🔬 Explore Sid's Data
Explore genomics and imaging data from Sid Sijbrandij's osteosarcoma tumor samples — openly shared to advance cancer research.
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Timeline
Sid was diagnosed with osteosarcoma in November 2022. The primary tumor was resected from the spine in December 2022 (T0). Disease recurred at the Th4 vertebra in June 2024 (T1, UCLA), at Th4–Th5 in January 2025 (T2, UCLA), and was excised in April 2025 (T3, MSKCC). The interactive Timeline tracks the clinical journey, including treatments, residual disease testing (MRD), flow cytometry measurements, and lab results.
| Date | Timepoint | Location | Assays |
|---|---|---|---|
| 2022-12-16 | T0 | UCSF (spine resection) | WES ×4, WGS, WTS |
| 2024-06-06 | T1 | UCLA (Th4 biopsy) | WES, WGS, WTS, scRNA-seq |
| 2025-01-28 | T2 | UCLA (Th4–Th5 biopsy) | WGS, WTS, scRNA-seq |
| 2025-04-17 | T3 | MSKCC (Th4–Th5 excision) | scRNA-seq |
Treatment Timeline
Interactive visualization of treatment history, MRD measurements, procedures, and imaging from November 2022 to present.
Genomics
Tumor and blood specimens have been profiled with whole-genome sequencing (WGS), whole-exome sequencing (WES), bulk RNA-seq, and single-cell RNA-seq across multiple timepoints and sequencing providers. These pages show complementary views of the molecular data: raw alignments, gene expression, pathway enrichment, copy-number changes, and neoantigen targets of personalized vaccines.
Genomics
Whole-genome, whole-exome, bulk and single-cell RNA-seq across multiple timepoints — variant calling pipelines, mutations, copy number, neoantigen vaccine targets, and transcriptomics.
Imaging & Pathology
Whole-body PET/CT imaging — serial FDG scans in the DICOM archive, plus a Ga-68 study with tracers targeting EphA2 and B7-H3 — tracks disease over time, while tumor tissue was profiled with complementary microscopy platforms: H&E histology of the resections and biopsies, Orion 18-plex immune imaging (HMS) of the T0 resection, immunohistochemistry (B7-H3, EphA2) of the April 2025 (T3) resection, and Xenium spatial transcriptomics across T0–T3 — characterizing the tumor microenvironment at the protein and transcript levels.
Imaging
Ga-68 EphA2 and B7-H3 PET tracers aligned by PUMA, plus the DICOM archive of diagnostic imaging, including serial FDG PET/CT scans.
Pathology
Interactive whole-slide microscopy of tumor tissue: H&E and IHC histology, Orion 18-plex imaging, and Xenium spatial transcriptomics.
Resources
Reference material for this dataset — osteosarcoma cell lines (HOS, U-2 OS, CAL-72) for comparative analyses, and a catalog of all raw and processed files (~37 TB) in the project bucket.
Cell Lines
Information about osteosarcoma cell lines including HOS, U-2 OS, and CAL-72 with genomic profiles and curated citations.
Data Files
~37 TB of data: bulk WGS, WES, RNA-seq, scRNA-seq, long-read sequencing (ONT), spatial transcriptomics, imaging (H&E, IHC), and HLA typing.