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prince-trial-data

Lacey J. Padrón, Deena M. Maurer, Mark H. O’ Hara, Eileen M. O’ Reilly, Robert A. Wolff, Zev A. Wainberg, Andrew H. Ko, George Fisher, Osama Rahma, Jaclyn P. Lyman, Christopher R. Cabanski, Jia Xin Yu, Shannon M. Pfeiffer, Marko Spasic, Jingying Xu, Pier Federico Gherardini, Joyson Karakunnel, Rosemarie Mick, Cécile Alanio, Katelyn T. Byrne, Travis J. Hollmann, Jonni S. Moore, Derek D. Jones, Marco Tognetti, Richard O. Chen, Xiaodong Yang, Lisa Salvador, E. John Wherry, Ute Dugan, Jill O’Donnell-Tormey, Lisa H. Butterfield, Vanessa M. Hubbard-Lucey, Ramy Ibrahim1, Justin Fairchild, Samantha Bucktrout, Theresa M. LaVallee and Robert H. Vonderheide. Sotigalimab and/or nivolumab with chemotherapy in first- line metastatic pancreatic cancer: clinical and immunologic analyses from the randomized phase 2 PRINCE trial. Nature Medicine, June 3, 2022.

https://doi.org/10.1038/s41591-022-01829-9

This repo contains the select cell populations, proteins, median fluorescence/ signal intensities, RNAseq counts and accompanying clinical/metadata that was used in the above Nature Medicine publication.

DATA DICTIONARY

Clinical

PICI0002_Labs_2021-03-24.csv

  • Deidentified.ID = Deidentified Subject ID
  • Visit = Cycle Timing of Lab Test
  • Study Day = Equivalent Study Day of Lab test
  • Lab Test = Lab Test Name
  • Result = Value of Lab Test
  • Units = Units of Lab Test
  • Normal Range - Low = Low limit of normal range
  • Normal Range - High = High limit of normal range
  • Result in Standard Units = Value of Lab Test in Standard Units
  • Standard Units = Standard Units
  • Standard Normal Range - Low = Low limit of normal range with standard units
  • Standard Normal Range - High = High limit of normal range with standard units
  • Reference Range Indicator = HIGH/NORMAL/LOW for how lab test fell in range
  • Baseline Flag = Y(Yes) if there were abnormal baseline levels

PICI0002_ph2_clinical.csv

  • Deidentified.ID = Deidentified Subject ID
  • Age = Age
  • Sex = Sex
  • Race = Race
  • Ethnicity = Ethnicity
  • HEIGHT (cm) = Height in centimeters
  • WEIGHT (lb) = Weight in pounds
  • Arm = Randomized Enrollment Arm
  • Arm Description = Description of Arm
  • Actual Arm = Actual Arm based on treatment received
  • Phase = Phase of Study When Patient Enrolled (Phase 1b/Phase 2)
  • Participant Dosed = Yes(Y)/No(N) if patient received any study agent
  • Received APX005M = Yes(Y)/No(N) if patient received sotigalimab
  • Received Nivolumab = Yes(Y)/No(N) if patient received nivolumab
  • DLT Evaluable = Dose limiting toxicity evaluable
  • Efficacy Population Flag = Yes(Y)/No(N) Efficacy Population Flag
  • Cancer Type = Type of Cancer (Adenocarcinoma)
  • Cancer Location = Site of Cancer in Pancrease (Head/Body/Tail)
  • Stage at Initial Diagnosis = Stage of disease when initially diagnosed (de novo vs recurrent)
  • Stage at Enrollment = Stage of disease on enrollment
  • Prior Cancer Surgery = History of cancer surgery prior to study enrollment
  • Prior Radiation = Use of radiation prior to study enrollment
  • Prior Chemo = Use of chemotherapy prior to study enrollment
  • ECOG at Screening = Eastern Cooperative Oncology Group (ECOG) Performance Status Scale at Screening
  • Tobacco History = History of Tobacco Usage e.g Smoking
  • Hematocrit (%) at Baseline = Percentage by volume of red blood cells in blood at baseline
  • BOR = Best Overall Response by RECIST
  • OS (days) = Overall Survival
  • OS Event = Death Event
  • PFS (days) = Progression free survival (days)
  • PFS Event = Progression Event
  • PFS Reason = reason for leaving study

CyTOF

NatureMed_CyTOF_metadata.csv

  • Deidentified.ID = Deidentified Subject ID
  • sample.id = sample identifier
  • ms = sample type/assay/%parent(par)/%leukocyte(leuk)
  • timepoint.id = timepoint of blood collection

NatureMed_CyTOF_select_cell_populations.csv

  • sample.id = sample identifier
  • value = fraction of population (parent or leukocyte respectively)
  • paper.name = Naming of cell population from publication

NatureMed_CyTOF_select_MSI.csv

  • sample.id = sample identifier
  • value = relative median signal intensity (arcsinh transformed raw intensity/150, normalized relative to upper (0.9) and lower (0.1) quantiles)
  • epitope.id = UniProt Protein Name
  • paper.name = Naming of cell population from publication

Olink

NatureMed_Olink_metadata.csv

  • Deidentified.ID = Deidentified Subject ID
  • sample.id = sample identifier
  • ms = sample type/assay
  • timepoint.id = timepoint of blood collection

NatureMed_Olink_select_proteins.csv

  • sample.id = sample identifier
  • value = log2(NPX) - Normalized Protein Expression from Olink
  • paper.name = Name used for protein from publication

RNAseq

NatureMed_GX_ph2_metadata

  • Deidentified.ID = Deidentified Subject ID
  • sample.id = sample identifier
  • timepoint.id = timepoint of tumor biopsy
  • filename = Name of respective processed data file
  • gdc.anatomic.site.name = GDC Anatomic Site of Biopsy

Data files

  • Gene Symbol = Gene Symbol
  • NCBI Gene ID = NCBI Gene Symbol
  • RNA-Seq Raw Counts = Raw Counts
  • FPKM = Fragments Per Kilobase of transcript per Million mapped reads
  • CPM = Reads per million mapped reads or Counts per million mapped reads
  • TPM = Transcripts per million
  • Percentile Rank = Percentile Rank
  • Is Expressed = Yes/No if gene is expressed
  • sample = sample identifier

Vectra

NatureMed_Vectra_metadata.csv

  • Deidentified.ID = Deidentified Subject ID
  • sample.id = sample identifier
  • ms = sample type/assay/%parent(par)/%total(tot)
  • timepoint.id = timepoint of tumor biopsy

NatureMed_Vectra_select_cell_counts.csv

  • sample.id = sample identifier
  • assay.name = Vectra assay
  • value = median cell count across all regions of interest (ROI)
  • timepoint.id = timepoint of tumor biopsy
  • gdc.anatomic.site.name = GDC Anatomic Site of Biopsy
  • variable = Naming of cell population from publication

NatureMed_Vectra_select_cell_populations.csv

  • sample.id = sample identifier
  • median.value = median fraction of population parent/total across all regions of interest (ROI)
  • variable = Naming of cell population from publication

X50

NatureMed_X50_metadata.csv

  • Deidentified.ID = Deidentified Subject ID
  • sample.id = sample identifier
  • ms = sample type/assay/%parent(par)/%leukocyte(leuk)
  • timepoint.id = timepoint of blood collection

NatureMed_X50_select_cell_populations.csv

  • sample.id = sample identifier
  • value = fraction of population (parent or leukocyte respectively)
  • paper.name = Naming of cell population from publication

NatureMed_X50_select_MFI.csv

  • sample.id = sample identifier
  • value = relative median fluorescence intensity (arcsinh transformed raw intensity/150, normalized relative to upper (0.9) and lower (0.1) quantiles)
  • epitope.id = UniProt Protein Name
  • paper.name = Naming of cell population from publication