Comprehensive next-generation cancer genome sequencing in the era of targeted therapy and personalized oncology

Abstract

DNA sequence analysis has become a significant laboratory test in oncology, permitting treatment to become increasingly personalized for both solid tumors and hematologic malignancies. Traditional approaches to sequence analysis, including Sanger sequencing, pyrosequencing and allele-specific PCR, are now widely used to guide therapy for patients diagnosed with lung and colorectal cancer as well as for melanoma, sarcomas (e.g., gastrointestinal stromal tumors) and subtypes of leukemia and lymphoma. Traditional sequence analysis has been limited in bandwidth and throughput and as a result, has been focused exclusively on testing the most common aberrations in key genes or fully sequencing single genes. The massively parallel or next-generation sequencing (NGS) approach to DNA analysis holds a number of potential advantages over the traditional methods, including the ability to fully sequence large numbers of genes (hundreds to thousands) in a single test. Furthermore, NGS can simultaneously detect deletions, insertions, copy number alterations, translocations and exome-wide base substitutions (including known hot-spot mutations) in all known cancer-related genes. However, significant challenges, particularly with respect to demands on expertise and infrastructure, will have to be overcome to translate NGS to the bedside of the cancer patient. Extensive computational expertise is required to bring NGS into clinical context, and a deep knowledge of cancer medicine and cancer biology will be required to generate truly useful, so-called 'clinically actionable' reports for clinicians. While NGS is on the cusp of being launched as a clinical test, it may be expected that the near future will continue to bring major advances in the technology that will lower the overall cost, speed up the turnaround time, increase the breadth of genome sequencing, and detect epigenetic markers and other important genomic parameters, while becoming applicable to smaller and smaller specimens, including circulating tumor cells and circulating free DNA in plasma.

CSF3R T618I, ASXL1 G942 fs and STAT5B N642H trimutation co‐contribute to a rare chronic neutrophilic leukaemia manifested by rapidly progressive leucocytosis, severe infections, persistent fever and deep venous thrombosis

“…Detection of the CSF3R mutation is essential to distinguish CNL from a leukaemoid reaction and other MPNs. Additionally, comprehensive NGS (Cronin & Ross, 2011;Patel et al, 2012) could reveal hidden pathogenic mutations, explore the pathogenesis, and explain the clinical manifestations in a rare case of CNL.…”

The potential for liquid biopsies in the precision medical treatment of breast cancer

“…Additionally, NGS panels for inherited cancer has increased the potential to identify pathogenic variants in genes that would not typically have been tested (in breast cancer, genes other than BRCA1/2) and to offer more tailored preventative management to patients and family members 132 . Each sequencing technique has specific advantages and disadvantages ( Table 2) [133][134][135][136][137][138][139][140][141][142][143][144] .…”

The Promise of Single Cell Omics for Onco-therapy

“…Genomic analysis is expected to untangle the complex nature of cancer biology and the extensive tumor heterogeneity leading to identification of new targets for more successful cancer therapy [68]. Current anticancer regimens mostly target the rapidly proliferating bulk tumor cells to shrink the tumor mass.…”

“…NGS can also simultaneously identify multiple genetic aberrations including insertions and deletions, CNVs, translocations and many more genetic perturbations. However, important challenges, particularly with respect to demands on expertise and infrastructure, need to be addressed in order to translate data generated by NGS to make it "clinically-actionable" [68]. Highly anticipated new technologies, far better than NGS and WGS, will soon emerge with clinically preferred features such as reduced overall cost, faster turnaround time, more genome coverage as well as epigenome interrogation, to be applied on ever-minute amounts of specimens including single CTCs and circulating free DNAs, RNAs and proteins in blood samples of cancer patients.…”