Rare Copy Number Changes Identified In Congenital Heart Disease Using ROMA
Genomic microarray analysis has recently revealed small-scale changes in gene copy number to be a major form of human variation. Congenital heart disease (CHD) is the most common human congenital malformation with a strong genetic component, yet most cases remain unexplained. CHD is a feature of most segmental aneuploidy syndromes and thus heart development must be sensitive to copy number changes (CNCs) in numerous parts of the genome. We hypothesize that small CNCs not detectable by standard cytogenetic analysis may be a significant cause of CHD.
We present preliminary data using ROMA (Representational Oligonucleotide Microarray Analysis) to look for CNCs in 22 patients with hypoplastic left heart syndrome and 12 patients with conotruncal defects. We performed reverse-color CGH on an 85K Nimblegen chip with 35kb resolution. CNCs were considered rare and of interest if they were not observed in a comparison sample of 500 previously studied cases. These include 175 normal individuals: the rest had various conditions such as autism but no CHD.
As expected, all CHD patients differed from control in 7 to 14 regions of the genome. Most of these changes were observed frequently in the comparison sample and are presumably polymorphic normal variants. We identified 18 rare CNCs in 13 patients. Two CNCs were greater than 1 Mb in size, which is rare for the common variants. Nine rare CNCs contained known genes. One overlapping deletion in 4p was observed in four patients with conotruncal disease. While intriguing, these studies are very preliminary. Verification by FISH and parental analyses to identify de novo changes are in progress. In addition, all confirmed de novo CNCs will be analyzed at a higher 6kb resolution using a custom-designed chip. However, these data suggest that rare CNCs may contribute significantly to the cause of CHD.