Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology

Abstract

Whole exome sequencing (WES) enables the analysis of all protein coding sequences in the human genome. This technology enables the investigation of cancer-related genetic aberrations that are predominantly located in the exonic regions. WES delivers high-throughput results at a reasonable price. Here, we review analysis tools enabling utilization of WES data in clinical and research settings. Technically, WES initially allows the detection of single nucleotide variants (SNVs) and copy number variations (CNVs), and data obtained through these methods can be combined and further utilized. Variant calling algorithms for SNVs range from standalone tools to machine learning-based combined pipelines. Tools for CNV detection compare the number of reads aligned to a dedicated segment. Both SNVs and CNVs help to identify mutations resulting in pharmacologically druggable alterations. The identification of homologous recombination deficiency enables the use of PARP inhibitors. Determining microsatellite instability and tumor mutation burden helps to select patients eligible for immunotherapy. To pave the way for clinical applications, we have to recognize some limitations of WES, including its restricted ability to detect CNVs, low coverage compared to targeted sequencing, and the missing consensus regarding references and minimal application requirements. Recently, Galaxy became the leading platform in non-command line-based WES data processing. The maturation of next-generation sequencing is reinforced by Food and Drug Administration (FDA)-approved methods for cancer screening, detection, and follow-up. WES is on the verge of becoming an affordable and sufficiently evolved technology for everyday clinical use.

Copy Number Variation: Methods and Clinical Applications

“…However, since most of the known disease-causing mutations fall into this category, exome sequencing significantly reduces sequencing cost in medical applications and is still sufficiently powerful. Moreover, targeted sequencing provides a greater depth of coverage in regions of interest for an even lower cost [43].…”

Role of Akt Activation in PARP Inhibitor Resistance in Cancer

“…For the development of novel rational combination therapies, enhanced genetic-interaction screens are needed that assumes integration of functional interaction data with orthogonal methods [145]. Additionally, heterogeneity of the patient population limits therapy development, and questions optimality of the applied treatment, a problem which can be amended by determining microsatellite instability and tumor mutation burden [146]. All these techniques, as they become affordable, pave the way toward the realm of personalized medicine [147].…”

Biomarkers for precision immunotherapy in the metastatic setting: hope or reality?

“…Generally, TMB is performed on the DNA extracted from tumour tissue, however, the analysis of circulating tumour DNA (ctDNA) is being investigated in the clinical practice, particularly in follow-up settings [ 102 , 103 ]. The gold standard method for assessing TMB is whole-exome sequencing (WES) by using NGS technology [ 104 ]. This technology estimates the neoantigen load based on somatic nonsynonymous coding mutations [ 95 ].…”