A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts

Abstract

Background: DNA copy number variants play an important part in the development of common birth defects such as oral clefts. Individual patients with multiple birth defects (including oral clefts) have been shown to carry small and large chromosomal deletions.

Methods: We investigated the role of polymorphic copy number deletions by comparing transmission rates of deletions from parents to offspring in case-parent trios of European ancestry ascertained through a cleft proband with trios ascertained through a normal offspring. DNA copy numbers in trios were called using the joint hidden Markov model in the freely available PennCNV software. All statistical analyses were performed using Bioconductor tools in the open source environment R.

Results: We identified a 67 kb region in the gene MGAM on chromosome 7q34, and a 206 kb region overlapping genes ADAM3A and ADAM5 on chromosome 8p11, where deletions are more frequently transmitted to cleft offspring than control offspring.

Conclusions: These genes or nearby regulatory elements may be involved in the etiology of oral clefts.

Keywords: DNA copy numbers; Oral clefts; case-parent trios; inherited deletions.

Figure 1

Left panel: Allele transmission rate estimates (cleft trios - solid circle; control trios - open circle) with unadjusted 95% confidence intervals, for the 13 copy number polymorphism regions identified. Expected transmission under independent assortment is 0.5. Right panel: The -log₁₀ p-values derived from one-sided Fisher's exact tests for equality of transmission rates in cleft and control trios, versus the alternative of increased transmission rates in the cleft group. The vertical lines indicate the nominal significance (-log₁₀(0.05) = 1.30), and the Bonferroni corrected p-values (-log₁₀(0.05/13) = 2.41).

Figure 2

Quantile-quantile plots of expected versus observed −log₁₀ p-values for the 13 CNP regions (A) and the corresponding 84 CNP components (B). The grey regions indicate confidence regions for the respective order statistics under an independence assumption, though the CNP components are highly correlated due to their proximity within regions.

Figure 3

Location of DNA copy number deletions and test results for equal transmission rates of copy number components between case and control trios in the MGAM region on chromosome 7q34 (left) and the ADAM3A / ADAM5 region on chromosome 8p11 (right). The genomic locations of the components are indicated by vertical bars on the ideograms (top panels), and overlapped with nearby genes (middle panels). Test results are shown as nominal −log₁₀(p) from Fisher's exact test for the respective CNV components, with the genome-wide significance level indicated by a dashed line (bottom panels). There is clear evidence of over-transmission of a deletion CNP in the MGAM region. The ADAM3A / ADAM5 region also contains a possible region of over-transmission.