Molecular Characterization And Discovery Of Novel Candidate Loci And Genes For Congenital Heart Disease By Chromosomal Microarray Analysis

Objective: This study aims to assess the diagnostic yields of clinical chromosomal microarray(CMA) testing for patients with syndromic or isolated congenital heart diseases(CHD), to characterize the association of patients’ clinical presentation with the clinical validity of the test, and to uncover novel CHD candidate loci and genes through gene prioritization.Methods: All patients with clinical presentation of CHD who underwent CMA testing at Boston Children’s Hospital(BCH) from December 2006 to April 2013 were reviewed. CHD patients from Shanghai Children’s Medical Center(SCMC) were also recruited. DNA samples from BCH cohort and SCMC cohort were tested on Agilent 4×180K SNP+CGH array platform and Affymetrix Cytoscan HD microarray platform respectively. Patients were first grouped as syndromic CHD or isolated CHD based on the presence or absence of extra-cardiac phenotypes. Patients were further subcategorized based on the presence of specific heart defects. The frequencies of pathogenic CNVs were evaluated for each group and subcategory. The diagnostic yields of CMA testing were compared between isolated CHD and syndromic CHD as well as among different sub-categories. Finally, genes encompassed in pathogenic/likely pathogenic CNVs were analyzed and prioritized by integrating several tools and public data sources for novel CHD candidate gene identification.Results: A genome-wide genotype(CNV)- phenotype(CHD and sub-categories) analysis on a total of 514 CHD cases(422 from BCH cohort and 92 from SCMC cohort) with CMA testing was conducted. Based on the BCH clinical cohort, the overall diagnostic yield of CMA testing for CHD patients is 12.8-18.48%. There were significantly higher frequency of non-polymorphic CNVs in syndromic CHD than that in isolated CHD(p=0.0078). The diagnostic yield of CMA for syndromic CHD is 14.11-20.56%, whereas the diagnostic yield for isolated CHD is 4.32-9.26%. Isolated conotruncal defects as well as complex conotruncal defects and septal defects are more likely to be associated with CNV than heterotaxy and valve defects. We detected a little lower rate(8.7-12%) in the SCMC cohort. Four recurrent genomic loci were significantly enriched in patients than in controls including 4q terminal region, 15q11.2, 16p12.2 and Yp11.2. They are considered as novel CHD candidate loci. Twenty genes were identified as the most likely novel CHD candidate genes through gene prioritization analysis.Conclusion: The high clinical diagnostic yield of CMA in this study provided evidence for supporting CMA as the first-line diagnostic tool for CHD patients. Syndromic CHD cases are more susceptible to pathogenic CNVs. CMA also provided diagnostic value for isolated CHD patients, particularly for patients with conotruncal defects and septal defects. The CNVs detected in CHD patients suggested a number of CHD candidate genes that warrant further investigation.