MSK SPECTRUM Tumor Microenvironment Study (2022)

Overview

The MSK-SPECTRUM project (canonical cBioPortal studyId msk_spectrum_tme_2022) is a prospective cohort study at Memorial Sloan Kettering Cancer Center characterizing the tumor microenvironment in high-grade serous ovarian cancer (HGSOC). Genomic profiling performed with MSK-IMPACT targeted hybrid-capture sequencing. Reference genome: hg19. PMID:35764743

Composition

  • Cancer type: HGSOC, predominantly stage III/IV.
  • 36 prospective MSK-SPECTRUM patients contributed to the Boehm et al. 2022 multimodal cohort (as part of 296 total MSKCC cases). PMID:35764743
  • MSK-IMPACT clinical sequencing used to infer HRD status via HRD-DDR gene variants (including BRCA1, BRCA2) and CCNE1 CNA, plus COSMIC SBS3 detection via SigMA. PMID:35764743

Assays / panels (linked)

  • MSK-IMPACT targeted hybrid-capture sequencing (HRD-DDR gene variants, CCNE1 CNA).

Papers using this cohort

  • PMID:35764743 — Boehm et al. 2022, Nature Cancer: 36 MSK-SPECTRUM patients (prospective arm) included as part of the 296-patient MSKCC cohort in the multimodal HGSOC late-fusion prognostic model.

Notable findings derived from this cohort

  • HRD status inferred from MSK-IMPACT sequencing plus SigMA COSMIC SBS3 detection; 130 MSKCC cases had research consent for HRD calling (high-confidence SBS3 n=48, low-confidence n=30). PMID:35764743
  • The full MSK-SPECTRUM + MSKCC cohort contributed CT imaging (adnexal and omental), H&E WSIs, and genomic data; the multimodal late-fusion model leveraged partial-data cases to avoid restricting training to the 114 patients with complete four-modality data. PMID:35764743
  • Characterized the ovarian cancer tumor microenvironment using scRNA-seq and spatial transcriptomics across 36 HGSOC samples, revealing immune cell composition and stromal cell interactions PMID:36517593

Sources

  • cBioPortal study: https://www.cbioportal.org/study/summary?id=msk_spectrum_tme_2022
  • PMID:35764743 — Boehm et al. 2022, Nature Cancer.

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