Dataset Submission Request – Curated Prostate Cancer Study (PEACE Cohort)

[Osvaldas Vainauskas]

Dear cBioPortal Team,

I am writing to express our interest in submitting a curated prostate cancer dataset for inclusion in the public cBioPortal.

Our study data has been fully generated, and we are currently in the manuscript drafting stage. We would ideally like to coordinate the public release of the dataset to coincide with the publication of the associated paper, and wanted to initiate this process early to ensure a smooth and timely submission.

Our dataset — the Prostate PEACE cohort — comprises sequential longitudinal samples (n=400 plasma and biopsies) and multi-region post-mortem samples (n=800) from 30 patients who died of prostate cancer. All samples have been sequenced at high depth (1000×) using a targeted panel covering 94 prostate cancer-specific genes. Additionally, a subset of samples has undergone whole-genome sequencing (60x; n=150), whole-transcriptome sequencing (n=300), and targeted methylation profiling (n=150). We have generated mutation and CNV data (hg19) for all samples.

We would greatly appreciate your guidance on the following:

• The recommended steps and timeline for submitting a new curated study

• Best practices for handling multi-region and longitudinal sample data

• Data formatting and curation requirements we should prepare in advance

• How to coordinate an embargo so the dataset goes live upon publication

Please let us know the best way to proceed. We are happy to provide any further details about the dataset at your convenience.

Thank you for your time and for the tremendous resource that cBioPortal represents to the cancer genomics community.

Best regards,

Osvaldas Vainauskas

UCL Cancer Institute

o.vain...@ucl.ac.uk