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Scripts for: Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction

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posted on 2022-12-05, 15:08 authored by Xinsong Chen, Emmanouil SifakisEmmanouil Sifakis, Seong-Hwan Jun, John LövrotJohn Lövrot, Johan Hartman

Description

This record includes scripts to reproduce the WGS and RNA-seq analysis as part of the study “Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction" by Chen et al., 2022. All scripts are available with a Creative Commons Attribution 4.0 International License (CC BY 4.0: http://creativecommons.org/licenses/by/4.0/).

WGS scripts

This script collection includes scripts to reproduce the WGS analysis as part of the study by Chen et al., 2022. It processes the outputs from Strelka/Mutect2 for somatic SNV calling and from Control-FREEC for somatic Copy Number Alteration (CNA) calling. Inputs the results of the somatic SNV and CNA calling, and outputs several informative plots. Further details are available in the Materials & Methods part of Chen et al., 2022 and in the corresponding README file.

RNA-seq R project

This script collection includes scripts to reproduce the RNA-seq analysis as part of the study by Chen et al., 2022. It is bundled as an R project. It performs quality control of the ex-vivo model of breast cancer, analyses 4OHT/NDT induced changes, and explores individual patients (as model for precision/personalized medicine). Inputs the RNA-seq gene count data and the patient clinical data, and outputs several informative plots. Further details are available in the Materials & Methods part of Chen et al., 2022 and in the corresponding README file.

Funding

Svenska Läkaresällskapet (Swedish Society of Medicine)

Svenska Sällskapet för Medicinsk Forskning (Swedish Society for Medical Research)

Cancerfonden (Swedish Cancer Society)

Radiumhemmets Forskningsfonders (Cancer Society in Stockholm)

Region Stockholm - Health, medicine and technology (Hälsa, medicin och teknik)

MedTechLabs

Bröstcancer Förbundet (Swedish Breast Cancer Association)

CIIR – Tumor-immune interactions and clinical applications

Swedish Research Council

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History

Publisher

Karolinska Institutet

Contact email

johan.hartman@ki.se

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    Johan Hartman research group

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