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

Int J Mol Sci. 2017 Mar 10;18(3):609. doi: 10.3390/ijms18030609.

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.

Keywords: CNV detection filters; agilent aberration call software; high density custom CGH array.

MeSH terms

  • Comparative Genomic Hybridization / methods
  • Comparative Genomic Hybridization / standards*
  • DNA / standards
  • Humans
  • Observer Variation
  • Signal-To-Noise Ratio
  • Software*

Substances

  • DNA