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Pipeline publication

[…] ted regions (UTRs) for all genes previously implicated in retinal degeneration as of early 2013, as listed by Retnet, were included as capture targets: a total of 3592 capture regions across 182 genes, spanning a total sequence size of 1.25 Mb, of which, 497 kb were coding exons, and the remainder UTRs (see S1)., , Captured patient DNA was multiplexed into a 96-sample pool, and sent for sequencing. Sequencing was performed off-site by BGI Tech using an Illumina HiSeq 2000 (Illumina, San Diego, California, USA). Confirmatory single-read sequencing was also performed to verify the presence of candidate mutations., Sequence data were demultiplexed and mapped to the human genome (hg19) using BWA V.0.7.4. Duplicate reads were flagged using Picard V.1.106, and downstream analysis and variant calling were performed using the GATK V.2.8 according to the protocol specified in the GATK Best Practices Workflow., The list of identified variants was annotated with snpEFF and dbNSFP. Synonymous and common variants were filtered out, and the remaining list of rare variants with the potential to affect protein sequence was output for manual curation., The proband presented at 80 years of age with a 6-month history of difficulties with steps. He commented on a lifelong history of night-blindness, which had remained unchanged throughout his life. There was no family history of night-blindness or day vision problems affecting either his parents, three siblings, ranging in age from 73 to 75 years or his three children aged 38–51 years. There was no history of parental consanguinity. His general health was good. He suffered for 10 years prior to presentation […]

Pipeline specifications

Software tools BWA, Picard, GATK, SnpEff
Organisms Homo sapiens, Mus musculus
Diseases Sensation Disorders, Neurologic Manifestations, Blindness, Retinal Degeneration, Retinal Diseases, Retinal Degeneration, Eye Diseases, Hereditary, Retinitis Pigmentosa, Genetic Diseases, Inborn