xchromosome219/spectrum-tme

Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"

Ovarian cancer mutational processes drive site-specific immune evasion

This repository contains supporting material for the manuscript:

I. Vázquez-García, F. Uhlitz et al, "Ovarian cancer mutational processes drive site-specific immune evasion", Nature (2022)

Table of Contents

• Code
• Data
  • Overview
  • Data availability
    • scRNA-seq
    • H&E
    • mpIF
    • Bulk WGS
    • MSK-IMPACT

Code

The source code contains RMarkdown notebooks to reproduce the manuscript figures and tables.

Data

Overview

The MSK SPECTRUM study is registered on dbGaP under accession number phs002857.v1.p1.

A Synapse page for the MSK SPECTRUM study is available to provide access to multi-modal datasets from one central location. This page can be accessed under accession number syn25569736.

Data availability

scRNA-seq

• Expression counts are available from NCBI Gene Expression Omnibus.
• Processed objects are available from Synapse.
• Interactive data visualizations are available via cellxgene.

Tumor-normal bulk WGS

• Raw sequencing reads are available for controlled access from the NCBI Sequence Read Archive via dbGaP.
• Somatic mutations and copy number data can be accessed from Synapse.
• Somatic mutations, copy number and structural variants can be visualized through cBioPortal.

Tumor-normal targeted panel sequencing (MSK-IMPACT)

• Somatic mutations, copy number and structural variants can be visualized through cBioPortal.

H&E

• Deidentified images are available via dbGaP.
• Cell segmentation, tissue segmentation and lymphocyte classification are available from Synapse.

mpIF

• Deidentified images are available via dbGaP.
• Cell segmentation, tissue segmentation and cell phenotyping are available from Synapse.