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. 2017 Dec;1(6):381-386.
doi: 10.1017/cts.2017.311.

Rapid Clinical Diagnostic Variant Investigation of Genomic Patient Sequencing Data With iobio Web Tools

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Free PMC article

Rapid Clinical Diagnostic Variant Investigation of Genomic Patient Sequencing Data With iobio Web Tools

Alistair Ward et al. J Clin Transl Sci. .
Free PMC article

Abstract

Introduction: Computational analysis of genome or exome sequences may improve inherited disease diagnosis, but is costly and time-consuming.

Methods: We describe the use of iobio, a web-based tool suite for intuitive, real-time genome diagnostic analyses.

Results: We used iobio to identify the disease-causing variant in a patient with early infantile epileptic encephalopathy with prior nondiagnostic genetic testing.

Conclusions: Iobio tools can be used by clinicians to rapidly identify disease-causing variants from genomic patient sequencing data.

Keywords: Genome sequencing; clinical diagnostic variant analysis; disease variant identification; early infantile epileptic encephalopathy; web-based data analysis.

Figures

Fig. 1
Fig. 1
Examining sequence alignment quality in the proband using the bam.iobio tool. Sequence coverage across all chromosomes (top middle), and relevant alignment metrics are visualized, including the distributions of read coverage, fragment length, and mapping quality (histograms on the right); as well as summary metrics including read mapping rate, and polymerase chain reaction (PCR) duplication rate (ring charts on left).
Fig. 2
Fig. 2
Identifying the causative variant in the proband using the gene.iobio tool. This tool facilitates sample data selection (i.e., sequence alignment and variant files for the proband and parents); candidate gene list generation according to the patient phenotype; variant filtering according, for example, to mode of inheritance, observed and/or predicted pathogenicity, and population frequency; and gene/variant ranking and prioritization. The insert shows the salient properties of the diagnostic de novo disease-causing variant in the proband pinpointed by the tool.

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