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Keywords: Exome sequencing; Microarrays; Copy number/structural variation; Genotype-phenotype correlations; Diagnostics

Authors:
E.A. Zanardo 1; F.P. Monteiro 2; A.T. Dias 1; S.N. Chehimi 1; Y.G. Oliveira 1; L.A. Costa 2; L.L. Ramos 2; G.M. Novo-Filho 1; G.F.S. Carvalho 1; M.M. Montenegro 1; M.V. Souza 1; A.B. Freitas 3; A.M. Nascimento 1; J.P. Kitajima 2; F. Kok 2; L.D. Kulikowski 1

Affiliations:
1) Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo; 2) Mendelics Analise Genomica; 3) Departamento de Obstetricia e Ginecologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo


Introduction: Detection of single nucleotide variants (SNVs) and copy number variations (CNVs) is essential for patient genotyping in cytogenomic diagnostic. Recently the screening of CNVs from whole exome sequencing (WES) data has become a common practice for routine diagnostic and allowed improving the accuracy of CNVs detection associated with phenotypes. Methods: In this study, we evaluated 38 patients with developmental delay and/or multiple congenital malformations and negative WES (Nextera Rapid Capture Exomes – Illumina) results for pathogenic SNVs. The WES data were submitted to ExomeDepth software in order to identify potential relevant CNVs. We performed genomic array using Infinium CytoSNP850K BeadChip (Illumina) and BlueFuse Multi v4.3 (BlueGnome - Illumina) software in all samples for comparison and confirmation of the CNVs. Those were classified as benign, VUS or pathogenic, and only the pathogenic CNVs were evaluated. Results: We identified 44.7% of the patients with pathogenic CNVs detected by both techniques including deletions and duplications in different chromosomal regions. Only one patient showed pathogenic CNV detected by array and missed by WES. Also, only the genomic array technique revealed cases with regions of homozygosity (8%) that led to correct diagnostic conclusion. Additionally, we performed a reevaluation and reanalysis of WES for normal results in attempt to reclassify variants originally classified as VUS based in relevant literature, updated available mutation/variant databases, and the latest research. The reanalysis improved the detection and cytogenomic diagnostic and showed 29.4% of the patients with SNV in a specific gene/region related to clinical phenotype. The extraction of CNVs information from WES data is an advantageous approach since it can improve the cost-effectiveness and reduces the number of genomic tests required in routine diagnostic.
Grants: FINEP-CT INFRA0160/12-SP8; CAPES-Finance Code 001.