SRodenburg

Labrecque et al. Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer

2

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763249/ Study with 98 PDX tumors, includes clinical data, RNA-Seq. - [x] [create an issue on datahub](https://github.com/cBioPortal/datahub/issues/new) before curating a study (one issue per study) and copy this checklist to...

Aggarwal et al. - Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study

2

https://pubmed.ncbi.nlm.nih.gov/29985747/ Study on treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) (n=202), includes targeted DNA-Seq and RNA-Seq. Clinical data needs to be requested at the authors. - [x] [create an issue on...

https://github.com/cBioPortal/datahub/blob/master/reference_data/gene_panels/data_gene_panel_sarc_mskcc.txt Refuses to import because it misses the `stable_id` field.

Alumkal et al. - Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance

1

https://www.pnas.org/doi/10.1073/pnas.1922207117 Phase II trial - study on castration-resistant prostate cancer (CRPC) (n=36). Targeted DNA-sequencing on 26 of 36 biopsies, and RNA-Seq was performed on 25 of 36 biopsies. We will...

Quigley et al. - Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

1

https://pubmed.ncbi.nlm.nih.gov/30033370/ Study (n=101) with focus on SVs, includes RNA-Seq and clinical data. We will need to request data to the authors. Mutation data is on hg38 so liftover required. -...

Possible mistake in .isNonExp function causes files (CNA etc) to be loaded as metadata?

4

Hello, I was loading a study using the function `loadStudy` and noticed that most data files are not being added to the `ExperimentList` of the `MultiAssayExperiment` object, but are loaded...