Computational protocol: A de novo missense mutation in ZMYND11 is associated with global developmental delay, seizures, and hypotonia

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Protocol publication

[…] DNA was extracted from blood obtained from the parents, proband, and an unaffected sibling. Exome libraries were prepared with the SureSelectXT2 Human All Exon V4 Kit (Agilent Technologies), followed by 100-bp paired-end sequencing on a HiSeq2000 instrument (Illumina Inc.) by GeneDX (GeneDX). Filtered reads were aligned to the human genome (Hg19/GRC37) using the Burrows–Wheeler transform (BWA-MEM) (). Reads were sorted and PCR duplicates were removed using Picard (). Base quality recalibration and indel realignment were performed using the Genome Analysis Toolkit (GATK) (). Variants were called jointly with HaplotypeCaller and recalibrated with GATK, annotated with SnpEff, and selected (SnpSift) for protein-coding events (). Prediction scores were loaded from dbNSFP (Database for Nonsynonymous SNPs' Functional Predictions) and used for filtering (Supplemental Table 3). Autosomal-recessive, autosomal-dominant, and X-linked inheritance models were considered when analyzing the data. Relatedness and gender of the four individuals were checked with Plink v1.07. […]

Pipeline specifications

Software tools BWA, Picard, GATK, SnpEff, SnpSift, PLINK
Databases dbNSFP
Applications WES analysis, GWAS
Organisms Homo sapiens
Diseases Congenital Abnormalities, Hypersensitivity, Movement Disorders, Angelman Syndrome, Eosinophilic Esophagitis
Chemicals Zinc