A new MIT lab unlocks the mysteries of extrachromosomal DNA

A new lab at the intersection of computation and biology

Professor Matt Jones' lab at MIT is working to understand how ecDNA shapes the microenvironment of a tumor, where it appears, how it may modulate cancer-immune interactions, and how it contributes to drug resistance. The lab brings computational advances and laboratory technologies under one roof to build predictive models with potential for clinical use.

Easy integration of spatial solutions with existing workflows

Among the technologies the Jones Lab uses are the Trekker Single-Cell Spatial Mapping Kit and Seeker Spatial Transcriptomics Kit. Trekker is designed as a simple reagent workflow that fits upstream of established single-cell library preparation platforms, spatially tagging nuclei while preserving the molecular resolution researchers already expect.

Because the workflow does not require a separate specialized instrument, teams can add spatial context without rebuilding their entire process. This makes single-cell spatial genomics more accessible while keeping familiar 10x- and Parse-style downstream workflows intact.

Maximizing technological development through a hybrid lab

The Jones Lab is building a hybrid model that gives experimental and computational teams equal weight. In Kendall Square's collaborative research environment, access to emerging research technologies enables the team to ask larger questions—and shorten the path from a new analytical idea to a validated experimental result.

The lab's scAmp probabilistic algorithm is one example: it detects and analyzes ecDNA from single-cell datasets and can extend into Trekker- and Seeker-enabled workflows. This combination of method development and accessible wet-lab tools helps the team investigate how ecDNA forms and what prognostic value it may provide.