Abstract
BackgroundCopy number variations (CNVs) of chromosomal region 22q11.2 are associated with a subset of patients with congenital heart disease (CHD). Accurate and efficient detection of CNV is important for genetic analysis of CHD. The aim of the study was to introduce a novel approach named CNVplex®, a high-throughput analysis technique designed for efficient detection of chromosomal CNVs, and to explore the prevalence of sub-chromosomal imbalances in 22q11.2 loci in patients with CHD from a single institute.ResultsWe developed a novel technique, CNVplex®, for high-throughput detection of sub-chromosomal copy number aberrations. Modified from the multiplex ligation-dependent probe amplification (MLPA) method, it introduced a lengthening ligation system and four universal primer sets, which simplified the synthesis of probes and significantly improved the flexibility of the experiment. We used 110 samples, which were extensively characterized with chromosomal microarray analysis and MLPA, to validate the performance of the newly developed method. Furthermore, CNVplex® was used to screen for sub-chromosomal imbalances in 22q11.2 loci in 818 CHD patients consecutively enrolled from Shanghai Children’s Medical Center. In the methodology development phase, CNVplex® detected all copy number aberrations that were previously identified with both chromosomal microarray analysis and MLPA, demonstrating 100% sensitivity and specificity. In the validation phase, 22q11.2 deletion and 22q11.2 duplication were detected in 39 and 1 of 818 patients with CHD by CNVplex®, respectively. Our data demonstrated that the frequency of 22q11.2 deletion varied among sub-groups of CHD patients. Notably, 22q11.2 deletion was more commonly observed in cases with conotruncal defect (CTD) than in cases with non-CTD (P < 0.001). With higher resolution and more probes against selected chromosomal loci, CNVplex® also identified several individuals with small CNVs and alterations in other chromosomes.ConclusionsCNVplex® is sensitive and specific in its detection of CNVs, and it is an alternative to MLPA for batch screening of pathogenetic CNVs in known genomic loci.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1590-5) contains supplementary material, which is available to authorized users.
Highlights
Copy number variations (CNVs) of chromosomal region 22q11.2 are associated with a subset of patients with congenital heart disease (CHD)
Performance of CNVplex® The 110 patients used in this study were initially characterized by chromosomal microarray analysis (CMA) and multiplex ligation-dependent probe amplification (MLPA)
We evaluated the performance of CNVplex® in the detection of selected genomic region CNVs with these extensively characterized samples
Summary
Copy number variations (CNVs) of chromosomal region 22q11.2 are associated with a subset of patients with congenital heart disease (CHD). Accurate and efficient detection of CNV is important for genetic analysis of CHD. The chromosome region 22q11.2 is a hotspot for genomic rearrangement and related disorders. Long-term studies carried out in several research centers indicate that children with CHD are most likely to undergo examinations for CNVs on chromosome 22q11.2 [5]. The results of such genetic testing are important for clinical decision makers because patients with 22q11.2 deletion need early medical intervention. A more detailed study on the mechanism of interaction between multiple genes is important to understand the exact cause of the 22q11 deletion syndrome [6]
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