> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/cci/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/cci/the-team/flagship-projects.md).

# Flagship Projects

## [**MSK-ACCESS**](https://www.mskcc.org/departments/division-solid-tumor-oncology/early-drug-development-service-phase-clinical-trials/precision-medicine-approach/msk-access) **(Research)** 

Developed by scientists in the CMO Technology Innovation Lab and Department of Pathology, this high-sensitivity assay is offered by the CMO to MSK researchers for profiling circulating tumor DNA derived from blood plasma. The inclusion of matched buffy coat DNA enables the identification and elimination of germline variants and mutations associated with clonal hematopoiesis, a significant confounder of most commercial assays. The assay is available for clinical use in the Molecular Diagnostics Service and for research projects in the Integrated Genomics Operations (IGO). CCI supports the data processing and analysis of research projects utilizing MSK-ACCESS in IGO and leads the ongoing development of the MSK-ACCESS pipeline for all applications. The current version of the pipeline is available here: [mskcc/ACCESS-Pipeline: cfDNA Sequencing Pipeline with UMI (github.com)](https://github.com/mskcc/ACCESS-Pipeline), and more details about the assay and analysis are described in this paper below as well as [here](/cci/the-onboarding/computational-biologist/msk-access-v1.md): 

[Brannon, A. R. et al. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell- free DNA via paired normal sequencing using MSK-ACCESS. Nat Commun 12, 3770 (2021).](https://www.nature.com/articles/s41467-021-24109-5)

![MSK-ACCESS Version 1 assay overview](https://1088897168-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWFNNHLutcLqVqWl5mCIq%2Fuploads%2FjeQp7dg7jHxBJf6XWjAy%2FScreen%20Shot%202022-02-07%20at%204.30.29%20PM.png?alt=media\&token=7d35fbfa-53f9-49d4-aabb-6fd4865c8565)

## **CMO-CH**

Developed by scientists in the CMO Technology Innovation Lab in collaboration with CCI and Clonal Hematopoiesis (CH) program, Diagnostic Molecular Pathology, Precision Interception, and Prevention Initiative & CCI, this assay utilizes the same barcoding and ultra-deep sequencing technology as MSK-ACCESS to detect CH mutations in white blood cells at high sensitivity. CMO-CH is offered by the CMO to MSK researchers for profiling white blood cell DNA to detect mutations in the most commonly altered CH-associated genes. The assay is run in IGO, and CCI supports the data processing and analysis. You can learn more about it [here](/cci/the-onboarding/computational-biologist/cmo-ch-v1.md)

For both projects, additional analysis packages and development versions of the workflows can be found here: [CMO Cell-Free DNA (cfDNA) Informatics Team (github.com)](https://github.com/msk-access)

 


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