title: Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics.
abstract: The correct interpretation of copy number gains in patients with developmental delay and multiple congenital anomalies is hampered by the large number of copy number variations (CNVs) encountered in healthy individuals. The variable phenotype associated with copy number gains makes interpretation even more difficult. Literature shows that inheritence, size and presence in healthy individuals are commonly used to decide whether a certain copy number gain is pathogenic, but no general consensus has been established. We aimed to develop guidelines for interpreting gains detected by array analysis using array CGH data of 300 patients analysed with the 105K Agilent oligo array in a diagnostic setting. We evaluated the guidelines in a second, independent, cohort of 300 patients. In the first 300 patients 797 gains of four or more adjacent oligonucleotides were observed. Of these, 45.4% were de novo and 54.6% were familial. In total, 94.8% of all de novo gains and 87.1% of all familial gains were concluded to be benign CNVs. Clinically relevant gains ranged from 288 to 7912 kb in size, and were significantly larger than benign gains and gains of unknown clinical relevance (P < 0.001). Our study showed that a threshold of 200 kb is acceptable in a clinical setting, whereas heritability does not exclude a pathogenic nature of a gain. Evaluation of the guidelines in the second cohort of 300 patients revealed that the interpretation guidelines were clear, easy to follow and efficient.
authors.affiliation: Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands.
authors.forename: Nicolien M
authors.initials: NM
authors.lastname: Hanemaaijer
authors.forename: Birgit
authors.initials: B
authors.lastname: Sikkema-Raddatz
authors.forename: Gerben
authors.initials: G
authors.lastname: van der Vries
authors.forename: Trijnie
authors.initials: T
authors.lastname: Dijkhuizen
authors.forename: Roel
authors.initials: R
authors.lastname: Hordijk
authors.forename: Anthonie J
authors.initials: AJ
authors.lastname: van Essen
authors.forename: Hermine E
authors.initials: HE
authors.lastname: Veenstra-Knol
authors.forename: Wilhelmina S
authors.initials: WS
authors.lastname: Kerstjens-Frederikse
authors.forename: Johanna C
authors.initials: JC
authors.lastname: Herkert
authors.forename: Erica H
authors.initials: EH
authors.lastname: Gerkes
authors.forename: Lamberta K
authors.initials: LK
authors.lastname: Leegte
authors.forename: Klaas
authors.initials: K
authors.lastname: Kok
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Sinke
authors.forename: Conny M A
authors.initials: CM
authors.lastname: van Ravenswaaij-Arts
mesh_terms: D000015:Abnormalities, Multiple / Q000175:diagnosis* / Q000235:genetics*; D015331:Cohort Studies; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D002658:Developmental Disabilities / Q000175:diagnosis* / Q000235:genetics*; D005260:Female; D006801:Humans; D008297:Male; D017410:Practice Guidelines as Topic