to phenotypes with other genetic changes • presently we do not yet know all the CNVs in the genome and their significance Kristiina Aitomäki HUSLAB 04.10.2012

11. Establishing the pathogenecity of a de novo CNV Extensive work-up for defining the clinical significance: • Size of the CNV • Review of relevant databases • Review of literature • Has the CNV been previously identified in patients / healthy controls • Is there a phenotype • What is the gene conent of the change • Deletions more often deleterious than duplications • Family history, variable penetrance and expressivity ... Kristiina Aitomäki HUSLAB 04.10.2012

12. CMA results Three categories of CMA results: • Normal • Abnormal • Variant on unknown significance (VOUS) • In post natal testing we do not know, if this finding will explain the disease in a child • In prenatal testing we do not know, if the fetus/child will be healthy or affected Kristiina Aitomäki HUSLAB 04.10.2012

13. CMA CMA can also identify • Incidental findings - assume deletions removing known disease genes • diagnosis of adult onset neurodegenerative disorder in the child • reveal the same diagnosis also in one of the healthy parents • diagnosis of cancer suceptibility in the child • carriership of recessive disorders • Non – paternity • Relatedness of parents (incest) Kristiina Aitomäki HUSLAB 04.10.2012

14. Example 1 • US finding: unilateral club foot • CMA: 1.6 Mb deletion in the area of known microdeletion syndrome • Found in patients with developmental delay • Familial and de novo cases • Cognitive ability normal to moderate mental retardation • The change pathogenic, but the phenotype unertain Kristiina Aitomäki HUSLAB 04.10.2012

15. Example 2 • Previous child with devopmental delay with known chromosome 21 trisomy • CVS: a deletion in chromosome 9 • The databases of literature does not reveal any similar cases • The change is de novo • Deleted region includes several known genes, three are potentially disease-causing with a known function in central nervous system • The change is a VOUS with unknown significance Kristiina Aitomäki HUSLAB 04.10.2012

16. Example 2 b • Previous child with devopmental delay with known chromosome 21 trisomy • CVS: a deletion in chromosome 1 • The databases and literature include many cases found in control populations • No genes in the region • A benign harmless CNV Kristiina Aitomäki HUSLAB 04.10.2012

17. CMA in PND • Several studies performed • Difficult to compare results, because • Different platforms used • Heterogeneous patient series • Differing indications • Definition of abnormal findings (VOUS included) • Definition of VOUS Kristiina Aitomäki HUSLAB 04.10.2012

18. The largest one study so far N=5003 from one lab • 2004-2011 (changing CMA platform over time) • Indications: • Known chromosome abnormality (648) • Chromosome abnormality in one of the parents (62) • Spontaneous abortion/foetus mortus (417) • US abnormality (2858) • Abnormal 1st or 2nd trimester screening (77) • Inherited disorder (non chromosomal) (487) • Advanced maternal age (417) • Parental concern (95) other (13) Kristiina Aitomäki HUSLAB 04.10.2012

19. N=5003 • Overall detection rate 5.3% • 5.5% (140/2533) with significant findings although normal karyotype • 71% of significant CNVs < 10kb (unlikely detection with karyotyping) • Turnaround time mean 7.5 days (median 6 days) • Frequency of VOUS 4.2%, de novo 0.4% Kristiina Aitomäki HUSLAB 04.10.2012

20. Prenatal chromosomal microarray analysis in a diagnostic laboratory; experience with < 1000 cases and review of literature Breman et al. Prenatal diagnosis 2012 • clinically significant CNVs 7.6% (85/1115) • clinically significant CNVs 4.2% without chromosomal indications • frequency of VOUS 1.6% Findings by incidation: • Abnormal US 8.8% • AMA 1.3% • Serum screening 5.4% • Parental concern 0 Kristiina Aitomäki HUSLAB 04.10.2012

