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Background  Copy number variants (CNVs) may play an important part in the development of common birth defects such as oral clefts, and individual patients with multiple birth defects (including clefts) have been shown to carry small and large chromosomal deletions. In this paper we investigate  de novo  deletions defined as DNA segments missing in an oral cleft proband but present in both unaffected parents. We compare  de novo  deletion frequencies in children of European ancestry with an isolated, non-syndromic oral cleft to frequencies in children of European ancestry from randomly sampled trios.    Results  We identified a genome-wide significant 62 kilo base (kb) non-coding region on chromosome 7p14.1 where  de novo  deletions occur more frequently among oral cleft cases than controls. We also observed wider  de novo  deletions among cleft lip and palate (CLP) cases than seen among cleft palate (CP) and cleft lip (CL) cases.    Conclusions  This study presents a region where  de novo  deletions appear to be involved in the etiology of oral clefts, although the underlying biological mechanisms are still unknown. Larger  de novo  deletions are more likely to interfere with normal craniofacial development and may result in more severe clefts. Study protocol and sample DNA source can severely affect estimates of  de novo  deletion frequencies. Follow-up studies are needed to further validate these findings and to potentially identify additional structural variants underlying oral clefts.

A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk