This readme file was generated on 2025-02-13 by Nona Struyf

Last updated: 2025-05-27 by Nona Struyf


GENERAL INFORMATION

Title of Dataset: 

Author/Principal Investigator
Name: Tom Erkers
ORCID: 0000-0002-2754-6287
Institution: Karolinska Institutet
Address: Tomtebodavägen 23, 171 65 Solna, Sweden
Email: tom.erkers@ki.se

Principal Investigator
Name: Olli Kallioniemi
ORCID: 0000-0002-3231-0332
Institution: Karolinska Institutet
Address: Tomtebodavägen 23, 171 65 Solna, Sweden
Email: olli.kallioniemi@ki.se

Principal Investigator
Name: Sören Lehmann
ORCID: 0000-0001-8374-8978
Institution: Karolinska Institutet
Address: NEO Medicinaren 25, HERM plan 7, 14157 Huddinge/Stockholm
Email: soren.lehmann@ki.se

Author
Name: Nona Struyf
ORCID: 0000-0002-6975-0753
Institution: Karolinska Institutet
Address: Tomtebodavägen 23, 171 65 Solna, Sweden
Email: nona.struyf@ki.se



Date of data collection: 2018-04-12 - 2024-04-21

Geographic location of data collection: Stockholm, Sweden

Information about funding sources that supported the collection of the data: Swedish childhood cancer fund (TJ2021-0080), Karolinska Institutet (2024-00304, 2020-01091, 2018-02283), Swedish foundation for strategic research (SB16-0058), Swedish research council (2017-06095), Knut and Alice Wallenberg foundation (2015.0291)



DATA & FILE OVERVIEW

File List: 
- sDSS.csv : sDSS table with response to 528 drug perturbations in FLT3 mutant patients.
- sDSS_FLT3i.csv : sDSS table with response to 8 FLT3i in FLT3 mutant and wild type patients.
- olink_NPX.csv : Soluble protein data table for 17 FLT3 mutant patients.
- pixelgen.RData : RData file containing a merged Seurat object with single-cell spatial proteomics data for 6 FLT3 mutant patients.
- annotation.csv : Annotation file for all samples.



DATA-SPECIFIC INFORMATION FOR: sDSS

Number of variables: 528

Number of cases/rows: 32

Variable List: Variables are selective drug sensitivity scores (sDSS) of 525 drugs and 3 drug combinations measured with drug sensitivity and resistance testing as previously described. (doi:10.1038/s41698-024-00528-7) Drug sensitivity scores (DSS) were calculated with Breeze (doi:10.1093/bioinformatics/btaa138) and healthy bone marrow control DSS were used to calculate the sDSS. sDSS is displayed for 32 FLT3 mutant patient samples. Responder status is available in annotation file.

Missing data codes: NA

Specialized formats or other abbreviations used: /



DATA-SPECIFIC INFORMATION FOR: sDSS_FLT3i

Number of variables: 8

Number of cases/rows: 175

Variable List: Variables are selective drug sensitivity scores (sDSS) of 8 FLT3 inhibitors measured with drug sensitivity and resistance testing as previously described. (doi:10.1038/s41698-024-00528-7) Drug sensitivity scores (DSS) were calculated with Breeze (doi:10.1093/bioinformatics/btaa138) and healthy bone marrow control DSS were used to calculate the sDSS. sDSS is displayed for 175 FLT3 mutant and wild type patient samples. Mutant and responder status is available in annotation file.

Missing data codes: NA



DATA-SPECIFIC INFORMATION FOR: olink_NPX

Number of variables: 89

Number of cases/rows: 17

Variable List: Variables consist of 89 soluble proteins measured in 17 bone marrow supernatants of FLT3 mutant patients with the Olink 96 Immuno-Oncology panel (Olink Proteomics, Uppsala, Sweden). Sample detection and analysis were done by real-time PCR analysis on the BioMarkTM HD System (Fluidigm, San Francisco, CA). Ct-data from the Fluidigm Real-Time PCR Analysis software (Fluidigm) was analyzed and normalized with the NPX Manager analysis software (Olink) based on internal and external assay controls resulting in Normalized Protein eXpression (NPX) values, a log2-scale relative quantification. Variables where none of the samples had a value above the limit of detection (LOD) were excluded.

Missing data codes: /



DATA-SPECIFIC INFORMATION FOR: pixelgen.RData

Number of variables: 76

Number of cases/rows: 8

Variable List: Variables consist of 76 surface proteins measured in 6 FLT3 mutant patients with the Single cell spatial proteomics kit, immunology panel I (Pixelgen Technologies, Stockholm, Sweden). Data for each patient sample was generated by running the raw fastq files through the nf-core/pixelator pipeline (v.0.15.2). The RData file contains merged information on expression, metadata, spatial features, and computed metrics (e.g. polarization, colocalization) for all 6 patients in the form of a Seurat object.

Missing data codes: /



DATA-SPECIFIC INFORMATION FOR: drug_class.csv 

Number of variables: 4

Number of cases/rows: 528

Variable List: drug: drug name. Class: Main drug class. subclass: Subclass with main drug targets. Final column: FIMM IDs for each drug

Missing data codes: /



DATA-SPECIFIC INFORMATION FOR: annotation.csv

Number of variables: 4

Number of cases/rows: 175

Variable List: ID: patient ID used in all data files. Group: FLT3 mutation status, wild type (wt) or mutated (mut). Response: Midostaurin response group as defined in the manuscript. Label: concatenated Group and Response label for analysis purposes-

Missing data codes: /



Code: All codes for data analysis are available at https://github.com/nstruyf/FLT3_SMAC
