Copy Number Variations in a Cohort of 420 Individuals with Neurodevelopmental Disorders From the South of Brazil

www.nature.com/scientificreports OPEN Copy Number Variations in a Cohort of 420 Individuals with Neurodevelopmental Disorders From the South of Brazil Tiago Fernando Chaves 1,5*, Nathacha Baretto1,5, Luan Freitas de Oliveira1, Maristela Ocampos2, Ingrid Tremel Barbato2, Mayara Anselmi1, Gisele Rozone De Luca3, Jorge Humberto Barbato Filho2, Louise Lapagesse de Camargo Pinto3, Pricila Bernardi4 & Angelica Francesca Maris1* Chromosomal microarray (CMA) is now recommended as first tier for the evaluation in individuals with unexplained neurodevelopmental disorders (ND). However, in developing countries such as Brazil, classical cytogenetic tests are still the most used in clinical practice, as reflected by the scarcity of publications of microarray investigation in larger cohorts. This is a retrospective study which analyses the reading files of CMA and available clinical data from 420 patients from the south of Brazil, mostly children, with neurodevelopmental disorders requested by medical geneticists and neurologists for diagnostic purpose. Previous karyotyping was reported for 138 and includes 17 with abnormal results. The platforms used for CMA were CYTOSCAN 750K (75%) and CYTOSCAN HD (25%). The sex ratio of the patients was 1.625 males :1 female and the mean age was 9.5 years. A total of 96 pathogenic copy number variations (CNVs), 58 deletions and 38 duplications, were found in 18% of the patients and in all chromosomes, except chromosome 11. For 12% of the patients only variants of uncertain clinical significance were found. No clinically relevant CNV was found in 70%. The main referrals for chromosomal microarrays (CMA) were developmental delay (DD), intellectual disability (ID), facial dysmorphism and autism spectrum disorder (ASD). DD/ID were present in 80%, facial dysmorphism in 52% and ASD in 32%. Some phenotypes in this population could be predictive of a higher probability to carry a pathogenic CNV, as follows: dysmorphic facial features (p-value = < 0.0001, OR = 0.32), obesity (p-value = 0.006, OR = 0.20), short stature (p-value = 0.032, OR = 0.44), genitourinary anomalies (pvalue = 0.032, OR = 0.63) and ASD (p-value = 0.039, OR = 1.94). The diagnostic rate for CMA in this study was 18%. We present the largest report of CMA data in a cohort with ND in Brazil. We characterize the rare CNVs found together with the main phenotypes presented by each patient, list phenotypes which could predict a higher diagnostic probability by CMA in patients with a neurodevelopmental disorder and show how CMA and classical karyotyping results are complementary. Neurodevelopmental disorders (ND), which mostly involve developmental delay (DD), intellectual disability (ID) and/or autism spectrum disorders (ASD), affect around 3–4% of the world’s population1,2. Such disorders, when isolated, are termed non-syndromic; when associated with the presence of dysmorphisms or apparent congenital anomalies (CA), are termed syndromic3. Individuals affected with ND usually present reduced adaptive skills and/or limited intellectual ability and face major challenges throughout their life, often including motor difficulties, CA and problems with social interaction. These are relevant characteristics which affect not only the patient, but also impact the daily life of family members due to their special care and dedication needs3,4. 1 Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil. 2Laboratory Neurogene, Florianópolis, SC, Brazil. Children’s Hospital Joana de Gusmão, Florianópolis, SC, Brazil. 4University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil. 5These authors contributed equally: Tiago Fernando Chaves and Nathacha Baretto. *email: ; 3 Scientific Reports | (2019) 9:17776 | https://doi.org/10.1038/s41598-019-54347-z 1 www.nature.com/scientificreports www.nature.com/scientificreports/ Study/Year Cohort CMA Platforms Detection Rate of Sample No Pathogenic CNVs Bruno et al.53 Australia patents with ID and CA AFFYMETRIX 250K microarrays 117 15% Kashevarova et al.11 Russian patients with ID AGILENT 44K e 60K. 79 28% Bartnik et al.13 Polish patients with neurodevelopmental disorder V8 OLIGO 180k (customized) 256 16% Preiksaitiene et al.15 Lithuanian patients with neurodevelopmental disorder AGILENT 105k and 400k 201 14% Roselló et al.5 Spanish children with neurodevelopmental disorder AGILENT 44K 246 30% Coutton et al.14 French children with moderate ID 4 × 180K OLIGONUCLEOTIDE ARRAY (AGILENT TECHNOLOGIES) 66 21% Lay-Son et al.16 Chilean patients with neurodevelopmental disorder CYTOSCAN HD, AFFYMETRIX 40 25% North American patients with disorder neurodevelopment CYTOSCAN DX, AFFYMETRIX (Platform similar to CYTOSCAN HD) 960 14% (first line test)* Quintela et al.26 Galician patients with neurodevelopmental disorder (Spain) CYTOGENETICS WHOLE-GENOME 2.7 M (n = 126) and CYTOSCAN HD (n = 447) 573 11,2% to 13,6% Wu et al. Pfundt et al. 9 Children with congenital heart disease (Chinese population) AFFYMETRIX CYTOSCAN HD 104 28% Borlot et al.24 Patients with unexplained childhood-onset epilepsy and intellectual disability (Toronto) 4 × 180K OLIGONUCLEOTIDE ARRAY (AGILENT TECHNOLOGIES) 134 16% HEIDE et al.27 Patients with both corpus callosum abnormality and intellectual disability (French) 370 CNV-QUAD (n = 7), CYTOSNP-12 (n = 121) our HUMANOMNIEXPRESS-24 (n = 21) (ILLUMINA) 149 13% Di Gregorio et al.54 Patients diagnosed with DD/ID in Turin, Italy AGILENT 60K 1015 11% Sansović et al. Patients with DD/ID with or without dysmorphism, ASD, and/or CA (Croatia) AGILENT SUREPRINT G3 UNRESTRICTED 337 CGH ISCA V2 22% Patients with ID/DD and epilepsy (Chinese population) AFFYMETRIX + SNP Microarray And ILLUMINA HUMANCYTOSNP-12 25% 12 55 Kessi et al.56 100 Table 1. Some recent studies that used chromosomal microarrays for diagnostic testing in cohorts of affected individuals and their diagnostic rates. *CMA used as a first line test (no screening with classical cytogenetics). CYTOSCAN HD platform validation study at FDA. DD = developmental delay; ID = intellectual disability; CA = congenital anomalies; ASD = autism spectrum disorder. Adequate diagnosis is necessary for the clinical follow-up of individuals with ND and to provide appropriate genetic counseling to the family, preventing the risk of recurrence. Hundreds of genes and many different chromosomal changes are associated with ND and, apart from the well-known and easy identifiable syndromes, the diagnosis of each affected individual remains a clinical challenge. Due to their high phenotypic and genetic heterogeneity, studies and diagnostics of ND are intricate. Additionally both, genetic and environmental factors, isolated or together, play an important role in their pathogenesis5,6. Currently, molecular karyotyping by chromosomal microarrays (CMA) has been clinically recommended as the first-tier cytogenetic (...truncated)