Despite significant advances, cancer remains one of the predominant causes of mortality in the modern world, and as such has remained a top research priority. It is a complex and continually evolving genetic disease and, as such, requires sophisticated tools for study. Traditional approaches have centred on histological classification, using karyotyping for the identification of gross chromosomal aberrations. Considering the vast underlying heterogeneity in the genetics of cancer, it is unsurprising that such techniques are no longer sufficient for progressing our understanding of this disease.
Consequently, molecular methods are becoming ever more popular in cancer research studies. Significant advances in our understanding of the underlying genetic aberrations have been aided by approaches such as microarrays and next generation sequencing (NGS), contributing to a 21% reduction in UK cancer mortality rates since 1990.1
Interestingly, these two mainstream molecular approaches of microarrays and NGS, which could be viewed as competing techniques are increasingly being regarded as complementary approaches for use in cancer research. With differing speed, resolution and ease of analysis, the utilisation of both techniques can be tailored to meet the individual requirements of the study at hand, with the two working together to reliably and accurately address a wider range of biological questions than either alone.
NGS for the targeted discovery of novel mutations
The development and progression of NGS is revolutionising genetic screening. By sequencing complete genes, chromosomes or even the genome in its entirety, researchers can detect novel sequence variants at single nucleotide resolution. Subsequent identification of new genomic aberrations may hold significant phenotypic implication and provide biomarkers of disease. This makes NGS a particularly powerful tool for cancer research, as cancer-causing mutations can be complex, diverse and unexpected.
To avoid the analysis and processing burdens of sequencing the entire genome, NGS experiments can be designed in a more focused manner. By sequencing defined stretches of the genome, for example genes known to be involved in specific cancers or genomic regions that have been implicated in cancer progression through earlier microarray studies, it permits a shorter turnaround time and generates smaller datasets for more manageable analysis. Exome sequencing is a selective and targeted sequencing approach allowing analysis of changes that are occurring in the coding regions of the genome. However, this approach forgoes analysis of most non-exonic variation, which can harbour important, disease-causing mutations. Of particular relevance to researchers in cancer genetics, is the increasing opportunity to utilise custom capture in NGS, which permits the targeted sequencing of specific, research-defined genomic regions. This enables focused analysis on regions of interest, for potential detection of novel point mutations, or to target known mutation hot-spots within the malignant genome in a highly customisable way.
While NGS provides nucleotide-level insights into the genetic causes and progression of cancer, this comes at a slightly higher cost than microarray analysis. The requirement to interpret larger amounts of data can be challenging if access to bioinformatic support is limited. Considering the complexity of experimental design and the extraordinary capacity for data generation via NGS, some vendors offer services to relieve these burdens, providing molecular biology and bioinformatics expertise. Some of these service providers further format the data into intuitive reports that highlight the biologically relevant results for additional investigation. OGT’s Genefficiency Cancer Sequencing Service is one such offering, presenting data in an intuitive, filterable report that includes links to external databases (such as the Catalogue of Somatic Mutations in Cancer [COSMIC]) for rapid insight into likely disease-associations. A further benefit of sequencing service providers is that they bear the significant expense of maintaining the ever-evolving equipment; ensuring staff are appropriately trained, implementing sophisticated laboratory information management systems (LIMS) and maintaining the latest analysis techniques. By outsourcing their sequencing requirements and utilising the expertise of external providers, cancer researchers can focus on interpreting their results rather than identifying which sequencing platform to use. With costs ever decreasing, and informatics improving, NGS certainly has the power to further expand its role in the detection of novel genomic aberrations within clinical research.
Combining Microarrays and NGS: The best of both worlds
Considering the differing strengths of microarrays and NGS, it is unsurprising that they are increasingly being thought of as complementary techniques for complex genetic research. When used together, researchers can detect a greater range of genomic aberrations, allowing in-depth and thorough analysis, which is ultimately important for the identification of genetic biomarkers for cancer prediction and progression.
Advantageously, the order of microarray and NGS use can be tailored depending upon the research question at hand. For the discovery of novel sequence variants, NGS is perfectly suited, following which new arrays can be developed to probe larger sample numbers. Alternatively, microarrays can be utilised initially for the genome wide screening of many samples, and then targeted NGS employed for more detailed analysis of particular genomic areas of interest. In this way, the two techniques can be tailored to answer a broader range of biologically relevant questions in cancer research. Furthermore, the ability to carry out more focused genomic screening has cost and time-associated benefits for researchers.
While these research techniques have been successful as individual methods for genetic investigation into cancer, the facility to combine practices could provide a more economical and tailored method for insightfully studying the cancer genome. The combined strength of the two processes offers an enhanced ability to detect de novo mutations across the genome and in many samples, raising the likelihood of discovering clinically relevant genomic aberrations. The identification of such biomarkers ultimately aims to permit patient screening via diagnostic arrays, leading the way towards personalised medicine and other development of optimised treatment plans for many forms of cancer.
1. Cancer Research UK, 2012. Cancer mortality for all cancers combined. [online] Available at: <http://www.cancerresearchuk.org/cancer-info/cancerstats/mortality/all-cancers-combined> [Accessed 11 December 2012].