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Background  Anophthalmia/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.    Methods  We used a pooled sequencing design, together with custom single nucleotide polymorphism (SNP) calling software. We verified predicted sequence alterations using Sanger sequencing.    Results  We verified three mutations - c.542delC in S OX2 , 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 .    Conclusions  Our 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.

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