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Clin Chem. 2018 Feb;64(2):307-316. doi: 10.1373/clinchem.2017.278911. Epub 2017 Oct 16.

Deactivated CRISPR Associated Protein 9 for Minor-Allele Enrichment in Cell-Free DNA.

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Department of Bioengineering, Stanford University School of Medicine, Stanford, CA.
Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA.
Department of Pathology, Stanford University School of Medicine, Stanford, CA.
Department of Radiology, Stanford University School of Medicine, Stanford, CA.
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA.
Stanford Cancer Institute, Stanford University, Stanford, CA.
Department of Genetics, Stanford University, Stanford, CA.
Department of Radiation Oncology, Stanford University, Stanford, CA.
Department of Bioengineering, Stanford University School of Medicine, Stanford, CA;
Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA.



Cell-free DNA (cfDNA) diagnostics are emerging as a new paradigm of disease monitoring and therapy management. The clinical utility of these diagnostics is relatively limited by a low signal-to-noise ratio, such as with low allele frequency (AF) mutations in cancer. While enriching for rare alleles to increase their AF before sample analysis is one strategy that can greatly improve detection capability, current methods are limited in their generalizability, ease of use, and applicability to point mutations.


Leveraging the robust single-base-pair specificity and generalizability of the CRISPR associated protein 9 (Cas9) system, we developed a deactivated Cas9 (dCas9)-based method of minor-allele enrichment capable of efficient single-target and multiplexed enrichment. The dCas9 protein was complexed with single guide RNAs targeted to mutations of interest and incubated with cfDNA samples containing mutant strands at low abundance. Mutation-bound dCas9 complexes were isolated, dissociated, and the captured DNA purified for downstream use.


Targeting the 3 most common epidermal growth factor receptor mutations (exon 19 deletion, T790M, L858R) found in non-small cell lung cancer (NSCLC), we achieved >20-fold increases in AF and detected mutations by use of qPCR at an AF of 0.1%. In a cohort of 18 NSCLC patient-derived cfDNA samples, our method enabled detection of 8 out of 13 mutations that were otherwise undetected by qPCR.


The dCas9 method provides an important application of the CRISPR/Cas9 system outside the realm of genome editing and can provide a step forward for the detection capability of cfDNA diagnostics.

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