Close
  Indian J Med Microbiol
 

Figure 3: HMVV workflow. HMVV integrates all workflow from NGS data processing through variant annotation. (a) The molecular technologist enters patient metadata such as name, medical record number, and order number using the “Enter Sample” interface. (b) The “Sample List” panel shows all samples in the database for the selected assay. The sample list can be sorted by clicking any column header. (c) The “Mutation List” panel shows key information for each variant detected for a selected sample. Fields include Gene-gene name – Exon: Exon location of the detected variant, HGVSc: Human Genome Variation Society Coding DNA nomenclature, HGVSp: Human Genome Variation Society Protein nomenclature, dbSNP: Link to the variant in the dbSNP database, cosmicID: Link to the variant in the COSMIC database, Type: Variant type, including snv, deletion, insertion, indel, Genotype: Impact as predicted by Variant Effect Predictor, Life Technologies assays – altFreq: Allele frequency based on Flow Evaluator observation counts, readDP: Flow Evaluator read depth at the locus to a position and used in variant calling, altReadDP: Flow Evaluator Alternate allele observations, Illumina assays – altFreq: The percentage of reads supporting the alternate allele, readDP: Number of base calls aligned to a position and used in variant calling, altReadDP: The number of alternate calls, Occurrence: Number of previous occurrences of the detected variant in our database, Annotation: The text entered by the pathologist to generate the clinical laboratory report, (d) The “Annotation” panel allows the pathologist to designate if the variant is known to be somatic/germline/unknown and benign/likely benign/likely pathogenic/pathogenic/unknown. The pathologist can also enter text to annotate the variant, such as its likely implication to prognosis and targeted therapy, to be used in the clinical laboratory report. HMVV: Houston Methodist Variant Viewer

Figure 3: HMVV workflow. HMVV integrates all workflow from NGS data processing through variant annotation. (a) The molecular technologist enters patient metadata such as name, medical record number, and order number using the “Enter Sample” interface. (b) The “Sample List” panel shows all samples in the database for the selected assay. The sample list can be sorted by clicking any column header. (c) The “Mutation List” panel shows key information for each variant detected for a selected sample. Fields include Gene-gene name – Exon: Exon location of the detected variant, HGVSc: Human Genome Variation Society Coding DNA nomenclature, HGVSp: Human Genome Variation Society Protein nomenclature, dbSNP: Link to the variant in the dbSNP database, cosmicID: Link to the variant in the COSMIC database, Type: Variant type, including snv, deletion, insertion, indel, Genotype: Impact as predicted by Variant Effect Predictor, Life Technologies assays – altFreq: Allele frequency based on Flow Evaluator observation counts, readDP: Flow Evaluator read depth at the locus to a position and used in variant calling, altReadDP: Flow Evaluator Alternate allele observations, Illumina assays – altFreq: The percentage of reads supporting the alternate allele, readDP: Number of base calls aligned to a position and used in variant calling, altReadDP: The number of alternate calls, Occurrence: Number of previous occurrences of the detected variant in our database, Annotation: The text entered by the pathologist to generate the clinical laboratory report, (d) The “Annotation” panel allows the pathologist to designate if the variant is known to be somatic/germline/unknown and benign/likely benign/likely pathogenic/pathogenic/unknown. The pathologist can also enter text to annotate the variant, such as its likely implication to prognosis and targeted therapy, to be used in the clinical laboratory report. HMVV: Houston Methodist Variant Viewer