Nav: Home

A new sequencing method to detect DNA modifications of relevance to cancer

February 25, 2019

FEBRUARY 25, 2019, NEW YORK - Ludwig Cancer Research scientists report in the current issue of Nature Biotechnology a new and improved method to detect chemical modifications to DNA. These modifications -- or "epigenetic" marks -- help control gene expression and their aberrant distribution across the genome contributes to cancer progression and resistance to therapy.

Led by Chunxiao Song and Benjamin Schuster-Boeckler, both assistant members of the Ludwig Institute for Cancer Research, Oxford, the study demonstrates that their method, dubbed TET-assisted pyridine borane sequencing, or TAPS, is a less damaging and more efficient replacement for bisulfite sequencing, the current gold standard for mapping epigenetic modifications to DNA.

"We think TAPS could directly replace bisulfite sequencing as a new standard in DNA epigenetic sequencing," said Song. "It makes DNA epigenetic sequencing more affordable and accessible to a wider range of academic research and clinical applications."

One class of epigenetic modifications involves the attachment of chemical groups to one of the four "letters," or bases, of DNA. These marks do not alter the DNA sequence itself, but rather influence the switching on and off of genes. Two of the most common modifications of this type involve the addition of chemical methyl and hydroxymethyl groups to cytosine to create 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). "Abnormal patterns of 5mC and 5hmC abundance are classic hallmarks of cancer," Song said.

For decades, biologists have relied on bisulfite to detect 5mC and 5hmC modifications, but the chemical is extremely destructive, degrading as much as 99% of the DNA it contacts. "You can imagine that if you're dealing with very limited genetic samples, such as cell-free DNA circulating in blood, bisulfite sequencing becomes very challenging," Song said.

Another limitation of bisulfite sequencing is that it detects 5mC and 5hmC only indirectly. The technique converts unmodified cytosine to a related base called uracil, while leaving methylated cytosine intact. "This is very inefficient and computation intensive," Song said. "It's like looking for Waldo by eliminating everyone who is not Waldo. TAPS allows us to find Waldo directly."

The new method involves two steps. The first uses an enzyme known as TET to convert 5mC and 5hmC to a third modification, 5-carboxylcytosine (5caC). The second step involves a new chemical reaction developed by Yibin Liu, a postdoctoral researcher in Song's lab, to convert 5caC into thymine - a DNA base that can be read by ordinary sequencing machines.

The process generated a new type of data, and the laboratory of Schuster-Boeckler developed the computational methodology required for its analysis. "Compared to bisulfite sequencing, processing TAPS data is not only twice as fast, it also retains a lot more information from the original sample. This makes it much easier to detect mutations and structural variations even while identifying DNA modifications," Schuster-Boeckler said.

After demonstrating that the core chemistry of TAPS worked, the team spent another year perfecting it, pushing the efficiency of the reaction from about 70% to over 95%. The researchers also developed two variations of the TAPS technique - TAPS-Beta and CAPS - which can be used to detect only 5mC or 5hmC, respectively.

In tests with mouse DNA, the researchers showed that TAPS can generate more accurate sequencing data at half the cost of bisulfite sequencing. "We can get twice as much useful data for the same amount of money," Song said.

Song, Schuster-Boeckler and colleagues are now refining TAPS to analyze cell-free DNA shed by tumors into the bloodstream with the goal of applying the technique to develop minimally invasive cancer diagnostics.
This study was supported by Ludwig Cancer Research, Cancer Research UK, NIHR Oxford Biomedical Research Centre and the Conrad N. Hilton Foundation.

Chunxiao Song is also a PI with the Target Discovery Institute at the University of Oxford, and Benjamin Schuster-Boeckler is a PI with the Big Data Institute at the University of Oxford.

