Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors.

"availability of data and materials the dataset supporting the conclusions of this article is available in the gene expression omnibus (geo) (processed gene count tables) under accession gse217517 [ 79 ] and database of genotypes and phenotypes (dbgap) (raw fastq files) under accession phs002262 v2 p1 [ 80 ]. it is also available through zenodo under doi 10 5281/zenodo 8475 [ 82 ]. we have included a tutorial on github for running new methods on this data (availability of data and materials). availability of data and materials the dataset supporting the conclusions of this article is available in the gene expression omnibus (geo) (processed gene count tables) under accession gse217517"

"we have included a tutorial on github for running new methods on this data (availability of data and materials).; the code for all the analyses performed in this paper is available at https://github com/greenelab/deconvolution_pilot under a bsd-3-clause license [ 81 ]."

"Declarations Ethics approval and consent to participateAll samples used in this study were obtained with patients’ written informed consent. All patients were de-identified. The protocol for tissue collection was reviewed and approved by an Institutional Review Board at the University of Pennsylvania (Protocol #702679). Competing interestsThe authors declare that they have no competing interests. Competing interests The authors declare that they have no competing interests."

"Funding Generation of the data used in this study was funded by a Hopkins-Penn Ovarian Cancer SPORE Developmental Research Program award, P50 CA228991. AAH, LMW, JAD, SCH, and CSG were also supported by the National Cancer Institute (NCI) from the National Institutes of Health (NIH) grant R01CA237170. DKO, EJ, RD, and The University of Pennsylvania Ovarian Cancer Research Center’s Tumor BioTrust Collection is funded by the DOD Omics Consortium W81XWH-22-1-0852 and the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."