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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Efficient detection of chromosome imbalances and single nucleotide variants using targeted sequencing in the clinical setting

Full text
Author(s):
Villela, Darine [1] ; Costa, Silvia Souza [1] ; Vianna-Morgante, Angela M. [1] ; Krepischi, Ana C. V. [1] ; Rosenberg, Carla [1]
Total Authors: 5
Affiliation:
[1] Univ Sao Paulo, Inst Biosci, Dept Genet & Evolutionary Biol, Rua Matao 277, BR-05508090 Sao Paulo, SP - Brazil
Total Affiliations: 1
Document type: Journal article
Source: EUROPEAN JOURNAL OF MEDICAL GENETICS; v. 60, n. 12, p. 667-674, DEC 2017.
Web of Science Citations: 2
Abstract

We evaluated an approach to detect copy number variants (CNVs) and single nucleotide changes (SNVs), using a clinically focused exome panel complemented with a backbone and SNP probes that allows for genome-wide copy number changes and copy-neutral absence of heterozygosity (AOH) calls; this approach potentially substitutes the use of chromosomal microarray testing and sequencing into a single test. A panel of 16 DNA samples with known alterations ranging from megabase-scale CNVs to single base modifications were used as positive controls for sequencing data analysis. The DNA panel included CNVs (n = 13) of variable sizes (23 Kb to 27 Mb), uniparental disomy (UPD; n = 1), and single point mutations (n = 2). All DNA sequence changes were identified by the current platform, showing that CNVs of at least 23 Kb can be properly detected. The estimated size of genomic imbalances detected by microarrays and next generation sequencing are virtually the same, indicating that the resolution and sensitivity of this approach are at least similar to those provided by DNA microarrays. Accordingly, our data show that the combination of a sequencing platform comprising focused exome and whole genome backbone, with appropriate algorithms, enables a cost-effective and efficient solution for the simultaneous detection of CNVs and SNVs. (C) 2017 Elsevier Masson SAS. All rights reserved. (AU)

FAPESP's process: 13/08028-1 - CEGH-CEL - Human Genome and Stem Cell Research Center
Grantee:Mayana Zatz
Support type: Research Grants - Research, Innovation and Dissemination Centers - RIDC
FAPESP's process: 14/17132-0 - Use of Next Generation Sequencing to study karyotypes with different number of X chromosome
Grantee:Darine Christina Maia Villela
Support type: Scholarships in Brazil - Post-Doctorate