By Neil Ward, vice President and general manager, PacBio EMEA
We’ve known for a long time that genomic sequencing can strengthen our understanding of cancer’s highly complex and variable pathology. But to date, embedding genomics into cancer research has been challenging because of limitations in sequencing technology. But with recent innovations, this is changing.
Genomic sequencing today
There are two main approaches to genomic sequencing used today – short- and long-read – each of which bring value to different cancer scenarios.
Short-read sequencing is used when the depth and length of long-read is unnecessary, such as single-nucleotide polymorphism (SNP) calling or sequencing microRNAs. Data from short-reads helps track residual disease, ongoing cancer screening, and early detection.
In contrast, long-reads are typically kilobases long, allowing them to span challenging variant types like large structural variants and tandem repeats. The accuracy and completeness of long-reads enables a deeper understanding of individual cancers, which supports a precision oncology approach. Historically, the use of long-reads in cancer studies has been limited by lower throughput, meaning trends in genetic change and new biomarkers associated with risk of cancer are less likely to be detected.
Sequencing-driven step change
The good news is that technology developments have made long-reads faster, more affordable, and even more accurate, while requiring fewer consumables. This means there’s less of a need to batch samples, unlocking the possibility of a $1,000 genome with a 24-hour turnaround time for patients.
Another significant change is the ability to gain both genetic and epigenetic insights in a single experiment. Many genetic changes related to cancer show in the methylation layer first; the potential to detect epigenetic variation presents new opportunities for diagnosing specific cancers before solid tumors begin to grow.
Significant improvements in the sensitivity and specificity of short-read sequencing are also increasing biological insight while decreasing the likelihood of false positives. This will drive development of diagnostic tools for detection therapy selection, and recurrence monitoring.
Finally, modern sequencing machines are backed by sophisticated AI and deep learning techniques. This enables researchers to conduct deeper analyses of large datasets to unlock insight into the pathology of cancer and its progression at a molecular level.
Innovation in both long- and short-read sequencing is leading a new era of cancer research. PacBio’s highly accurate sequencing technology can assemble complete genomes and drive advancements in scientific discovery, by allowing researchers to explore variations in the genome that were not previously detected.
We’ve already seen the benefits, with one breast cancer study using long-reads to reveal 3,059 breast tumor-specific splicing events, including 35 significantly associated with patient survival. Such technology edges us closer to the goal of diagnosing at the earliest possible stage and informing precision oncology treatment decisions.