# SaferSeqS (Watson and Crick strand sequencing)

Source: https://onco.cc/technologies/saferseqs/  
OnCo record `saferseqs` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

A way of reading both strands of each DNA molecule in a blood sample, so a real mutation can be told from a copying error even when only one molecule in 100,000 carries it.

## Summary

SaferSeqS (Cohen et al., Nature Biotechnology 2021, Johns Hopkins) introduces identical molecular barcodes on the Watson and Crick strands of each template molecule and enriches targets with strand-specific PCR. It detects variants below 1 in 100,000 template molecules with a background mutation rate below 5 x 10^-7 mutants per base pair, can assess one or several amplicons, recovers both strands well from limited cell-free DNA, and cuts the error rate of existing barcoding approaches by more than 100-fold. It reaches that level per locus, for the few mutations it assays. Haystack MRD describes its chemistry as an optimised version of the earlier Safe-SeqS method from the same group.

## Fields

- Kind: Technology
- Status: emerging
- Last checked: 2026-11-04
- Also known as: SaferSeqS
- Principle: A true mutation is present on both strands of a double-stranded molecule; an error made while copying is usually on one. Requiring both strands, tied together by barcodes, removes most errors.
- Since: 2021
- Strengths: Error rate low enough to read single rare molecules; Works on small amounts of cell-free DNA
- Limitations: Amplicon based: each assay reads few loci, so the total number of informative molecules is small; A per-locus limit, not a whole-sample limit

## Sources

- Cohen et al., Nat Biotechnol 2021 (SaferSeqS): https://doi.org/10.1038/s41587-021-00900-z

## Connected records

- drugs: [Haystack MRD](https://onco.cc/drugs/haystack-mrd/)
- ideas: [Read methylation and mutation on the same cell-free DNA fragment to tell what kind of cancer is left](https://onco.cc/ideas/idea-same-fragment-methylation-and-mutation/)
- fronts: [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/)
- technologies: [Liquid biopsy (ctDNA)](https://onco.cc/technologies/liquid-biopsy/), [MRD / molecular residual disease testing](https://onco.cc/technologies/mrd-testing/)
- terms: [Circulating tumour DNA (ctDNA)](https://onco.cc/terms/ctdna/), [Next-generation sequencing (NGS)](https://onco.cc/terms/ngs/)
- key papers: [Detection of low-frequency DNA variants by targeted sequencing of the Watson and Crick strands](https://onco.cc/key-papers/paper-cohen-saferseqs-nat-biotechnol-2021/)

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