Evidence for replicative mechanism in a CHD7 rearrangement in a patient with CHARGE syndrome

• Published in: American journal of medical genetics. Part A Vol. 161A; no. 12; pp. 3182 - 3186
• Main Authors: Vatta, Matteo, Niu, Zhiyv, Lupski, James R., Putnam, Philip, Spoonamore, Katherine G., Fang, Ping, Eng, Christine M., Willis, Alecia S.
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 01-12-2013; Wiley Subscription Services, Inc
• Subjects: Abnormalities, Multiple - genetics; Abnormalities, Multiple - physiopathology; Breakpoints; CHARGE syndrome; CHARGE Syndrome - genetics; CHARGE Syndrome - physiopathology; CHD7; Child; Diagnosis; DNA Helicases - genetics; DNA Replication - genetics; DNA-Binding Proteins - genetics; Exons; Female; FoSTeS/MMBIR; Gene Deletion; Haploinsufficiency; Humans; Lymphocytes; MLPA; Mutation; Peripheral blood; CHARGE syndrome; MLPA; FoSTeS/MMBIR; CHD7
• ISSN: 1552-4825; 1552-4833
• DOI: 10.1002/ajmg.a.36178

Haploinsufficiency of CHD7 (OMIM# 608892) is known to cause CHARGE syndrome (OMIM# 214800). Molecular testing supports a definitive diagnosis in approximately 65–70% of cases. Most CHD7 mutations arise de novo, and no mutations affecting exon‐7 have been reported to date. We report on an 8‐year‐old girl diagnosed with CHARGE syndrome that was referred to our laboratory for comprehensive CHD7 gene screening. Genomic DNA from the subject with a suspected diagnosis of CHARGE was isolated from peripheral blood lymphocytes and comprehensive Sanger sequencing, along with deletion/duplication analysis of the CHD7 gene using multiplex ligation‐dependent probe amplification (MLPA), was performed. MLPA analysis identified a reduced single probe signal for exon‐7 of the CHD7 gene consistent with potential heterozygous deletion. Long‐range PCR breakpoint analysis identified a complex genomic rearrangement (CGR) leading to the deletion of exon‐7 and breakpoints consistent with a replicative mechanism such as fork stalling and template switching (FoSTeS) or microhomology‐mediated break‐induced replication (MMBIR). Taken together this represents the first evidence for a CHD7 intragenic CGR in a patient with CHARGE syndrome leading to what appears to be also the first report of a mutation specifically disrupting exon‐7. Although likely rare, CGR may represent an overlooked mechanism in subjects with CHARGE syndrome that can be missed by current sequencing and dosage assays. © 2013 Wiley Periodicals, Inc.