Abstract
BackgroundThe use of Microarray (array CGH) analysis has become a widely accepted front-line test replacing G banded chromosome studies for patients with an unexplained phenotype. We detail our findings of over 5300 cases.ResultsOf 5369 pre and postnatal samples, copy number variants (CNVs) were detected in 28.3 %, of which ~40 % were deletions and ~60 % were duplications. 96.8 % of cases with a CNV <5 Mb would not have been detected by G banding. At least 4.9 % were determined to meet the minimum criteria for a known syndrome. Chromosome 17 provided the greatest proportion of pathogenic CNVs with 65 % classified as (likely) pathogenic. X chromosome CNVs were the most commonly detected accounting for 4.2 % of cases, 0.7 % of these being classified as cryptic (likely) pathogenic CNVs.ConclusionsMicroarray analysis as a primary testing strategy has led to a significant increase in the detection of CNVs (~29 % overall), with ~9 % carrying pathogenic CNVs and one syndromic case identified per 20 referred patients. We suggest these frequencies are consistent with other heterogeneous studies. Conversely, (likely) pathogenic X chromosome CNVs appear to be greater compared with previous studies.
Highlights
The use of Microarray analysis has become a widely accepted front-line test replacing G banded chromosome studies for patients with an unexplained phenotype
As the technology has developed, it has aided in the diagnosis of pathogenic copy number variants (CNVs) and genotype-phenotype correlations
Much larger scale array sample numbers have included Shaffer et al [2] who reported on 8800 patients with an overall CNV yield of ~12 %, and Ahn et al [3] who reported on a similar-sized sample number
Summary
The use of Microarray (array CGH) analysis has become a widely accepted front-line test replacing G banded chromosome studies for patients with an unexplained phenotype. Reported findings have varied due mainly to sample numbers, different platforms, variation in probe coverage and analysis and reporting guidelines. Published reports tend to fall into three groups. Those based on sample sizes such as Park et al [1] who arrayed 407 peripheral bloods, and found an 8.3 % pathogenic rate. Much larger scale array sample numbers have included Shaffer et al [2] who reported on 8800 patients with an overall CNV yield of ~12 %, and Ahn et al [3] who reported on a similar-sized sample number
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