Computational protocol: Mutations in CTNNA1 cause butterfly-shaped pigment dystrophy and perturbed retinal pigment epithelium integrity

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Protocol publication

[…] To identify the genetic defect in a large Dutch family with nine individuals affected by butterfly-shaped pigment dystrophy (family A; ), the DNA of two affected individuals (A-III:7 and A-III:11) was analyzed using whole exome sequencing. The exomes were enriched using the SureSelect Human All Exon v.2 Kit (50Mb), which targets the exonic sequences of approximately 21,000 genes, according to the manufacturer's protocol (Agilent). Sequencing was performed on a 5500xl SOLiD sequencing platform (Life Technologies). BioScope software v.1.3 (Life Technologies) was used to map color space reads along the hg19 reference genome assembly. The high-stringency calling DiBayes algorithm was used for single-nucleotide variant calling, and small insertions and deletions were detected using the small Indel Tool.All coding exons and intron-exon boundaries of the CTNNA1 gene were screened for mutations in 93 unrelated probands with butterfly-shaped pigment dystrophy (N=19) or other pattern dystrophies (N=74) by Sanger sequencing. Primers for PCR amplification and sequencing were designed with Primer3 software (). Missense variants detected in the CTNNA1 gene were analyzed in ethnically matched control individuals by restriction enzyme analysis (TaqI for c.953T>C; and BccI for c.1293T>G;), allele-specific PCR (c.919G>A), or Sanger sequencing (c.160C>T). […]

Pipeline specifications

Software tools SOLiD BioScope Software, Primer3
Applications WES analysis, qPCR
Organisms Mus musculus
Diseases Eye Diseases, Macular Degeneration, Retinal Diseases