Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

Abstract

Lung cancer detection and monitoring are hampered by a lack of sensitive biomarkers, which results in diagnosis at late stages and difficulty in tracking response to treatment. Recent developments have established liquid biopsies as promising non-invasive methods for detecting biomarkers in lung cancer patients. With concurrent advances in high-throughput sequencing technologies and bioinformatics tools, new approaches for biomarker discovery have emerged. In this article, we survey established and emerging biomarker discovery methods using nucleic acid materials derived from bodily fluids in the context of lung cancer. We introduce nucleic acid biomarkers extracted from liquid biopsies and outline biological sources and methods of isolation. We discuss next-generation sequencing (NGS) platforms commonly used to identify novel biomarkers and describe how these have been applied to liquid biopsy. We highlight emerging biomarker discovery methods, including applications of long-read sequencing, fragmentomics, whole-genome amplification methods for single-cell analysis, and whole-genome methylation assays. Finally, we discuss advanced bioinformatics tools, describing methods for processing NGS data, as well as recently developed software tailored for liquid biopsy biomarker detection, which holds promise for early diagnosis of lung cancer.

HTR2B as a novel biomarker of chronic obstructive pulmonary disease with lung squamous cell carcinoma

“…Despite such advances in lung cancer treatment, increasing the efficiency of early detection is the most promising strategy for improving long-term survival of patients with lung cancer 24 . In recent years, the rapid development of high-throughput technology has generated large amounts of high-throughput sequencing data and expression profile data in oncology 25 . The combination of big data and different data types presents an entirely new perspective on the analysis of such data 26 .…”

Liquid Biopsy in Lung Cancer: Biomarkers for the Management of Recurrence and Metastasis

“…The most common approaches for nucleic-acid-based detection in liquid biopsy samples include multiplex-hybridization-based methods, PCR-based methods, and NGS. These approaches vary in sensitivity and in the variants that they are capable of detecting, as reviewed in our previous paper [45]. Table 2 displays the technical approaches based on their sensitivity, multiplexing capability, turnaround time (TAT), and limit of detection (LOD).…”

“…In addition, the evaluation of acquired resistance in samples such as peripheral blood is a supplementary tool to tissue analysis used in clinical examination [33]. Currently, with the implementation of broad-based platforms such as next-generation sequencing (NGS), the additional genotyping of oncogene drivers supports the utility of plasma ctDNA, as reviewed elsewhere [45][46][47][48]; in fact, the absence of detectable alterations in plasma has been associated with a lower tumor burden [49]. However, the use of plasma is not sufficient for patients with metastasis exclusive to the brain or leptomeninges, and, for these cases, the use of CSF arises as an alternative source of ctDNA [50].…”

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

“…Thus, the idea to use methylation as a biomarker for cancer detection is not far to seek. Due to its prognostic property, DNA methylation was already applied as a prognostic marker in several cancer types, including prostate, bladder, colorectal, non-small-cell lung, breast, ovarian, cervical cancer, and liver malignancies [ 125 , 126 ].…”