🔬 Explore Sid's Data
Explore genomics and imaging data from Sid Sijbrandij's osteosarcoma tumor samples — openly shared to advance cancer research.
Please contact us with any questions or comments.
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) | 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
Longitudinal whole-body PET/CT scans — nine FDG timepoints plus Ga-68 tracers targeting EphA2 and B7-H3 — track disease across timepoints, while tissue from the T0 resection was profiled with complementary microscopy platforms: H&E histology, immunohistochemistry (B7-H3, EphA2), Orion 18-plex immune imaging (HMS), and Xenium spatial transcriptomics — characterizing the tumor microenvironment at the protein and transcript levels.
Imaging
Nine whole-body FDG PET/CT timepoints with LION tumor segmentation, plus Ga-68 EphA2 and B7-H3 tracers aligned by PUMA.
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 (~25 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
25TB of data: bulk WGS, WES, RNA-seq, scRNA-seq, long-read sequencing (ONT), spatial transcriptomics, imaging (H&E, IHC), and HLA typing.
