Good news!
"A new, error-corrected method for detecting cancer from blood samples is much more sensitive and accurate than prior methods and may be useful for monitoring disease status in patients following treatment ...
The method, based on whole-genome sequencing of DNA, also represents an important step toward the goal of routine blood test-based screening for early cancer detection. ...
the researchers benchmarked the cancer-detection performance of a new commercial sequencing platform from Ultima Genomics. They demonstrated that a low-cost platform such as this one enables a very high “depth” of coverage – a measure of the sequencing data quality – allowing investigators to detect extremely low concentrations of circulating tumor DNA. Adding an error-correcting method greatly improved the accuracy of the technique.
“We’re now entering an era of low-cost DNA sequencing, and in this study, we took advantage of that to apply whole-genome sequencing techniques that in the past would have been considered wildly impractical,” ...
Blood-test-based “liquid biopsy” technology for early cancer detection and monitoring of cancer burden in patients could revolutionize cancer care. However, sensitively and accurately identifying the mutational signatures of cancer, just from tiny concentrations of tumor DNA in blood samples, has involved major challenges. ... using methods based on whole-genome sequencing – not just targeted sequencing of stretches of DNA where mutations are expected. In a study published last year, they showed that they could reliably detect advanced melanoma and lung cancer from patient blood samples, even without access to sequence data from tumor samples.
In the new study, they took their approach a step further. First, they showed that the low cost of a new sequencing platform enables a depth of whole-genome sequencing that would have been prohibitively expensive with older technology. Using that platform alone, and having the known mutational patterns in patient tumors as a guide, they were able to detect tumor DNA in patient blood samples at concentrations in the part per million range. ..."
From the abstract:
"Differentiating sequencing errors from true variants is a central genomics challenge, calling for error suppression strategies that balance costs and sensitivity. For example, circulating cell-free DNA (ccfDNA) sequencing for cancer monitoring is limited by sparsity of circulating tumor DNA, abundance of genomic material in samples and preanalytical error rates.
Whole-genome sequencing (WGS) can overcome the low abundance of ccfDNA by integrating signals across the mutation landscape, but higher costs limit its wide adoption.
Here, we applied deep (~120×) lower-cost WGS (Ultima Genomics) for tumor-informed circulating tumor DNA detection within the part-per-million range.
We further leveraged lower-cost sequencing by developing duplex error-corrected WGS of ccfDNA, achieving 7.7 × 10−7 error rates, allowing us to assess disease burden in individuals with melanoma and urothelial cancer without matched tumor sequencing.
This error-corrected WGS approach will have broad applicability across genomics, allowing for accurate calling of low-abundance variants at efficient cost and enabling deeper mapping of somatic mosaicism as an emerging central aspect of aging and disease."
Whole genome error-corrected sequencing for sensitive circulating tumor DNA cancer monitoring (preprint, open access, but it was published in November 2022 and was apparently never updated since, possibly quite outdated)
Fig. 1 Ultralow ctDNA detection requires deep sequencing coverage and low error rates.
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