Validation and Clinical Applications of a Comprehensive Next Generation Sequencing System for Molecular Characterization of Solid Cancer Tissues

Identification of somatic molecular alterations in primary and metastatic solid tumor specimens can provide critical information regarding tumor biology and its heterogeneity, and enables the detection of molecular markers for clinical personalized treatment assignment. However, the optimal methods and target genes for clinical use are still being in development. Toward this end, we validated a targeted amplification-based NGS panel (Oncomine comprehensive assay v1) on a personal genome machine sequencer for molecular profiling of solid tumors. This panel covers 143 genes, and requires low amounts of DNA (20 ng) and RNA (10 ng). We used 27 FFPE tissue specimens, 10 cell lines, and 24 commercial reference materials to evaluate the performance characteristics of this assay. We also evaluated the performance of the assay on 26 OCT-embedded fresh frozen specimens (OEFF). The assay was found to be highly specific (>99%) and sensitive (>99%), with low false-positive and false-negative rates for single-nucleotide variants, indels, copy number alterations, and gene fusions. Our results indicate that this is a reliable method to determine molecular alterations in both fixed and fresh frozen solid tumor samples, including core needle biopsies.

Clinical pharmacogenomics testing in the era of next generation sequencing: challenges and opportunities for precision medicine

INTRODUCTION

The rapid development and dramatic decrease in cost of sequencing techniques have ushered the implementation of genomic testing in patient care. Next generation DNA sequencing (NGS) techniques have been used increasingly in clinical laboratories to scan the whole or part of the human genome in order to facilitate diagnosis and/or prognostics of genetic disease. Despite many hurdles and debates, pharmacogenomics (PGx) is believed to be an area of genomic medicine where precision medicine could have immediate impact in the near future. Areas covered: This review focuses on lessons learned through early attempts of clinically implementing PGx testing; the challenges and opportunities that PGx testing brings to precision medicine in the era of NGS. Expert commentary: Replacing targeted analysis approach with NGS for PGx testing is neither technically feasible nor necessary currently due to several technical limitations and uncertainty involved in interpreting variants of uncertain significance for PGx variants. However, reporting PGx variants out of clinical whole exome or whole genome sequencing (WES/WGS) might represent additional benefits for patients who are tested by WES/WGS.

The challenges of tumor genetic diversity

The authors review and discuss the implications of genomic analyses documenting the diversity of tumors, both among patients and within individual tumors. Genetic diversity among solid tumors limits targeted therapies, because few mutations that drive tumors are both targetable and at high prevalence. Many more driver mutations and how they affect cellular signaling pathways must be identified if targeted therapy is to become widely useful. Genetic diversity within a tumor-intratumor genetic heterogeneity-makes the tumor a collection of subclones: related yet distinct cancers. Selection for pre-existing, resistant subclones by conventional or targeted therapies may explain many treatment failures. Immune therapy faces the same fundamental challenges. Nevertheless, the processes that generate and maintain heterogeneity might provide novel therapeutic targets. Addressing both types of diversity requires genomic tumor analyses linked to detailed clinical data. The trend toward sequencing restricted cancer gene panels, however, limits the ability to discover new driver mutations and assess intratumor heterogeneity. Clinical data currently collected with genomic analyses often lack critical information, substantially limiting their use in understanding tumor diversity. Now that diversity among and within tumors can no longer be ignored, research and clinical practice must adapt to take diversity into account. Cancer 2017;123:917-27. © 2016 American Cancer Society.

Targeted next-generation sequencing panels for monogenetic disorders in clinical diagnostics: the opportunities and challenges

Next-generation sequencing (NGS) will soon be used for clinically heterogeneous, inherited disorders and the increasing number of disease-causing genes reported. Diagnostic laboratories therefore need to decide which NGS methods they are going to invest in and how to implement them. We discuss here the challenges and opportunities of using targeted resequencing (TRS) panels for diagnosing monogenetic disorders. Of the different NGS approaches available, TRS panels offer the opportunity to sequence and analyze a limited set of predetermined target genes. At present, TRS panels offer better base-pair coverage, running times, costs and dataset handling than other NGS applications such as whole genome sequencing and whole exome sequencing. However, working with TRS panels also poses new challenges in variant interpretation, data handling and bioinformatic analyses. To optimize the analyses, TRS panel testing should be performed by bioinformaticians, clinicians and laboratory staff in close collaboration.

