Computational protocol: CIB2, defective in isolated deafness, is key for auditory hair cell mechanotransduction and survival

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Protocol publication

[…] Targeted genomic enrichment (TGE) and massively parallel sequencing (MPS) using the OtoSCOPE® platform was performed on the proband in Trio‐A and one affected individual from family L‐700, to screen all known genes implicated in NSHL and USH for possible mutations as previously described (Booth et al, ; Sloan‐Heggen et al, ). Enriched libraries were sequenced at the University of Iowa Genomics Core on an Illumina HiSeq 2000 (Illumina, Inc., San Diego, CA) using 100‐bp paired‐end reads. Data analysis was performed using a custom Galaxy annotation pipeline as previously described (Azaiez et al, , ; Booth et al, ). After mapping and variant calling, variants were annotated, filtered and prioritized as previously described (Azaiez et al, ; Booth et al, ). Briefly, variants were initially filtered based on depth (> 10) and quality score (> 30). Variant was further filtered based on minor allele frequency (MAF) < 2% in Genome Aggregation Database (gnomAD), 1000 Genomes Project database, the Exome Aggregation Consortium (ExAC) and the National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project Exome Variant Server (EVS). Next variants were prioritized based on mutation type (missense, nonsense, indel or splice site), conservation (GERP and PhyloP) and predicted deleteriousness (SIFT, PolyPhen2, MutationTaster, LRT and the Combined Annotation Dependent Depletion (CADD)). Additionally, samples were analysed for CNVs using a sliding window method to assess read‐depth ratios (Nord et al, ). The two reported variants and relevant data have been submitted to the University of Iowa Deafness Variation Database (http://deafnessvariationdatabase.org/) for expert curation and integration. […]

Pipeline specifications

Software tools GERP, PHAST, SIFT, PolyPhen, MutationTaster, CADD
Databases Exome Variant Server gnomAD
Applications WGS analysis, WES analysis
Organisms Homo sapiens, Mus musculus
Diseases Congenital Abnormalities, Retinal Diseases