Source 1primary paper2021Molecular Oncology
Toolkit/H3K36me3 cfChIP followed by droplet digital PCR
H3K36me3 cfChIP followed by droplet digital PCR
Also known as: H3K36me3 cfChIP followed by ddPCR
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
H3K36me3 cfChIP followed by droplet digital PCR is a cell-free chromatin immunoprecipitation assay that enriches plasma cfDNA associated with the transcription-linked histone mark H3K36me3 and then quantifies specific alleles by ddPCR. In a 2021 NSCLC study, it detected greater enrichment of EGFR-L858R fragments than EGFR wild-type fragments, providing proof of principle for identifying tumor-specific transcriptional activity of mutated alleles.
Usefulness & Problems
Why this is useful
This assay is useful for linking circulating tumor-derived DNA fragments to a chromatin mark associated with transcription, rather than measuring only mutation presence. The cited study indicates that H3K36me3-associated cfDNA can help delineate whether transcription of a particular gene is occurring in the cells from which the cfDNA originates.
Problem solved
It addresses the problem of inferring tumor-specific transcriptional activity of mutant alleles from blood plasma. Specifically, it was applied to distinguish transcription-linked enrichment of EGFR-L858R cfDNA fragments relative to EGFR-WT fragments in NSCLC patients.
Problem links
Need better screening or enrichment leverage
DerivedH3K36me3 cfChIP followed by droplet digital PCR is a cell-free chromatin immunoprecipitation assay that enriches plasma cfDNA associated with the transcription-linked histone mark H3K36me3 and then quantifies specific alleles by ddPCR. In the cited NSCLC study, it was used to detect enrichment of EGFR-L858R fragments relative to EGFR-WT fragments, providing proof of principle for identifying tumor-specific transcriptional activity of mutated alleles.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Mechanisms
digital pcr-based allele-specific quantificationdigital pcr-based allele-specific quantificationimmunoenrichment of cfdna associated with h3k36me3-marked chromatinimmunoenrichment of cfdna associated with h3k36me3-marked chromatinTechniques
Functional AssayFunctional AssayFunctional AssaySelection / EnrichmentSelection / EnrichmentSelection / EnrichmentTarget processes
selectionImplementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensor
The assay format consists of cfChIP targeting H3K36me3-associated plasma cfDNA followed by droplet digital PCR for allele-specific quantification. The supplied evidence supports use in blood plasma from NSCLC patients harboring EGFR-L858R. Details on antibody clone, cfDNA input, preanalytical handling, and ddPCR primer/probe design are not provided in the supplied evidence.
The available evidence is limited to a proof-of-principle study in NSCLC focused on EGFR-L858R versus EGFR-WT. No broader validation across additional genes, cancer types, histone marks, or orthogonal assays is described in the supplied evidence. Practical performance characteristics such as sensitivity, input requirements, and reproducibility are not provided here.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
cfChIP of H3K36me3-associated cfDNA has the potential to delineate whether transcription of a particular gene is occurring in the cells from which its cfDNA originates.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
This study provides proof of principle that cfChIP can be used to identify tumor-specific transcriptional activity of mutated alleles.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
In representative NSCLC cell lines, both wild-type EGFR and EGFR-L858R are transcribed, and mRNA is similarly expressed per EGFR copy.
Approval Evidence
1 source1 linked approval claimfirst-pass slug h3k36me3-cfchip-followed-by-droplet-digital-pcr
H3K36me3 cfChIP followed by droplet digital PCR (ddPCR)
Source:
enrichment resultsupports
In blood plasma from NSCLC patients harboring EGFR-L858R, H3K36me3 cfChIP followed by ddPCR revealed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments.
Source:
Comparisons
Source-backed strengths
The method combines histone-mark-specific immunoenrichment with allele-specific digital PCR, enabling targeted assessment of mutant versus wild-type cfDNA fragments. In the cited NSCLC cohort, H3K36me3 cfChIP followed by ddPCR showed significantly higher enrichment of EGFR-L858R fragments than EGFR-WT fragments. The study explicitly presents this as proof of principle for detecting tumor-specific transcriptional activity of mutated alleles.
Compared with high throughput screening
H3K36me3 cfChIP followed by droplet digital PCR and high throughput screening address a similar problem space because they share selection.
Shared frame: same top-level item type; shared target processes: selection
Compared with LC-MS analysis of fittest binders
H3K36me3 cfChIP followed by droplet digital PCR and LC-MS analysis of fittest binders address a similar problem space because they share selection.
Shared frame: same top-level item type; shared target processes: selection
Compared with whole genome screening of gene knockout mutants
H3K36me3 cfChIP followed by droplet digital PCR and whole genome screening of gene knockout mutants address a similar problem space because they share selection.
Shared frame: same top-level item type; shared target processes: selection
Ranked Citations
- 1.