SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.
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.
Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania. Electronic address: roys@upmc.edu.
Somak
S
Roy
Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
Mary Beth
MB
Durso
Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
Abigail
A
Wald
Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.
Yuri E
YE
Nikiforov
Division of Molecular and Genomic Pathology, Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania. Electronic address: nikiforovamn@upmc.edu.
Marina N
MN
Nikiforova
D000465:Algorithms; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020407:Internet; D008491:Medical Informatics Applications; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software