Usability study of clinical exome analysis software: top lessons learned and recommendations

OBJECTIVES

New DNA sequencing technologies have revolutionized the search for genetic disruptions. Targeted sequencing of all protein coding regions of the genome, called exome analysis, is actively used in research-oriented genetics clinics, with the transition to exomes as a standard procedure underway. This transition is challenging; identification of potentially causal mutation(s) amongst ∼10(6) variants requires specialized computation in combination with expert assessment. This study analyzes the usability of user interfaces for clinical exome analysis software. There are two study objectives: (1) To ascertain the key features of successful user interfaces for clinical exome analysis software based on the perspective of expert clinical geneticists, (2) To assess user-system interactions in order to reveal strengths and weaknesses of existing software, inform future design, and accelerate the clinical uptake of exome analysis.

METHODS

Surveys, interviews, and cognitive task analysis were performed for the assessment of two next-generation exome sequence analysis software packages. The subjects included ten clinical geneticists who interacted with the software packages using the "think aloud" method. Subjects' interactions with the software were recorded in their clinical office within an urban research and teaching hospital. All major user interface events (from the user interactions with the packages) were time-stamped and annotated with coding categories to identify usability issues in order to characterize desired features and deficiencies in the user experience.

RESULTS

We detected 193 usability issues, the majority of which concern interface layout and navigation, and the resolution of reports. Our study highlights gaps in specific software features typical within exome analysis. The clinicians perform best when the flow of the system is structured into well-defined yet customizable layers for incorporation within the clinical workflow. The results highlight opportunities to dramatically accelerate clinician analysis and interpretation of patient genomic data.

CONCLUSION

We present the first application of usability methods to evaluate software interfaces in the context of exome analysis. Our results highlight how the study of user responses can lead to identification of usability issues and challenges and reveal software reengineering opportunities for improving clinical next-generation sequencing analysis. While the evaluation focused on two distinctive software tools, the results are general and should inform active and future software development for genome analysis software. As large-scale genome analysis becomes increasingly common in healthcare, it is critical that efficient and effective software interfaces are provided to accelerate clinical adoption of the technology. Implications for improved design of such applications are discussed.

Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics

Mutation detection through exome sequencing allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace Sanger sequencing (SS) in diagnostics because of incomplete representation and coverage of exons leading to missing clinically relevant mutations. Targeted next-generation sequencing (NGS), in which a selected fraction of genes is sequenced, may circumvent these shortcomings. We aimed to determine whether the sensitivity and specificity of targeted NGS is equal to those of SS. We constructed a targeted enrichment kit that includes 48 genes associated with hereditary cardiomyopathies. In total, 84 individuals with cardiomyopathies were sequenced using 151 bp paired-end reads on an Illumina MiSeq sequencer. The reproducibility was tested by repeating the entire procedure for five patients. The coverage of ≥30 reads per nucleotide, our major quality criterion, was 99% and in total ∼21,000 variants were identified. Confirmation with SS was performed for 168 variants (155 substitutions, 13 indels). All were confirmed, including a deletion of 18 bp and an insertion of 6 bp. The reproducibility was nearly 100%. We demonstrate that targeted NGS of a disease-specific subset of genes is equal to the quality of SS and it can therefore be reliably implemented as a stand-alone diagnostic test.

Developing genome and exome sequencing for candidate gene identification in inherited disorders: an integrated technical and bioinformatics approach

CONTEXT

Advances in sequencing technology with the commercialization of next-generation sequencing (NGS) has substantially increased the feasibility of sequencing human genomes and exomes. Next-generation sequencing has been successfully applied to the discovery of disease-causing genes in rare, inherited disorders. By necessity, the advent of NGS has fostered the concurrent development of bioinformatics approaches to expeditiously analyze the large data sets generated. Next-generation sequencing has been used for important discoveries in the research setting and is now being implemented into the clinical diagnostic arena.

OBJECTIVE

To review the current literature on technical and bioinformatics approaches for exome and genome sequencing and highlight examples of successful disease gene discovery in inherited disorders. To discuss the challenges for implementing NGS in the clinical research and diagnostic arenas.

DATA SOURCES

Literature review and authors' experience.

CONCLUSIONS

Next-generation sequencing approaches are powerful and require an investment in infrastructure and personnel expertise for effective use; however, the potential for improvement of patient care through faster and more accurate molecular diagnoses is high.