title: Chromosomal microarray analysis as a first-tier clinical diagnostic test: Estonian experience.
abstract: Chromosomal microarray analysis (CMA) is now established as the first-tier cytogenetic diagnostic test for fast and accurate detection of chromosomal abnormalities in patients with developmental delay/intellectual disability (DD/ID), multiple congenital anomalies (MCA), and autism spectrum disorders (ASD). We present our experience with using CMA for postnatal and prenatal diagnosis in Estonian patients during 2009-2012. Since 2011, CMA is on the official service list of the Estonian Health Insurance Fund and is performed as the first-tier cytogenetic test for patients with DD/ID, MCA or ASD. A total of 1191 patients were analyzed, including postnatal (1072 [90%] patients and 59 [5%] family members) and prenatal referrals (60 [5%] fetuses). Abnormal results were reported in 298 (25%) patients, with a total of 351 findings (1-3 per individual): 147 (42%) deletions, 106 (30%) duplications, 89 (25%) long contiguous stretches of homozygosity (LCSH) events (>5 Mb), and nine (3%) aneuploidies. Of all findings, 143 (41%) were defined as pathogenic or likely pathogenic; for another 143 findings (41%), most of which were LCSH, the clinical significance remained unknown, while 61 (18%) reported findings can now be reclassified as benign or likely benign. Clinically relevant findings were detected in 126 (11%) patients. However, the proportion of variants of unknown clinical significance was quite high (41% of all findings). It seems that our ability to detect chromosomal abnormalities has far outpaced our ability to understand their role in disease. Thus, the interpretation of CMA findings remains a rather difficult task requiring a close collaboration between clinicians and cytogeneticists.
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia ; Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu Tartu, Estonia.
authors.forename: Olga
authors.initials: O
authors.lastname: Zilina
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia ; Department of Pediatrics, University of Tartu Tartu, Estonia.
authors.forename: Rita
authors.initials: R
authors.lastname: Teek
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia.
authors.forename: Pille
authors.initials: P
authors.lastname: Tammur
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia.
authors.forename: Kati
authors.initials: K
authors.lastname: Kuuse
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia ; Department of Biomedicine, Institute of Biomedicine and Translation Medicine, University of Tartu Tartu, Estonia.
authors.forename: Maria
authors.initials: M
authors.lastname: Yakoreva
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia.
authors.forename: Eve
authors.initials: E
authors.lastname: Vaidla
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia.
authors.forename: Triin
authors.initials: T
authors.lastname: Mölter-Väär
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia ; Department of Pediatrics, University of Tartu Tartu, Estonia ; Department of Biomedicine, Institute of Biomedicine and Translation Medicine, University of Tartu Tartu, Estonia.
authors.forename: Tiia
authors.initials: T
authors.lastname: Reimand
authors.affiliation: Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu Tartu, Estonia.
authors.forename: Ants
authors.initials: A
authors.lastname: Kurg
authors.affiliation: Department of Genetics, United Laboratories, Tartu University Hospital Tartu, Estonia ; Department of Pediatrics, University of Tartu Tartu, Estonia.
authors.forename: Katrin
authors.initials: K
authors.lastname: Ounap
keywords: Chromosomal microarray analysis; copy-number variation; developmental delay; first-tier testing; intellectual disability; postnatal diagnosis; prenatal diagnosis