Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies

Abstract

Background: Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician.

Method: We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016. The aim of the study was to analyze clinical and molecular cytogenetic data in order to identify what elements could be useful to interpret unknown or poorly described aberrations. Comparison of phenotype and cytogenetic characteristics through univariate analysis and multivariate logistic regression was performed.

Results: Copy number variations (CNVs) with a frequency < 1% were detected in 225 patients of the total sample, while 68 patients presented only variants with higher frequency (heterozygous deletions or amplification) and were considered to have negative aCGH. Proved pathogenic CNVs were detected in 70 patients (20.6%). Delayed psychomotor development, intellectual disability, intrauterine growth retardation (IUGR), prematurity, congenital heart disease, cerebral malformations and dysmorphisms correlated to reported pathogenic CNVs. Prematurity, ventricular septal defect and dysmorphisms remained significant predictors of pathogenic CNVs in the multivariate logistic model whereas abnormal EEG and limb dysmorphisms were mainly detected in the group with likely pathogenic VOUS. A flow-chart regarding the care for patients with NDD and/or MCA and/or dysmorphisms and the interpretation of aCGH has been made on the basis of the data inferred from this study and literature.

Conclusion: Our work contributes to make the investigative process of CNVs more informative and suggests possible directions in aCGH interpretation and phenotype correlation.

Keywords: Array-CGH; Dysmorphisms; Interpretation; Multiple congenital anomalies; Neurodevelopmental disorders.

Fig. 1

Description of the total sample enrolled investigated through aCGH until 07–31-2016. Red rectangle includes the patient group (293/339) on which the statistical analysis was performed

Fig. 2

a percentages of CNVs distinct for type of aberrations; (b) percentages of CNVs distinct for hereditary pattern [NA: not available]

Fig. 3

a CNVs distribution on chromosomes; b Correlation of chromosomes’ size (Mb) and number of CNVs for each chromosome; c Correlation of gene density and number of CNVs for each chromosome; d Pathogenic CNVs distribution on chromosomes

Fig. 4

Comparison of phenotypic features between pathogenic CNVs, likely pathogenic CNVs and likely benign CNVs. Representation of variables with statistically significant difference between the three groups. Post-hoc comparison indicates to which groups this difference specifically refers. [*p < 0.05; ^† p < 0.0001]

Fig. 5

Flow-chart in patients with NDD and/or MCA and/or Dysmorphisms. The first step is the collection of appropriate family and clinical history and physical/dysmorphological evaluation. If the patient has a recognizable syndrome, we have to confirm it with specific genetic tests. Otherwise, except for other possible neurological or metabolic implications, we will proceed by considering aCGH (in case of male subjects with ID, it would be appropriate to consider the molecular survey for Fragile X syndrome). The blood draw should always be done on the trio in order to perform aCGH on parent’s sample if anomalous in the child. If aCGH detects CNVs, they will be carefully interpreted. Some CNVs can be classified as pathogenic because linked to known syndromes or to “new microdeletion/microduplication syndromes”. If CNVs are less known or poorly described they have an uncertain clinical significance (VOUS): we suggest some variables that might be useful in distinguishing likely pathogenic from likely benign CNVs (continuous box). Additionally, the presence of some phenotypic variables, as well as the analysis of non-coding regions, could be useful in classifying VOUS as likely pathogenic (dashed box) [* Phenotypic variables significant for pathogenic CNVs: developmental delay, ID, prematurity, IUGR, dysmorphisms, congenital heart disease, hypotonia, cerebral malformations; Phenotypic variables significant for likely pathogenic CNVs: abnormal EEG, hand and lower limb dysmorphisms; Independent predictive factors for pathogenic CNVs: prematurity, ventricular septal defect, dysmorphisms]. In the case of normal chromosomal pattern or likely benign CNVs, it will be necessary to re-evaluate the patient. If the clinical features are strongly suggestive of a genetic/syndromic condition further genetic investigations will be carried out. These may include targeted sequencing, exome sequencing and, in selected cases, genome sequencing. Otherwise clinical follow up should be implemented in the event that evocative elements could emerge over time recommending future genetic investigations