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Tools — SITC 2026

The second primary artifact: one Markdown file per biomarker / immune-profiling method or pipeline. SITC programs methods talks adjacent to drug readouts — multiplex IF panels, TCR repertoire pipelines, ctDNA-MRD assays, microbiome sequencing protocols, single-cell + spatial classifiers. Each gets a tools/<slug>.md entry. The drug / cell-therapy side lives in trials/.

Status: Template stub. We're carrying over the per-tool format from EuroBioC 2025 tools, with one modification: SITC is not a Bioconductor venue — many tools are commercial platforms (Akoya, Standard BioTools / IonPath MIBI, NanoString CosMx, 10x Xenium / Visium HD, Adaptive immunoSEQ), not R packages. The "Status" badge swaps Bioconductor for Platform / vendor / open-source repo / vignette / preprint. Once the program-at-a-glance posts in September, ~15–20 entries get populated from the methods + immune-monitoring sessions.

Per-tool entry template

Each tool gets its own page (tools/<slug>.md) following this structure:

# <Tool / panel / platform name>

**One-line description** — what the assay / pipeline does in plain language.

- **Group / vendor:** <academic lab / commercial vendor>
- **Platform / format:** <multiplex IF / spatial-transcriptomics / TCR-seq / single-cell / ctDNA / 16S+shotgun / image-analysis / classifier>
- **Repo / vendor page:** [link]
- **Vignette / protocol:** [link]
- **Preprint / paper:** [DOI]
- **Status at SITC 2026:** <new release / major update / methods talk / case-study readout / pre-conference workshop>

## Talk at SITC 2026

- **Speaker:** ...
- **Day / session:** ...
- **Slides:** [link if shared]
- **Video:** [SITC virtual link if recorded]
- **Abstract:** [JITC DOI]

## What it does

2–3 sentences: the immune-profiling problem it solves, key methodological idea,
what it consumes / produces. Be explicit about the **IO use case** — biomarker
of response, mechanism-of-resistance characterization, MRD, neoantigen
prediction, TCR-clonotype tracking, immune-cell-state classification.

## Where it fits in the corpus

- **SITC 2026 trials:** [link to any `trials/<x>.md` that used this assay for correlatives]
- **AACR 2026:** [link if mentioned in an AACR talk or poster]
- **EuroBioC 2025:** [link if the same / analogous package was shown]
- **GBCC 2025 / RECOMB 2026 / ISMB 2026:** [link if mentioned]
- **JPM 2026:** [link if commercial vendor presented]

## Notes

Free-form impressions: validation data shown, comparisons to alternatives,
batch / cross-site reproducibility claims, sample-prep requirements,
turnaround time, regulatory status (CDx / CLIA / RUO).

Tool index

Pre-meeting shortlist of the categories we expect to populate. The specific named platforms below are expected, subject to program release — derived from SITC 2025 program shape, AACR 2026 method-talk overlap, and active commercial / academic platforms in IO biomarker development. To be replaced with named talks once SITC posts the program-at-a-glance.

Category Representative platforms / packages Anticipated SITC angle Cross-vault link
Multiplex IF / IHC Akoya PhenoCycler-Fusion, Standard BioTools / IonPath MIBI, Lunaphore COMET TME phenotyping panels keyed to cell-therapy / bispecific cohorts AACR 2026 spatial sessions; SpatialData
Spatial transcriptomics 10x Xenium, NanoString CosMx, Curio Seeker, Vizgen MERSCOPE Pre/post-treatment biopsy spatial-immune profiling AACR 2026 spatial; DESpace, spatialFDA
TCR repertoire Adaptive immunoSEQ, MiXCR, Mvision, Repertoire AI Clonotype tracking pre/post-treatment; neoantigen-vaccine response EuroBioC 2025 clonal-tracking (barbieQ)
scRNA-seq + scTCR 10x Chromium, Parse, Scale; downstream Seurat / scanpy Cell-therapy product profiling + TIL state characterization AACR 2026 single-cell axis; EuroBioC2025 single-cell short talks
ctDNA-MRD Signatera (Natera), RaDaR (NeoGenomics), Guardant Reveal, Tempus xM Surrogate endpoint for adjuvant IO / vaccine trials ASCO 2026 trials with ctDNA-defined cohorts
Neoantigen prediction NetMHCpan family, MHCflurry, Personalis NeXT, Gritstone EDGE, BioNTech iNeST The Wu Smalley lecture substrate; vaccine selection pipelines AACR 2026 bioinfo-tools axis
Microbiome profiling Shotgun metagenomics (illumina + nanopore), 16S, metabolomics Stool + tissue panels in microbiome × IO cohorts EuroBioC 2025 mia, miaTime
Spatial-immune classifiers Lunaphore-derived signatures, NeoGenomics MultiOmyx, academic CODEX/MIBI pipelines Response / resistance classifiers; biomarker development AACR 2026 sessions on TME spatial atlases
Cytometry (mass + spectral) Cytek Aurora, Standard BioTools Helios (CyTOF), spectral flow standardization Deep immune-monitoring panels for clinical trial correlatives Methods workshops
HLA typing + class-I/II profiling OptiType, Polysolver, arcasHLA, Personalis ImmunoID Required upstream of TCR-T and personalized-vaccine trials Neoantigen / TCR-T trial cross-links
Image-analysis pipelines (digital pathology) QuPath, Stardist, HALO (Indica Labs), PathAI TIL counting, multiplex-IF segmentation, response classifiers EuroBioC 2025 HistoImagePlot
Soluble biomarker panels Olink, SomaScan, Luminex multiplex Cytokine release / IO toxicity / pharmacodynamic monitoring Trial-correlative panel cross-links

Additional candidates once the program lands:

  • Single-cell proteomics — emerging in cell-therapy product characterization; EuroBioC scp-distributional cross-link
  • Foundation models for TCR / antigen prediction — TCRBert-class, ESM-2 derivatives applied to immunogenicity
  • CITE-seq + cell hashing — high-parameter single-cell for cell-therapy product release testing
  • CTC / cellular MRD in solid tumors — Bio-Techne, Epic Sciences platforms
  • Imaging mass cytometry — Hyperion / Standard BioTools, academic IMC pipelines

Why this format

  • Cross-vault links matter most here — a multiplex-IF panel from SITC anchors trial correlatives at AACR, biomarker classifiers at RECOMB, and Bioconductor analysis packages at EuroBioC. The tool entry is the join key.
  • Trial ↔ tool linking is the unique value of the SITC vault: every tools/<x>.md should link to the trials/<y>.md where it appeared as correlative data, and vice versa.
  • Platform vs package distinction is explicit. Unlike EuroBioC (all R packages), SITC mixes commercial platforms, academic open-source pipelines, and clinical assays — the Status field surfaces that.

Open questions for the build

  1. Commercial vendor sessions — SITC has industry-symposia where vendors (Akoya, 10x, Adaptive, NanoString) present case studies. Treat these as tools/ entries with Status: vendor case-study?
  2. CDx / IVD status — for assays moving toward companion-diagnostic status (Signatera, Akoya panels in trials), surface FDA / EU regulatory state as a separate field?
  3. Workshops vs talks — pre-conference workshops on cellular-therapy immune-monitoring and biomarker development warrant fuller treatment than a single talk; consider a workshop-detail subsection in the template.