Computational protocol: Mutations in N-acetylglucosamine (O-GlcNAc) transferase in patients with X-linked intellectual disability

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Protocol publication

[…] For patient 1, whole exome sequencing was performed in a trio diagnostic approach as described before (). Exome capture was performed with the SureSelect Human All Exon v4 enrichment kit (Agilent, Santa Clara, CA). Whole exome sequencing was performed on the Illumina HiSeq platform (San Diego, CA). Data were analyzed with the BWA (read alignment) and GATK (variant calling) software packages. Variants were annotated using an in-house developed pipeline. Prioritization of variants was done by an in-house designed “variant interface” and manual curation.Exomes of patient 2 and parents were enriched using the SureSelect XT Human All Exon V5 kit (Agilent) and sequenced in rapid run mode on the HiSeq2500 sequencing system (Illumina) at a mean target depth of 100×. The target is defined as all coding exons of UCSC and Ensembl ± 20-bp intron flanks. At this depth >95% of the target is covered at least 15 times. Reads were aligned to hg19 using BWA (BWA-MEM v0.7.5a), and variants were called using the GATK haplotype caller (v2.7-2). Detected variants were annotated, filtered, and prioritized using the Bench NGS Lab platform (Cartagenia; Agilent). The OGT gene sequences of the grandmother and great-grandmother were analyzed to study the origin of the mutation. All potentially causative variants were confirmed by Sanger sequencing. [...] Scatter plots indicate ratios of any given normalized signal as averaged from three biological replicates, with the error bars representing standard deviation. Variations in data were calculated by Mann–Whitney U test using GraphPad Prism 5.0. Power calculations were performed using G*Power 3.1. […]

Pipeline specifications

Software tools BWA, GATK, G*Power
Applications Miscellaneous, WES analysis
Organisms Homo sapiens
Diseases Congenital Abnormalities, Neurodegenerative Diseases, Genetic Diseases, X-Linked