Computational protocol: Recurrent candidiasis and early-onset gastric cancer in a patient with a genetically defined partial MYD88 defect

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Protocol publication

[…] Genomic DNA was extracted from peripheral blood cells and hybridized to Affymetrix SNP6.0 arrays (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol. The genotype was generated using the Birdseed analysis software incorporated in the Affymetrix Genotyping Console v2.1 (Affymetrix). Detected copy number variants (CNVs) were compared to a set of healthy controls, as described previously [], to exclude regions of normal variation.Massive parallel whole-exome sequencing was performed after DNA enrichment using the human SureSelect 50 Mb kit (version 2, Agilent Technologies, Santa Clara, CA, United States) on a 5500XL SOLiD platform (Life Technologies, Bleiswijk, The Netherlands). Reads were mapped to the hg19 reference genome using SOLiD BioScope software (Life Technologies) []. Variants were annotated using an in-house annotation pipeline, as described previously []. Briefly, from our total set of variants we selected high-confidence (≥5 variant reads and/or ≥20 % variant reads) non-synonymous variants with a SNP frequency in dbSNP (v132) below 1 % that were present at most once in our in-house variant database containing 2096 exomes (the majority of European ancestry) [].Missense variants were considered putatively pathogenic when the affected nucleotide was highly conserved (PhyloP ≥ 3.0) and if two of the following three in silico prediction programs considered this variant deleterious/damaging: SIFT [], PolyPhen-2 [], and Align GVGD [] [all incorporated in the Alamut 2.0 software package (Interactive Biosoftware, Rouen, France)]. […]

Pipeline specifications

Software tools SOLiD BioScope Software, PHAST, SIFT, PolyPhen, Align-GVGD
Databases dbSNP
Application WES analysis
Organisms Candida albicans, Homo sapiens
Diseases Candidiasis, Stomach Neoplasms, Genetic Diseases, Inborn