Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants.

Maria Delio,Nichelle Simmons,Wilber Quispe-Tintaya,Cristina Montagna,Michal Bejerano-Sagie,Dennis Y.S. Kuo,Kunjan Patel,Jenna Marcus Zechmeister,Nicole E. Patterson,Nivedita Ravi,Rouzan G. Karabakhtsian,Alexander Maslov,Jan Vijg,John M. Greally,Eirwen M. Miller,Maria Castaldi

doi:10.18632/oncotarget.22116

Maria Delio, Nichelle Simmons + Show 14 more

Open Access

https://doi.org/10.18632/oncotarget.22116

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Abstract

Next generation sequencing (NGS) technologies have revolutionized our approach to genomic research. The use of whole genome sequencing (WGS), whole exome sequencing (WES), transcriptome profiling, and targeted DNA sequencing has exponentially improved our understanding of the human genome and the genetic complexities underlying malignancy. Yet, WGS and WES clinical applications remain limited due to high costs and the large volume of data generated. When utilized to address biological questions in basic science studies, targeted sequencing panels have proven extremely valuable due to reduced costs and higher sequencing depth. However, the routine application of targeted sequencing to the clinical setting is limited to a few cancer subtypes. Some highly aggressive tumor types, like type 2 endometrial cancer (EC), could greatly benefit from routine genomic analysis using targeted sequencing. To explore the potential utility of a mid size panel (~150 genes) in the clinical setting, we developed and validated a custom panel against WGS, WES, and another commercially available targeted panel. Our results indicate that a mid size custom designed panel is as efficient as WGS and WES in mapping variants of biological and clinical relevance, rendering higher coverage, at a lower cost, with fewer variants of uncertain significance. Because of the much higher sequencing depth that could be achieved, our results demonstrate that targeted sequencing outperformed WGS and WES in the mapping of pathogenic variants in a breast cancer case, as well as a case of mixed serous and high-grade endometrioid EC, the most aggressive EC subtype.

Highlights

whole genome sequencing (WGS) and whole exome sequencing (WES) have emerged as valuable tools for the identification of driver mutations in a variety of tumor types, as well as for the identification of actionable mutations [1,2,3]
To investigate somatic genomic alterations common to a variety of solid tumors, including breast and gynecologic malignancies, we developed the Einstein Custom Cancer Panel (ECCP), a custom cancerfocused targeted gene panel
On the basis of an extensive literature review, 156 highly cited and frequently mutated oncogenes and tumor suppressor genes were strategically selected for inclusion in the panel design based on their molecular pathways and their mutation frequency in solid tumors as assessed by mining The Cancer Genome Atlas (TCGA) through the cBioPortal [14,15] and the Catalogue Of Somatic Mutations In Cancer (COSMIC) [16]

Summary

Introduction

WGS and WES have emerged as valuable tools for the identification of driver mutations in a variety of tumor types, as well as for the identification of actionable mutations [1,2,3]. Though targeted therapies have shown promise in chronic myeloid leukemia, lung cancer, and melanoma, actionable mutations are currently limited to a few dozen genes due to the small number of compounds on the market that are mutation specific [4,5,6,7]. The panel we designed and validated in this study differs from the design commonly used in targeted sequencing profiling because of the larger size (~150 genes compared with a dozen commonly used in clinical settings). This offers the advantage of being suited to the analysis of a variety of cancer subtypes, even those with a more unique genomic profile

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