Cancer Genomics

Cancer is caused by changes in a once-normal cell, which accumulates genetic damage and mutations in the cell’s “instruction book”, the DNA, causing the cell to grow and multiply uncontrollably. Today, we know much about the many mutations which can contribute to cancer, some mutations which can be inherited, as well as the many gene mutations which arise randomly and due to environmental exposures. Increasingly, these mutations can be targeted by approved drugs as well as dozens of therapeutics currently in development around the world.

An accurate snapshot of the current state

It has been known for decades that DNA from cells can escape and circulate as free-floating DNA, so-called cell-free DNA (cfDNA), in the bloodstream. In a cancer patient, the mutated DNA from tumor cells also escapes into the blood stream. This happens in proportion to the number of tumors and cancer cells in the body. In this case the DNA is called circulating tumor DNA (ctDNA). All circulating DNA is rapidly degraded to short fragments. Therefore, the quantity of ctDNA at a given time point provides a precise snapshot of the current tumor burden. Importantly, the ctDNA also makes its way into other bodily fluids such as the urine, and depending on the location of the tumor, also into saliva/sputum, cerebrospinal fluid, and other secretions. Together, the interrogation of these fluids as a source of diagnostic specimens is known as the minimally-invasive “liquid biopsy”. Until recently, however, the technology has not existed to accurately and reliably distinguish the ctDNA from the normal-cell-derived cfDNA.

Our research as well as the work of others has indicated that ctDNA is an excellent cancer biomarker. The reasons are manifold:

  • ctDNA is released by all tumors in the body, thus a blood sample will provide a diagnostic result for all cancer clones at the same time in a single test;
  • The quantity of ctDNA is proportional to the number of cancer cells and tumors in the body, therefore ctDNA quantity gives a read-out of the total amount of cancer in a patient;
  • All types of DNA alterations such as the gene mutations and chromosomal rearrangements present in the patient’s cancer are represented in the ctDNA, thus ctDNA gives an accurate picture of the complete genetic makeup of the cancer including information on the mutations that are drug targets;
  • Liquid biopsy sampling, such as a blood draw, is a simple and inexpensive procedure that can be performed by any medical personnel, can be easily repeated at multiple time points, and the samples obtained can be handled and shipped at room temperature.

A cancer tumor releases ctDNA into the blood stream. A liquid biopsy, in this case a blood sample, shows the current quantity of ctDNA. The quantity of ctDNA at a given time point provides a precise snapshot of the current tumor burden.

Liquid Biopsy

– A minimally-invasive diagnostic method

In direct comparisons, ctDNA has been shown to be superior to conventional serum protein biomarkers, circulating tumor cells, and radiographic imaging. Analysis of ctDNA in liquid biopsies is rapidly becoming one of the most important minimally invasive diagnostic methods used in oncology since it has overcome the many limitations of traditional diagnostic methods used today.

Treatment decisions will rely more and more on the genetic variant profile of a tumor derived from the patient’s cancer cells. Thus, liquid biopsy tests that can capture and analyze tumor cells and/or circulating tumor DNA hold great promise for current and future cancer applications.

Benefits of the SAGA technology

With SAGA technology, you can be certain you have chosen the best possible tool to assist you in your task. With SAGAsafe® and SAGAsign®, you get new information, vital for the results in clinical studies and for development of new therapies. Both are ultrasensitive and highly cost-effective methods with a short turn-around time. The possibility to choose between a biopsy based on tissue or any suitable body liquid adds flexibility. The stability seen with chromosomal rearrangements, which are used in SAGAsign®, enables long-term use of the same initial fingerprint to monitor clonal evolution throughout a patient’s journey.

SAGAsafe® assays can be ordered for RUO purpose, and all of our assays and tests can also be ordered as a service from our laboratory in Lund.

SAGA's R&D

We have made it SAGA’s mission to develop further unique platform technologies that have the potential to change patient outcome. To remain on forefront of the ctDNA liquid biopsy field, SAGA has established its own R&D laboratory in Lund and is also collaborating with prominent researchers and clinicians in the field of cancer liquid biopsies.

SAGAsafe®

We have over 250 SAGAsafe® ultrasensitive tests developed, and are continually expanding our portfolio.  For a customer, typically we can generate a custom test within 4-6 weeks. Moreover, a number of CE-IVD marked validated tests will be released going forward. SAGAsafe® tests can be ordered as kits, or performed in our central lab as a service.

SAGAsign®

At present, SAGAsign® chromosomal rearrangement monitoring of tumor burden, residual disease, and early detection of relapse, can only be performed as a service in our central lab.  However, we are currently working towards a distributable kit solution.

SAGAseq®

SAGA is currently developing the SAGAseq® platform, a broader gene-panel sequencing-based approach that can analyze tens to hundreds of mutations simultaneously. SAGAseq® marries panel gene sequencing with computationally-augmented error correction – the lower limit of detection is anticipated to approach the range of 0.1% to 0.05% ctDNA variant allele frequency which is highly competitive in the wider panel area. SAGAseq® has the potential to provide a higher performance than the competition mainly due to improved error correction. SAGA also aims to provide panels which are better adapted to their respective use with only relevant genes.

SAGAseq® will feature:

  • Pan-cancer panel
  • Cancer type-specific gene panels
  • Microsatellite instability (MSI) panel
  • Tumor mutational burden (TMB) panel
  • Customizable panels
  • Computationally-enhanced machine-learning error correction
  • Limit of detection to 0.05%

Scientific Collaborations

We collaborate with world leading academic institutions:

  • Karolinska Institute (Sweden)
  • Keio University (Japan)
  • Lund University (Sweden)
  • The Francis Crick Institute / UCL Cancer Institute (UK)
  • Uppsala University (Sweden)
  • Queens University Belfast (UK)
  • Örebro University (Sweden)

Our Publications