Multiplexed Spatial Proteomics Services: Phenocycler aka CODEX

Introduction

Highly multiplexed spatial proteomics makes it possible to visualize 10s of proteins and biomarkers, within multiple cell and tissue structures on a single tissue section, thus providing meaningful context. This enables powerful modeling of biological processes in context to and relationship with the multitude of proteins and biomarkers that define specific cell phenotypes and tissue architecture. One such technology, pioneered and developed in Dr. Nolan’s lab at Stanford and now licensed to Akoya Biosciences, is "CODEX" aka "PhenoCycler". This technology makes use of a DNA barcode technology comprised of unique, complimentary, oligonucleotide sequences. One unique oligo sequence is conjugated to a primary antibody (against a protein or other biomarker target); the complimentary oligo sequence is conjugated to a fluorescent reporter dye. DNA base pairing, between the conjugated complimentary oligonucleotides, then enables highly specific detection. Iterative cycles of imaging 3 different conjugated fluorophores (reports) at a time, plus a DNA dye, results in detection of >50 biomarkers in a single tissue slice.

The CSIF offers a full array of highly multiplexed spatial proteomics services to Stanford researchers as well as to external researchers from academia and industry. These services include:

Custom panel development for mouse and human FFPE and FF tissue samples.
Custom antibody conjugation and validation.
Highly multiplexed Akoya or custom panel runs on PhenoCycler (coverslip) and Phenocycler Fusion (whole slide) instruments.
Data processing using Akoya’s processing software.
Data analysis using Multiplex Analysis Viewer (MAV) or VisioPharm-Phenoplex software.