MRD & ctDNA Markers

MRD & ctDNA Markers

Minimal residual disease (MRD) testing

Testing for minimal residual disease (MRD) is routine in paediatric leukemia and Cergentis supports multiple leading pediatric hospitals in personalized MRD test development.

TLA uniquely enables detection of gene fusion breakpoint sequences at nucleotide resolution. Since gene fusions in leukemia are known to be cancer-driving, clonal events, these breakpoint sequences are ideal markers for sensitive and quantitative MRD testing with PCR.


Circulating tumor DNA (ctDNA) testing

Solid tumors shed DNA and recent years have seen a surge in interest in the use of ctDNA testing on liquid biopsies as part of cancer diagnosis. The most developed and promising application is the use of ctDNA levels to monitor disease progression after initial surgery and/or therapy. Such tests can further help select patients that require, or do not require, therapy or a change of therapy after resistance to an initial treatment occurs.

For reasons outlined above, breakpoint sequences of driving rearrangements are also ideal targets for personalized ctDNA testing with PCR.  

For example, TMPRSS2-ERG fusions are found in approximately 50% of prostate cancers. There is currently no targeted therapy available, and fusion detection is therefore less relevant for diagnostics. However, since TMPRSS2-ERG fusions are known to be cancer-driving, clonal events, using TLA for detection of the breakpoint sequences at nucleotide resolution creates ideal markers for sensitive ctDNA testing with PCR.

Cancers caused by viruses, such as cervical cancers, frequently have unique viral integration sites in the host genome, and breakpoints of these integration sites can serve as monitoring markers.

Other cancers with recurrent SVs, such as colorectal cancer, may also benefit from this strategy.



An ALL patient was monitored using an IGH rearrangement (blue) and a TCRD (red) rearrangement as well as the junction region of a CRLF2 deletion (green). The quantitative ranges were 5x10-4 (TCRD) and 1x10-4 (IGH and CRLF2), whereas the sensitivities were 10-4 (CRLF2) and 10-5 (TCRD and IGH). The IGH and TCRD rearrangements and CRLF2 deletion junction gave highly comparable MRD data. Relapse refers to an extramedullary relapse.
Detection of TMPRSS2-ERG fusions in prostate cancer (together with CharlieMassie). While the LNCAP cell line shows no SVs in the TMPRSS2 locus (green arrow), theVCAP cell line shows an extra peak (blue arrow) indicating a translocation.
Detection of TMPRSS2-ERG fusions in prostate cancer (together with CharlieMassie). More detailed analysis reveals a complex TMPRSS2-ERG fusion, which is shownschematically. All breakpoints could be identified (green arrows).
Detection of TMPRSS2-ERG fusions in prostate cancer (together with CharlieMassie). Example of breakpoint sequence detection.
Detection of genomic insertion of HPV DNA (together with Matthias Dürst)A) By targeting HPV sequences in cervical cancer samples, we can detect thepositions at which HPV DNA has integrated into the cancer genome, includingthe exact breakpoints of those insertions.B) This panel shows an example of HPV integration in chromosome 13 in SiHa cells.
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