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. 2024 Mar 23;15(4):396.
doi: 10.3390/genes15040396.

Comprehensive Analysis of Clinically Relevant Copy Number Alterations (CNAs) Using a 523-Gene Next-Generation Sequencing Panel and NxClinical Software in Solid Tumors

Vivek Gupta  1   2 , Vishakha Vashisht  2 , Ashutosh Vashisht  2 , Ashis K Mondal  2 , Ahmet Alptekin  2 , Harmanpreet Singh  2 , Ravindra Kolhe  2
Affiliations

Comprehensive Analysis of Clinically Relevant Copy Number Alterations (CNAs) Using a 523-Gene Next-Generation Sequencing Panel and NxClinical Software in Solid Tumors

Vivek Gupta et al. Genes (Basel). .

Abstract

Copy number alterations (CNAs) are significant in tumor initiation and progression. Identifying these aberrations is crucial for targeted therapies and personalized cancer diagnostics. Next-generation sequencing (NGS) methods present advantages in scalability and cost-effectiveness, surpassing limitations associated with reference assemblies and probe capacities in traditional laboratory approaches. This retrospective study evaluated CNAs in 50 FFPE tumor samples (breast cancer, ovarian carcinoma, pancreatic cancer, melanoma, and prostate carcinoma) using Illumina's TruSight Oncology 500 (TSO500) and the Affymetrix Oncoscan Molecular Inversion Probe (OS-MIP) (ThermoFisher Scientific, Waltham, MA, USA). NGS analysis with the NxClinical 6.2 software demonstrated a high sensitivity and specificity (100%) for CNA detection, with a complete concordance rate as compared to the OS-MIP. All 54 known CNAs were identified by NGS, with gains being the most prevalent (63%). Notable CNAs were observed in MYC (18%), TP53 (12%), BRAF (8%), PIK3CA, EGFR, and FGFR1 (6%) genes. The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis.

Keywords: Copy Number Alterations; FFPE Solid Tumor; Molecular Inversion Probe; Next-Generation Sequencing; NxClinical Software.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Workflow for copy number alteration (CNA) detection and analysis using Oncoscan Molecular Inversion Probe (OS-MIP) and Next Generation Sequencing (NGS) (TSO500) on NxClinical 6.2 software.
Figure 2
Figure 2
Bar chart of CNAs detected (A) in 24 cancer genes (B) in different tumor samples in 50 patients of the retrospective cohort, including breast, ovary, pancreas, melanoma, and prostate tumors.
Figure 3
Figure 3
Heatmap of CNAs detected by NGS using NxClinical 6.2 software; BR = Breast; ML = Melanoma; OV = Ovary; PN = Pancreas; PRO = Prostate.
Figure 4
Figure 4
A representation of copy number analysis from NxClinical software version 6.2 using OS-MIP and NGS data; (A) shows 3q and 7q gain in ovary cancer sample (Case No. 14268) (B) shows 3q amplification 5q gain, 12q gain in melanoma sample (Case No. 14467). Gain/amplifications in specific genes are indicated by red arrows and boxes.
See this image and copyright information in PMC

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