As the second leading cause of death worldwide, cancer has complex genetic and molecular drivers that researchers must examine to inform personalized approaches to care.1 Next-generation sequencing (NGS) powers these inquiries by enabling the rapid and accurate analysis of large amounts of genomic and transcriptomic data. May is National Cancer Research Month.2 To promote this lifesaving field, we wanted to outline the impact that NGS has had on our understanding of how cancer begins, spreads, and responds to potential treatments.
Read on to learn about the applications of NGS in cancer research as well as some factors that may limit accessibility for smaller labs. This blog also addresses how the right library prep tools can boost the possibilities for a myriad of oncology applications.
NGS Fuels Cancer Research and Care
Since the early 2000s, the speed and depth of NGS technology has opened up rich avenues of discovery in several key cancer-related applications.3
- Targeted sequencing: Using predetermined NGS panels to rapidly sequence only a specific set of genes or gene regions enables a more cost-effective and concise analysis compared to other approaches. This also allows for deeper sequencing at specific loci to enable analysis of the heterogeneity of tumorous cells.4 Targeted sequencing has led to the detection of novel pathways and targetable driver mutations. As a result, new biomarker tests, such as noninvasive blood-based liquid biopsies, have been made accessible to more patients for diagnosis and monitoring.5
- Whole-genome sequencing (WGS): Prior to NGS, sequencing an entire genome was expensive and time-consuming. Now researchers can harness NGS to perform WGS, which enables a detailed level of sequencing that helps researchers identify large structural variations in the genome, such as translocations and inversions, which play a major role in cancer development and progression. These factors make WGS well-suited for comparing tumor and matched normal samples.6
The end goal of these applications is to improve cancer care. Thanks to the consistent decline in the cost of NGS, precision medicine—tailored treatment that better targets the characteristics of each unique tumor while minimizing adverse effects—has become a reality for a growing number of patients with cancer. Genetically informed tools like comprehensive genomic profiling, liquid biopsy, immunotherapy, and combination therapy routinely help clinicians and researchers diagnose, treat, monitor, and understand cancer more effectively.
Innovation is Not Free of Challenges
As with many advanced biotechnologies, implementation of NGS can pose significant challenges, especially for smaller or emerging labs.
Although the price of NGS has fallen dramatically in recent years (Illumina’s NovaSeq X system is designed to produce a $200 human genome7), cost can still be a barrier. The price to sequence a single sample varies based on the size of the region being sequenced, the sequencing system used, the depth of coverage required, and the number of samples run at once. Adding high-quality bioinformatics also raises the price tag, especially for larger-scale studies. The complexity of NGS data analysis also means that bioinformatics can be time-consuming and computationally intensive, requiring significant IT resources and an expertise in computational biology.
Ensuring consistency in NGS protocols is critical for reproducing and comparing results across different studies and research groups. However, complex NGS workflows are subject to variability in sample preparation, library construction, sequencing, data analysis, and quality control. For NGS research findings to make the coveted leap to clinical practice, labs must expend resources to standardize protocols all the way from sample to results.
Despite these challenges, NGS still plays a critical role in oncology. It continues to drive research that could lead to even more life-changing revolutions to care.
Leveraging Long-Read Sequencing
Long-read sequencing, also known as third-generation sequencing, generates DNA or RNA reads with lengths ranging from thousands to hundreds of thousands of bases.
Historically, long-read sequencing technology has demonstrated a lower accuracy per read and higher cost per base compared to short read sequencing. However, industry-leading long-read players like PacBio and Oxford Nanopore Technologies have strived to improve the cost-effectiveness and scalability of their instruments to improve accessibility and adoption.
For now, combining short- and long-read data with sophisticated analysis may provide a more realistic solution for cancer researchers delving into questions of complex rearrangements and phase haplotypes. To this end, seqWell is developing a tool that enables short reads to be connected across multiple DNA fragments. This library prep workflow will allow for the simultaneous phasing of many samples while boosting efficiency and scalability.8
Driving Gene Editing
CRISPR is helping scientists find and replace specific targets, such as DNA from cancer-causing viruses and RNA from cancer cells, with relative ease.9 By leveraging CRISPR gene editing, researchers can identify and validate the role of specific genetic mutations in tumor development and disease progression.
However, maintaining safe and ethical care are major considerations within this new frontier of gene editing. NGS can be integrated into the CRISPR workflow to confirm, at a high resolution, which cells have taken on the desired on-target edits and determine if other off-targets edits to the genome were made.
Tn5 transposases allows for easier and safer gene editing and analysis.10 As an example, Editas Medicine harnessed the power of seqWell’s custom-loaded Tn5 transposase enzyme to quickly and efficiently tag DNA fragments with adapters using UDiTaS, their method for assessing CRISPR on-target editing and structural changes.11 To learn more about our Tn5-based solutions for gene editing quality control, check out our webinar collaboration with Editas.12
Hope for the Future of NGS in Cancer Research
Over the past two decades, cancer mortality rates have consistently decreased.13 That success wouldn’t be possible without the labors of cancer researchers and clinicians—and the NGS innovations that drive their work. With accelerating advances in instruments and supporting technologies like seqWell’s library prep workflows, we can see that downward trend continue.
This blog is the first published in honor of NCRM. Click here to read the second blog in this series titled “Navigating Variants of Uncertain Significance”.