AUG 05, 2020 12:08 PM PDT

A New Test to Analyze Cell-Free DNA in Cancer Diagnostics

WRITTEN BY: Jasper Cantrell

Cell-free DNA (cfDNA) are small pieces of genomic DNA that have escaped into the bloodstream either through active release by the cell or are remnants of a terminated cell. In recent years, identification and profiling of cfDNA by size was found to be an early indicator of early-stage cancers. Cancer has a higher ratio of small/large cfDNA than normal cfDNA profiles, which could be seen in tests.

Current methods of analyzing cfDNA in the blood suffer from some issues. Samples are often contaminated with genomic DNA from cells accidentally lysed during handling. Contaminating DNA degrading enzymes can also affect cfDNA levels in a sample. On top of it all, cfDNA is not abundant in the blood, so enrichment is needed before testing can be done.

A team from Simon Fraser University in Canada developed a possible method to overcome these downfalls of current cfDNA analysis methods. They would use droplet digital PCR, which combines PCR (which is used to amplify the cfDNA signal so it can be analyzed) with droplet formation (which is used to get many tests from one sample).

They started with 117 samples from patients with and without cancer. To determine the size profile, they used primers targeted for specific marker genes with known sizes alongside an internal control. They then compared the results of the droplet digital PCR test with the current tests to measure accuracy. Their assay’s results were in line with the current methodology. They observed that samples from cancer patients had a higher ratio of small/medium cfDNA fragments compared to samples from healthy patients.

To counter the possible genomic DNA contamination, the team utilized a profiling method of separating cfDNA into three sizes; small, medium, and large. Genomic DNA is often far larger than the short or medium, so a ratio of small/medium cfDNA was used to determine if a sample had higher DNA fragmentation than normal. They note that although cutting out the larger DNA fragments made the test resistant to genomic DNA contamination, to much genomic DNA could still interfere with the results.

This digital droplet PCR assay uses a small amount of cfDNA to generate analyzable datasets. The profiling method used by this assay is simple and is resistant to contaminating genomic DNA. The team also found that a high small/medium cfDNA ratio seems to be indicative of cancer, which is in line with many other studies. Unfortunately, the team notes that any mutations in the marker genes used in this test could ruin test results.

The study concludes, “Taken together, our data show that assays inferring ctDNA levels from cfDNA size distributions are a convenient approach to identify candidate samples with high ctDNA but these measurements must be always corroborated by complementary methods.”

Sources: Nature Scientific Reports, NEJMvideo

About the Author
  • Hey everyone! My name is Jasper and, considering I am pretty new here to Labroots, I figured I would introduce myself. I received my bachelor’s from the University of California at Riverside back in 2016. I started off my career a few years ago with a job at a University over in New York, before moving over into the industry. I'm happy to be writing content for Labroots, and I hope you enjoy it!
You May Also Like
MAY 16, 2021
Cancer
Can you guess which drug is both antiviral and immunotherapeutic?
MAY 16, 2021
Can you guess which drug is both antiviral and immunotherapeutic?
Hepatitis B virus (HBV) is the most common cause of liver cancer in the world, resulting in approximately 880,000 deaths ...
JUN 16, 2021
Cancer
New drug attacks pancreatic tumors with mutant KRAS addiction
JUN 16, 2021
New drug attacks pancreatic tumors with mutant KRAS addiction
Pancreatic cancer is notoriously difficult to detect in early stages, which is why it is associated with a low survival ...
AUG 19, 2021
Cancer
Japanese Berry Vine Could Treat Lung Cancer
AUG 19, 2021
Japanese Berry Vine Could Treat Lung Cancer
A berry-producing vine in Japan has shown promise in mouse models for treating lung cancer. The corresponding study was ...
AUG 30, 2021
Cancer
A Hot Approach to CAR T Cells
AUG 30, 2021
A Hot Approach to CAR T Cells
Immunotherapy, a type of treatment that targets a patient’s immune system to enhance the natural ability to attack ...
SEP 06, 2021
Cancer
A New Biomarker to Personalize Breast Cancer Therapy
SEP 06, 2021
A New Biomarker to Personalize Breast Cancer Therapy
The American Cancer Society estimates that over 280,000 women in the United States will be diagnosed with breast cancer ...
SEP 18, 2021
Genetics & Genomics
Cancer Genes Might Aim for the Immune System, Not Growth Promotion
SEP 18, 2021
Cancer Genes Might Aim for the Immune System, Not Growth Promotion
The DNA in our cells can accumulate damage over may years. Environmental influences like UV light or cigarette smoke may ...
Loading Comments...