title: Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation.
abstract: The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software. The Aberration Detection Method 2 (ADM-2) algorithm with a threshold of 6 performed quite well, and the array design proved to be reliable, provided that some additional filters are applied, such as considering only intervals with average absolute log₂ratio above 0.3. We also propose an additional filter that takes into account the proportion of probes with log₂ratio exceeding suggestive values for gain or loss. In addition, the quality of samples was confirmed to be a crucial parameter. Finally, this work raises the importance of evaluating the samples profiles by eye and the necessity of validating the imbalances detected.
authors.affiliation: Dipartimento di Scienzedella Salute, Sezione di Biostatistica, Università degli Studi di Genova, Via Pastore 1, 16132 Genoa, Italy. f.lantieri@unige.it.
authors.forename: Francesca
authors.initials: F
authors.lastname: Lantieri
authors.affiliation: Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy. michela.malacarne@galliera.it.
authors.forename: Michela
authors.initials: M
authors.lastname: Malacarne
authors.affiliation: Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Bâtiment de Base 8C-3-840.3, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland. stefania.gimelli@gmail.com.
authors.forename: Stefania
authors.initials: S
authors.lastname: Gimelli
authors.affiliation: UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy. giuseppesantamaria@gaslini.org.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Santamaria
authors.affiliation: Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy. domenico.coviello@galliera.it.
authors.forename: Domenico
authors.initials: D
authors.lastname: Coviello
authors.affiliation: UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy. isa.c@unige.it.
authors.forename: Isabella
authors.initials: I
authors.lastname: Ceccherini
mesh_terms: D055028:Comparative Genomic Hybridization / Q000379:methods / Q000592:standards*; D004247:DNA / Q000592:standards; D006801:Humans; D015588:Observer Variation; D059629:Signal-To-Noise Ratio; D012984:Software
chemical_list: D004247:DNA
keywords: CNV detection filters; agilent aberration call software; high density custom CGH array