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Int. J. Mol. Sci. 2017, 18(3), 609; doi:10.3390/ijms18030609

Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation

1
Dipartimento di Scienzedella Salute, Sezione di Biostatistica, Università degli Studi di Genova, Via Pastore 1, 16132 Genoa, Italy
2
Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy
3
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
4
UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy
*
Author to whom correspondence should be addressed.
Academic Editor: Ali Mobasheri
Received: 7 February 2017 / Revised: 1 March 2017 / Accepted: 7 March 2017 / Published: 10 March 2017
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
View Full-Text   |   Download PDF [3305 KB, uploaded 10 March 2017]   |  

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. View Full-Text
Keywords: high density custom CGH array; agilent aberration call software; CNV detection filters high density custom CGH array; agilent aberration call software; CNV detection filters
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Lantieri, F.; Malacarne, M.; Gimelli, S.; Santamaria, G.; Coviello, D.; Ceccherini, I. Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation. Int. J. Mol. Sci. 2017, 18, 609.

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