Copy number variations in 375 patients with oesophageal atresia and/or tracheoesophageal fistula

Abstract

Oesophageal atresia (OA) with or without tracheoesophageal fistula (TOF) are rare anatomical congenital malformations whose cause is unknown in over 90% of patients. A genetic background is suggested, and among the reported genetic defects are copy number variations (CNVs). We hypothesized that CNVs contribute to OA/TOF development. Quantifying their prevalence could aid in genetic diagnosis and clinical care strategies. Therefore, we profiled 375 patients in a combined Dutch, American and German cohort via genomic microarray and compared the CNV profiles with their unaffected parents and published control cohorts. We identified 167 rare CNVs containing genes (frequency<0.0005 in our in-house cohort). Eight rare CNVs - in six patients - were de novo, including one CNV previously associated with oesophageal disease. (hg19 chr7:g.(143820444_143839360)_(159119486_159138663)del) 1.55% of isolated OA/TOF patients and 1.62% of patients with additional congenital anomalies had de novo CNVs. Furthermore, three (15q13.3, 16p13.3 and 22q11.2) susceptibility loci were identified based on their overlap with known OA/TOF-associated CNV syndromes and overlap with loci in published CNV association case-control studies in developmental delay. Our study suggests that CNVs contribute to OA/TOF development. In addition to the identified likely deleterious de novo CNVs, we detected 167 rare CNVs. Although not directly disease-causing, these CNVs might be of interest, as they can act as a modifier in a multiple hit model, or as the second hit in a recessive condition.

Figure 1

Filtering and prioritizing CNVs. After quality control and manual evaluation of CNVs, 374 CNVs larger than 30 kb, either absent or rare in the modified Database of Genomic Variants incorporated in the Nexus software, remained. Out of 374, 123 did not contain genes. In all, 257 were absent and 5 were present once in our in-house control database. These 262 CNVs were either gene-rich – containing genes – (n=167) or gene-poor (n=95). Two gene-poor CNVs were suspected of being de novo in microarray trio analysis. Eight out of 74 evaluated CNVs were de novo. Almost all of the rare CNVs (140) were widely distributed over the genome. However, our analysis yielded a total of 12 loci – containing 29 CNVs – which were affected by a rare CNV more than once and were present in more than one patient.

Figure 2

Size and type distribution of rare CNV. Total number of rare CNVs in the Erasmus MC – Sophia, Baylor College of Medicine and University of Bonn OA/TOF cohort (=375). Homozygous loss is counted as loss. Bins represent size ranges, for example, the 50–100 kb bin contains all CNVs within the size range of 50–100 kb.

Figure 3

De novo deletion ranging from chromosomal band 7q35 to 7q36.3. Note the loss (red) in the patients logR track and the loss of heterozygosity (yellow) in the patients B-allele frequency (BAF) plot. qPCR/FISH/MAQ assay validation results in Supplementary Figure 1.

Figure 4

De novo duplication on chromosome 8p22. Note the gain (blue dots/arrow) in the patients' logR track and allelic imbalance (purple dots/arrow) in the patients BAF plot. qPCR/FISH/MAQ assay validation results in Supplementary Figure 1.