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Cancers
Special Issues
Application of Genomic Testing in Precision Oncology
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Application of Genomic Testing in Precision Oncology

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Methods and Technologies Development".

Deadline for manuscript submissions: closed (31 March 2025) | Viewed by 2814

Special Issue Editor

Dr. Gowhar Shafi

E-Mail Website
Guest Editor
OneCell Diagnostics, 20380 Town Center Lane, Cupertino, CA 95014, USA
Interests: cancer; precision oncology; genomics; AI in precision oncology; immuno-oncology; data analytics; big data

Special Issue Information

Dear Colleagues,

Genomics has emerged and become one of the major components of precision oncology in the last decade. DNA, being a component of higher stability among the nucleotides, has become a component of preliminary importance. With transcriptomics and proteomics still in the emerging phase, genomics has gained more momentum in recent times. Besides just cancer diagnosis and therapy, genomics is also very functional in disease risk prediction, pharmacological response prediction, and drug toxicity and response predictions, including nutrigenomics. Cancer is not just a lonely disease but a multifactorial complexity which involves nucleotide omics, nutritional profiling, pharmacogenomic factors, etc., to combinedly function for overall prediction.

Altogether, these individual attributes work together to enable precision oncology. Since precision oncology is involved in achieving personalized disease intervention approaches, considering complex parameters is important. Above all, determining the clinical importance of these findings to enable precise diagnoses is important to progress.

Papers related to these areas are welcome to be submitted for this Special Issue, whether they are about personalized therapies, therapy response monitoring, treatment toxicities, immune-related adverse events, supportive care, palliative care or diagnostics, etc.

Dr. Gowhar Shafi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cancers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • precision oncology
  • genomics
  • immunotherapy
  • targeted therapy
  • AI in precision oncology
  • prognosis
  • predictive

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Published Papers (2 papers)

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Research

16 pages, 987 KiB  
Article
Analytical Validation and Performance Evaluation of Amplicon-Based Next-Generation Sequencing Assays for Detecting ERBB2 and Other Gene Amplifications in Solid Tumors
by Ekaterina Olkhov-Mitsel, Danny Chan, Kenneth J. Craddock, August Lin, Grace Luk, Rashmi S. Goswami, Hong Wang, Anna Plotkin, Sharon Nofech-Mozes, David M. Hwang and Weei-Yuarn Huang
Cancers 2024, 16(23), 3927; https://doi.org/10.3390/cancers16233927 - 23 Nov 2024
Viewed by 869
Abstract
Background: Targeted next-generation sequencing (NGS) panels are increasingly being utilized to identify actionable gene amplifications (copy number > 4) among solid tumors. Methods: This study validated the analytical performance of two amplicon-based NGS assays, the Oncomine Comprehensive Panel (OCAv3) and the Oncomine Focus [...] Read more.
Background: Targeted next-generation sequencing (NGS) panels are increasingly being utilized to identify actionable gene amplifications (copy number > 4) among solid tumors. Methods: This study validated the analytical performance of two amplicon-based NGS assays, the Oncomine Comprehensive Panel (OCAv3) and the Oncomine Focus Assay (OFA), for detecting gene amplification in formalin-fixed paraffin-embedded (FFPE) tumors of varying cellularity. OCAv3 was assessed for amplification detection in 756 FFPE samples comprising various tumor types. Results: We demonstrated that with standardized quality control metrics, including median absolute pairwise difference score, these assays can achieve a near-perfect positive predictive value, although their sensitivity for detecting amplifications significantly decreased in tumors with cellularity below 30%. Stratifying tumor cellularity into 10–30%, 31–60%, and 61–95% groups revealed significantly higher gene amplification detection rates in the 31–60% and 61–95% groups versus the 10–30% group (20.6% and 26.7% vs. 9.2%, p < 0.0001). When considering all detected gene amplifications, the average amplification calling per sample was nearly five-fold lower in the 10–30% group versus the 61–95% group (0.11 vs. 0.52; p < 0.0001). To further investigate the analytic performance of OCAv3 in detecting ERBB2 amplification, we analyzed a cohort of 121 uterine carcinomas with confirmed ERBB2 status by HER2 IHC or FISH, in which a threshold incorporating amplifications and tumor cellularity achieved 79% sensitivity and 100% specificity, potentially eliminating the need for FISH analysis in 34% of equivocal cases. In a separate validation cohort, similar analytical performance was observed, with the threshold demonstrating consistent sensitivity and specificity. Conclusions: This study highlights the strengths and limitations of amplicon-based NGS assays in detecting amplifications using real-world data. Full article
(This article belongs to the Special Issue Application of Genomic Testing in Precision Oncology)
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13 pages, 2280 KiB  
Article
Clinical and Technical Validation of OncoIndx® Assay—A Comprehensive Genome Profiling Assay for Pan-Cancer Investigations
by Aarthi Ramesh, Atul Bharde, Alain D’Souza, Bhagwat Jadhav, Sangeeta Prajapati, Kanchan Hariramani, Madhura Basavalingegowda, Sandhya Iyer, Sumit Halder, Mahesh Deochake, Hrishita Kothavade, Aravindan Vasudevan, Mohan Uttarwar, Jayant Khandare and Gowhar Shafi
Cancers 2024, 16(19), 3415; https://doi.org/10.3390/cancers16193415 - 8 Oct 2024
Viewed by 1415
Abstract
Comprehensive next-generation sequencing (NGS) assays enable the identification of clinically relevant mutations, enhancing the capability for targeted therapeutic interventions. In addition, genomic alterations driving the oncogenic roadmap and leading to resistance mechanisms are reshaping precision oncology. We report the workflow and clinical and [...] Read more.
Comprehensive next-generation sequencing (NGS) assays enable the identification of clinically relevant mutations, enhancing the capability for targeted therapeutic interventions. In addition, genomic alterations driving the oncogenic roadmap and leading to resistance mechanisms are reshaping precision oncology. We report the workflow and clinical and technical validation of the OncoIndx® NGS platform—a comprehensive genomic profiling (CGP)-based assay for pan-cancer investigation. We evaluated the concordance between the OncoIndx® test findings and clinically established hotspot detection using SeraSeq reference standards. OncoIndx is a hybridization capture-based NGS assay for the targeted deep sequencing of all exons and selected introns of 1080 cancer-related genes. We show the outcome in the form of tier I and tier II single nucleotide variants (SNVs), copy number alterations (CNAs), and specific gene fusions. OncoIndx® also informs genome-wide tumor mutational burden (TMB), microsatellite instability (MSI), homologous recombination deficiency (HRD), and genomic loss of heterozygosity (gLOH). A total of 63 samples were utilized for validation with reference standards, clinical samples, and orthogonal assessment for genomic alterations. In addition, 49 cross-laboratory samples were validated for microsatellite instability (MSI), and for the tumor mutation burden (TMB), 18 samples as reference standards, 6 cross-laboratory samples, and 29 TCGA samples were utilized. We show a maximum clinical sensitivity of 98% and a positive predictive value (PPV) of 100% for the clinically actionable genomic variants detected by the assay. In addition, we demonstrate analytical validation with the performance of the assay, limit of detection (LoD), precision, and orthogonal concordance for various types of SVs, CNAs, genomic rearrangements, and complex biomarkers like TMB, MSI, and HRD. The assay offers reliable genomic predictions with the high-precision detection of actionable variants, validated by established reference standards. Full article
(This article belongs to the Special Issue Application of Genomic Testing in Precision Oncology)
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