About Ludwig Cancer Research

Ludwig Cancer Research is an international collaborative network of acclaimed scientists that has pioneered cancer research and landmark discovery for more than 40 years. Ludwig combines basic science with the ability to translate its discoveries and conduct clinical trials to accelerate the development of new cancer diagnostics and therapies. Since 1971, Ludwig has invested $2.7 billion in life-changing science through the not-for-profit Ludwig Institute for Cancer Research and the six U.S.-based Ludwig Centers. To learn more, visit

For further information please contact Rachel Reinhardt, or +1-212-450-1582.

Ludwig Institute for Cancer Research

Related Cancer Articles:

Radiotherapy for invasive breast cancer increases the risk of second primary lung cancer
East Asian female breast cancer patients receiving radiotherapy have a higher risk of developing second primary lung cancer.
Cancer genomics continued: Triple negative breast cancer and cancer immunotherapy
Continuing PLOS Medicine's special issue on cancer genomics, Christos Hatzis of Yale University, New Haven, Conn., USA and colleagues describe a new subtype of triple negative breast cancer that may be more amenable to treatment than other cases of this difficult-to-treat disease.
Metabolite that promotes cancer cell transformation and colorectal cancer spread identified
Osaka University researchers revealed that the metabolite D-2-hydroxyglurate (D-2HG) promotes epithelial-mesenchymal transition of colorectal cancer cells, leading them to develop features of lower adherence to neighboring cells, increased invasiveness, and greater likelihood of metastatic spread.
UH Cancer Center researcher finds new driver of an aggressive form of brain cancer
University of Hawai'i Cancer Center researchers have identified an essential driver of tumor cell invasion in glioblastoma, the most aggressive form of brain cancer that can occur at any age.
UH Cancer Center researchers develop algorithm to find precise cancer treatments
University of Hawai'i Cancer Center researchers developed a computational algorithm to analyze 'Big Data' obtained from tumor samples to better understand and treat cancer.
New analytical technology to quantify anti-cancer drugs inside cancer cells
University of Oklahoma researchers will apply a new analytical technology that could ultimately provide a powerful tool for improved treatment of cancer patients in Oklahoma and beyond.
Radiotherapy for lung cancer patients is linked to increased risk of non-cancer deaths
Researchers have found that treating patients who have early stage non-small cell lung cancer with a type of radiotherapy called stereotactic body radiation therapy is associated with a small but increased risk of death from causes other than cancer.
Cancer expert says public health and prevention measures are key to defeating cancer
Is investment in research to develop new treatments the best approach to controlling cancer?
UI Cancer Center, Governors State to address cancer disparities in south suburbs
The University of Illinois Cancer Center and Governors State University have received a joint four-year, $1.5 million grant from the National Cancer Institute to help both institutions conduct community-based research to reduce cancer-related health disparities in Chicago's south suburbs.
Leading cancer research organizations to host international cancer immunotherapy conference
The Cancer Research Institute, the Association for Cancer Immunotherapy, the European Academy of Tumor Immunology, and the American Association for Cancer Research will join forces to sponsor the first International Cancer Immunotherapy Conference at the Sheraton New York Times Square Hotel in New York, Sept.

Related Cancer Reading:

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Climate Crisis
There's no greater threat to humanity than climate change. What can we do to stop the worst consequences? This hour, TED speakers explore how we can save our planet and whether we can do it in time. Guests include climate activist Greta Thunberg, chemical engineer Jennifer Wilcox, research scientist Sean Davis, food innovator Bruce Friedrich, and psychologist Per Espen Stoknes.
Now Playing: Science for the People

#527 Honey I CRISPR'd the Kids
This week we're coming to you from Awesome Con in Washington, D.C. There, host Bethany Brookshire led a panel of three amazing guests to talk about the promise and perils of CRISPR, and what happens now that CRISPR babies have (maybe?) been born. Featuring science writer Tina Saey, molecular biologist Anne Simon, and bioethicist Alan Regenberg. A Nobel Prize winner argues banning CRISPR babies won’t work Geneticists push for a 5-year global ban on gene-edited babies A CRISPR spin-off causes unintended typos in DNA News of the first gene-edited babies ignited a firestorm The researcher who created CRISPR twins defends...