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Pipeline publication

[…] h various form of retinal degeneration (including LCA, RP, Stargardt disease, CORD, and achromatopsia) to the Penn Genome Frontiers Institute were evaluated by WES (). Samples had previously been screened using Asper Ophthalmics (Tartu, Estonia) arrayed primer extension (APEX) multigene panels for the relevant disease (using panels that were available from 2009 to 2014) and no disease-causing variants had been identified. Target enrichment was performed with the Agilent SureSelect target enrichment system (Agilent Technologies, Santa Clara, CA, USA), and the sequencing was performed on Illumina HiSeq2000 (Illumina, San Diego, CA, USA)., Mapping and variant identification was performed using Galaxy. The FASTQ files for each patient were mapped to the reference human genome (hg18) using Burrows-Wheeler Aligner for Ilumina. Variants were identified using freebayes. Variants were annotated using Annovar., A semi-masked analysis was used to identify potentially pathogenic mutations without knowledge of the type of retinal degeneration. We created a curated list of genes linked to any form of retinal degeneration and used a python script (Python Software Foundation, Fredericksburg, VA, USA) to create a customized list of potential pathogenic variants for each patient. This list consisted of retinal degeneration genes with variants with an allele frequency of ,0.05. Those mutations were then prioritized based on mutation type and known facts about the mutations from the Single Nucleotide Polymorphism Database (dbSNP) (https://www.ncbi.nlm.nih.gov/projects/SNP/) and the Universal Protei […]

Pipeline specifications

Software tools Galaxy, BWA, FreeBayes, ANNOVAR
Databases UniProt