Accurate detection of copy number alterations (CNAs) has become increasingly important in clinical oncology for the purpose of diagnosis, prognostication, and disease management. Cytogenetic approaches for the detection of CNAs, including karyotype, fluorescence in situ hybridization (FISH), and chromosomal microarray, remain mainstays in clinical laboratories. Yet, with rapidly decreasing costs and improved accuracy of CNA detection using emerging technologies such as next-generation sequencing and optical genome mapping, we are approaching a new era of cytogenomics and molecular oncology. The aim of this review is to describe the benefits and limitations associated with the routine clinical application of available classic, emerging, and projected future technologies for the detection of CNAs in oncology.
Somatic CNAs yield a wealth of clinically relevant and actionable information, with an enormous potential to refine personalized cancer medicine for solid tumors and hematologic malignancies.
As the diversity of approaches for CNA detection rapidly evolves, selection of the most appropriate technology may be a challenge, confounded by competing advantages and limitations in any given clinical context.
This review describes the unique technical and interpretative considerations that are encountered in the detection and analysis of somatic CNAs.
Comprehensive genomic characterization of cancers has rapidly transitioned from research innovations to diagnostic applications. Increasingly, in accordance with continual revisions to the World Health Organization (WHO), many solid tumors and hematologic malignancies alike require the detection or exclusion of pathognomonic single-nucleotide variants (SNV), structural variants (SVs) and copy number variants (CNVs) to achieve diagnosis and/or appropriate clinical management.
Somatic CNVs, referred to as copy number alterations (CNAs) in this review, have long been recognized as an important component of neoplastic transformation, resulting in the activation of proto-oncogenes, or disruption of tumor suppressor genes. CNAs can be observed in ∼50% of cancers, substantiating a greater degree of alteration than any other type of somatic variation and CNAs that are of potential clinical actionability are identified frequently in tumor specimens lacking single-nucleotide driver variants. CNAs range dramatically in size–from highly targeted focal alterations, less than ∼5 megabases (Mb) in size, to whole-genome doubling events–and amplitude–from homozygous deletions resulting in biallelic inactivation to amplifications.
Essential to our understanding of the detection of CNAs in cancer is the knowledge that the mechanism, size, and functional consequence of these alterations are highly variable, thus necessitating diverse approaches to the detection of these alterations depending on the tumor context (summarized in Table 1 ). There is a tendency for similar CNAs to be found in a spectrum of distinct cancer types, suggesting that the neoplastic process that gives rise to many CNVs is often tumor-agnostic. Many cancer cells also demonstrate polyploidy (ie, a gain or loss of a complete haploid or diploid set of chromosomes), whereby the relative imbalance of large chromosomal gains or losses is attenuated by gains of a near-complete chromosome complement. It has also been demonstrated that the level of allelic imbalance or overall CNA burden, which can be defined as the degree to which a tumor cell genome is altered, is directly associated with prognosis, recurrence, and disease outcome in some cancer types and that there is a direct correlation between CNAs and differential gene expression across cancer types.