Computational protocol: Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

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Protocol publication

[…] Image analysis was performed with the default parameters of Illumina RTA pipeline, and base calling was carried out using CASAVA. The sequence reads were mapped and aligned to the Human Reference Genome (UCSC hg19, NCBI build 37) using the Burrows-Wheeler transformation algorithm, and duplicated reads were removed using Picard [, ]. FastQC was used to check the quality of sequence data []. Calling of SNPs and InDels was done using GATK Unified Genotyper, which uses a Bayesian genotype likelihood model to report alleles and Phred-scaled confidence values []. Variants (SNVs and indels) were called with SAMTools, with reference to public databases including dbSNP and 1000Genomes and gnomAD []. Analysis was performed with preference to variants located in genes implicated in atypical non-autoimmune forms of diabetes and early-onset obesity. The prioritized candidate gene list was obtained by reviewing publications in PubMed and OMIM. Analysis focused on non-synonymous coding variants, frameshift indels, and variants affecting splice sites, as these are most likely to be pathogenic. Non-exonic and synonymous variants were excluded from further analysis. Missense variants were evaluated for functional impact using a variety of in-silico prediction tools including SIFT [], Polyphen2 [], MelaLR [], MetaSVN [], fathmm-MKL [], DANN [], CADD [], MutationTaster [], Mutation Assesser [] and LRT []. […]

Pipeline specifications

Software tools BaseSpace, Picard, FastQC, GATK, SAMtools, SIFT, PolyPhen, FATHMM-XF, DANN, CADD, MutationTaster
Databases dbSNP OMIM gnomAD
Applications WGS analysis, WES analysis
Organisms Homo sapiens
Diseases Congenital Abnormalities, Diabetes Mellitus, Diabetes Mellitus, Type 2, Diabetic Nephropathies, Kidney Diseases, Liver Diseases