Evaluation of Commercial Next-Generation Sequencing Bioinformatics Software Solutions.

07:00 EST 18th November 2019 | BioPortfolio

Summary of "Evaluation of Commercial Next-Generation Sequencing Bioinformatics Software Solutions."

Next-generation sequencing (NGS) diagnostics continue to expand rapidly in clinical medicine. An ever-expanding menu of molecular biomarkers are deemed important for diagnostic, prognostic, and therapeutic assessment in patients. The increasing role of NGS in the clinic is driven mainly by the falling costs of sequencing. However, the data-intensive nature of NGS makes bioinformatic analysis a major challenge to many clinical laboratories. Critically needed NGS bioinformatics personnel are hard to recruit and retain in small- to mid-size clinical laboratories. Also, NGS software often lacks the scalability necessary for expanded clinical laboratory testing volumes. Commercial software solutions aim to bridge the bioinformatics "barrier" via turnkey informatics solutions tailored specifically for the clinical workplace. Yet, there has been no systematic assessment of these software solutions thus far. This paper presents our end-to-end vendor evaluation experience of commercial NGS bioinformatics solutions. Six different commercial vendor solutions were assessed systematically. Key metrics of NGS software evaluation to aid in the robust assessment of software solutions are described. Comprehensive feedback provided by the TriCore molecular pathology team enabled the final vendor selection. Many key lessons were learned during the software evaluation process, which are described here. This manuscript aims to provide a detailed road map for small- to mid-size clinical laboratories interested in evaluating commercial bioinformatics solutions available in the marketplace.


Journal Details

This article was published in the following journal.

Name: The Journal of molecular diagnostics : JMD
ISSN: 1943-7811


DeepDyve research library

PubMed Articles [15697 Associated PubMed Articles listed on BioPortfolio]

Using R and Bioconductor in Clinical Genomics and Transcriptomics.

Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data generated by next-generation sequencing. Recent guidelines emphasize the need for rigorous validation and asse...

ClinVAP: A reporting strategy from variants to therapeutic options.

Next-generation sequencing (NGS) has become routine in oncology and opens up new avenues of therapies, particularly in personalized oncology setting. An increasing number of cases also implies a need ...

Application of next-generation sequencing for the identification of herbal products.

Conventional Sanger sequencing for authentication of herbal products is difficult since they are mixture of herbs with fragmented DNA. Next-generation sequencing (NGS) techniques give massive parallel...

VikNGS: A C ++ Variant Integration Kit for Next Generation Sequencing Association Analysis.

Integration of next generation sequencing data (NGS) across different research studies can improve the power of genetic association testing by increasing sample size and can obviate the need for seque...

SCSsim: an integrated tool for simulating single-cell genome sequencing data.

Allele dropout (ADO) and unbalanced amplification of alleles are main technical issues of single-cell sequencing (SCS), and effectively emulating these issues is necessary for reliably benchmarking SC...

Clinical Trials [4302 Associated Clinical Trials listed on BioPortfolio]

Enhancing Diagnosis in Chronic B-cell Lymphoproliferative Disorders Using Next-Generation Sequencing

To enhance the diagnosis of unclassifiable, non-CLL B-LPDs using next-generation sequencing technology.

Development of Biomarker for the Evaluation of Response After Neoadjuvant Therapy in Patients With Pancreatic Cancer

The purpose of this study is to identify and apply biomarkers that can provide better information than previous imaging and blood tests when evaluating the response after neoadjuvant chemo...

Molecular Profiling to Improve Outcome of Patients in Cancer. A Pilot Study

Next Generation Sequencing in cancer: a feasibility study in France to assess sample circuit and to perform analyzes within a limited time.

Diagnosis of Lynch Syndrome Based on Next-generation Sequencing in Colorectal Cancer

The purpose of this study is to determine the proportion of patients diagnosed with Lynch syndrome in colorectal cancer patients with the loss of staining by immunohistochemistry (IHC) of ...

Personalized Therapy of Molecular Tumor Board Participation With the Guidance of Next Generation Sequencing

This study seeks to evaluate the clinical value of the personalized therapy model with the guidance of Molecular Tumor Board (MTB) after Next Generation Sequencing(NGS), and to track patie...

Medical and Biotech [MESH] Definitions

Sterile solutions, essentially free from foreign particles and suitably compounded and dispensed, for instillation into the eye. It does not include solutions for cleaning eyeglasses or CONTACT LENS SOLUTIONS. (From Dorland, 27th ed)

The act of testing the software for compliance with a standard.

Specifications and instructions applied to the software.

Software capable of recognizing dictation and transcribing the spoken words into written text.

Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.

Quick Search

DeepDyve research library

Relevant Topic

DNA sequencing
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...

Searches Linking to this Article