Computational protocol: Loss of function of the E3 ubiquitin-protein ligase UBE3B causes Kaufman oculocerebrofacial syndrome

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Protocol publication

[…] Targeted enrichment and massively parallel sequencing were performed on genomic DNA extracted from circulating leucocytes of patient UCSC-KS01. Exome capture was performed using NimbleGen SeqCap EZ Exome V. 2.0 (Roche), and sequencing using a HiSeq2000 instrument (Illumina). Paired-end reads were aligned to human genome (UCSC GRCh37/hg19) with the Burrows–Wheeler Aligner (BWA V. 0.5.9-rc1). Presumed PCR duplicates were discarded with the Picard's MarkDuplicates utility (http://picard.sourceforge.net). Local realignment and base-quality-score recalibration were performed with the Genome Analysis Toolkit (GATK). Single nucleotide polymorphisms (SNPs) and indels were identified with the GATK Unified Genotyper, excluding from further analyses variants which failed to meet any of the following criteria: alignment quality >50; quality-by-depth score >1.5; variant resulting from >3 reads having unambiguous mapping (the number being >1/10 of all aligned reads). Variants were filtered against available public (1000 Genomes Project and dbSNP135) and in-house databases. Functional annotation of variants was performed by using snpEff V. 2.0.5d. Variants within segmental duplications and variants outside highly conserved regions in vertebrates were filtered using wAnnovar (http://wannovar.usc.edu). […]

Pipeline specifications

Software tools BWA, Picard, GATK, SnpEff, wANNOVAR
Databases dbSNP
Application WES analysis
Diseases Eye Abnormalities, Microcephaly, Myopia
Chemicals Etodolac