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J Mol Diagn. 2014 Jan;16(1):11-22. doi: 10.1016/j.jmoldx.2013.08.005. Epub 2013 Nov 9.

SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.

Author information

1
Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania. Electronic address: roys@upmc.edu.
2
Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
3
Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania. Electronic address: nikiforovamn@upmc.edu.

Abstract

A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was designed using HTML5, CSS3, and Javascript. The server-side processing (VB.NET) relied on interaction with a customized SQL server 2008 R2 database. Overall, 104 cases (1062 variant calls) were analyzed by SeqReporter. Each variant call was classified into one of five report levels: i) known clinical significance, ii) uncertain clinical significance, iii) pending pathologists' review, iv) synonymous and deep intronic, and v) platform and panel-specific sequence errors. SeqReporter correctly annotated and classified 99.9% (859 of 860) of sequence variants, including 68.7% synonymous single-nucleotide variants, 28.3% nonsynonymous single-nucleotide variants, 1.7% insertions, and 1.3% deletions. One variant of potential clinical significance was re-classified after pathologist review. Laboratory information system-compatible clinical reports were generated automatically. SeqReporter also facilitated quality management activities. SeqReporter is an example of a customized and well-designed informatics solution to optimize and automate the downstream analysis of clinical next-generation sequencing data. We propose it as a model that may envisage the development of a comprehensive clinical informatics solution.

PMID:
24220144
DOI:
10.1016/j.jmoldx.2013.08.005
[Indexed for MEDLINE]

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