21. Non-targeted whole genome 250K SNP array analysis as replacement for karyotyping in fetuses wth structural ultrasound anomalies: evaluation of a one-year experience Faas et al. Prenatal diagnosis 2012 • Upon US detection of fetal anomalies couples were offered counselling for alternative methods and a choice of • Trisomy screening and CMA (QF/array) or • Trisomy screenig and karyotyping (QF/karyo) Results • 153/220, 70% choseQF/array (later <82%) • 35/153 an abnormal finding in QR-PCR • 5/118 a microdeletion syndrome was identified • 3/118 variant of uncertain significance • Inherited CNVs 11/118 • homozygous stretches 3/67 • 67/220 30% chose QF/karyo • 23/67 an abnormal QF-PCR • 3/67 abnormal karyotype Kristiina Aitomäki HUSLAB 04.10.2012

22. Non-targeted whole genome 250K SNP array analysis as replacement for karyotyping in fetuses wth structural ultrasound anomalies: evaluation of a one-year experience Faas et al. Prenatal diagnosis 2012 For recieving results, • 46% of couples chose to receive information of CNVs unrelated to fetal US findings regardless of the availability of current treatment for a late-onset disease • 33% chose not to recieve such information • 21% chose to recieve the information only when threre was either screening or treatment available • in all but two cases both parents chose the same options • Couples have different views to incidental findings Kristiina Aitomäki HUSLAB 04.10.2012

23. We now know • CMA identifies more unbalanced abnormalities than karyotyping in prenatal and postnatal diagnostis • Pre and postnatal testing have differences • CMA gives important additional information in many abnormalities found in karyotyping • CMA is less labour intensive and has a better turnaround time Kristiina Aitomäki HUSLAB 04.10.2012

24. CMA • will identify CNVs of unknown significance, presently with 1.5 (-5%) frequency • can produce incidental findings of late- onset diseases Both may cause sometimes long-lasting concern and anxiety in parents Is this a reason not to do CMA? No, because • also in these cases you still have excluded a large number of known abnormalities • the uncertainty about the health of the fetus/child remains, but on a higher level if no studies are done Kristiina Aitomäki HUSLAB 04.10.2012

25. CMA • will identify CNVs of unknown significance • can produce incidental findings of late-onset diseases which may cause sometimes long-lasting concern and anxiety in parents Is this a reason to withold information from parents (in relevance to the aims of PND)? Absolutely NO, because • that would be dishonest and paternalistic Kristiina Aitomäki HUSLAB 04.10.2012

26. Informed consent needed for CMA Before prenatal CMA patients need counselling for • Possibility of identifying VOUS • Possibility of incidental findings Patients need to decide what information they want to receive, particularly concerning incidental findings Kristiina Aitomäki HUSLAB 04.10.2012

27. In conclusion • We should provide our patients with the benefits or modern genetic technology in prenatal testing • We should provide patients/couples with adequate choice and counselling • We need to educate professionals to provide the counselling • We need to provide patients with all our best information but also all the support they may need Kristiina Aitomäki HUSLAB 04.10.2012

28. Towards genomic testing in antenatal care – are we ready? YES, we are!

29. Thank you!

30. Poikkeavan löydöksen selvittely sikiötutkimuksissa Lapsiveden soluissa havaittiin kromosomin 16 lyhyessä käsivarressa ylimääräistä materiaalia, 46,XX,add(16)(p13) Vanhempien kromosomitutkimuksen tulos oli normaali. Trisomia 16p? Krittinen alue 16p13.1-13.3. Oireet: mm. vaikea kehitysviivästymä, epilepsia, CHD, raaja-anomalioita, persoonalliset ulkonäköpiirteet Dignoosilla olisi tärkeä merkitys pariskunnalle, joten päätettiin tehdä molekyylikaryotyypitys. K. Aittomäki / Kirsi Jänkälä

31. aVGH tulos Tutkimus tehtiin 244k sirulla. Duplikoitunut 16p13.11p13.3 sikiöllä Vanhemmat päätyivät keskeytykseen. Sikiöllä todettiin mm. VSD ja muita 16p trisomiaan sopivia oireita. Sikiö Äiti Isä K. Aittomäki / Kirsi Jänkälä