Targeted 'Next-Generation' sequencing in anophthalmia and microphthalmia patients confirms SOX2, OTX2 and FOXE3 mutations

BMC Medical Genetics

Research Article

Jason Flannick¹  Jiang Li²  Mani Yahyavi³  Nelson Lopez Jimenez³  Tanya Bardakjian⁴ 

[1] Broad Institute of Harvard and MIT, Cambridge MA Massachusetts General Hospital, Boston, Massachusetts, USA;Department of Neurology, University of California, San Francisco, 94143-0114, San Francisco, California, USA;Department of Pediatrics, Division of Genetics, University of California, San Francisco, 533 Parnassus St, Room U585P, 94143-0748, San Francisco, CA, USA;Division of Genetics, Department of Pediatrics, Albert Einstein Medical Center, 19141, Philadelphia, Pennsylvania, USA;

关键词: anophthalmia;    microphthalmia;    next-generation sequencing;    SOX2;    OTX2;    FOXE3;   

DOI  :  10.1186/1471-2350-12-172

 received in 2011-10-11, accepted in 2011-12-28,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundAnophthalmia/microphthalmia (A/M) is caused by mutations in several different transcription factors, but mutations in each causative gene are relatively rare, emphasizing the need for a testing approach that screens multiple genes simultaneously. We used next-generation sequencing to screen 15 A/M patients for mutations in 9 pathogenic genes to evaluate this technology for screening in A/M.MethodsWe used a pooled sequencing design, together with custom single nucleotide polymorphism (SNP) calling software. We verified predicted sequence alterations using Sanger sequencing.ResultsWe verified three mutations - c.542delC in SOX2, resulting in p.Pro181Argfs*22, p.Glu105X in OTX2 and p.Cys240X in FOXE3. We found several novel sequence alterations and SNPs that were likely to be non-pathogenic - p.Glu42Lys in CRYBA4, p.Val201Met in FOXE3 and p.Asp291Asn in VSX2. Our analysis methodology gave one false positive result comprising a mutation in PAX6 (c.1268A > T, predicting p.X423LeuextX*15) that was not verified by Sanger sequencing. We also failed to detect one 20 base pair (bp) deletion and one 3 bp duplication in SOX2.ConclusionsOur results demonstrated the power of next-generation sequencing with pooled sample groups for the rapid screening of candidate genes for A/M as we were correctly able to identify disease-causing mutations. However, next-generation sequencing was less useful for small, intragenic deletions and duplications. We did not find mutations in 10/15 patients and conclude that there is a need for further gene discovery in A/M.

【 授权许可】

Unknown   
© LopezJimenez et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.