Initial Array CGH Screening
Using BAC clone and oligonucleotide array CGH, we identified overlapping microdeletions in 16q24.1q24.2, ranging in size from ∼100 kb to ∼3.5 Mb, in seven patients referred for high-resolution genome analysis (Figures 1A and 1C, Table 1). The first of these patients (D1) was ascertained through our study of the genetic basis of esophageal atresia, for which, to date, 80 syndromic cases have been studied. The remainder were ascertained by queries of databases of patients referred for high-resolution genome analysis for a variety of reasons. Parental samples were available in six out of seven patients (not D2). One deletion (D7) was inherited from a phenotypically abnormal parent; the remaining five were de novo, supporting their likely pathogenic effect. No deletion CNVs in this genomic region were found, either in the Database of Genomic Variants or in the BCM and Signature Genomics databases of over 30,000 patients studied by array CGH. Five of the seven deletions (D2–D5 and D7) were independently verified by FISH analysis (Figure 1D). High-resolution oligonucleotide array CGH (385K or 2.1M NimbleGen) confirmed the deletions and enabled breakpoint characterization in all seven cases (Figures 1E and 1F).
The deletions centered around the FOX transcription factor gene cluster at 16q24.1. All but one harbored FOXF1, a gene with a role in lung and foregut development ascertained on the basis of previous studies of mice.18–20 Patient D7 had an ∼131 kb deletion encompassing FOXC2 and FOXL1 but not FOXF1.