Data types

KPMP Data Types

‍

Clinical data

A wide variety of clinical phenotype data is being collected about each participant in the KPMP, including longitudinal follow-up data. The KPMP REDCap codebook outlines all of the collected clinical phenotype data. View the REDCap Codebook.

‍

KPMP has created a baseline clinical phenotyping data file that allows for a faster turnaround time for clinical data requests once a Data Use Agreement (DUA) has been completed. This file can be sent to users both internally and externally with DUAs. Variables include sex, age, race, disease type, condition, KDIGO stage, duration, comorbidities, family and personal history, frequently requested lab values, and medications. To find out more about the contents of this baseline clinical file, view the Baseline Clinical Phenotyping Data Dictionary.

‍

Pathology data

‍

Whole slide images

KPMP biopsy tissue is processed for light microscopy, immunofluorescence microscopy, and electron microscopy. Standard light microscopic stains for the KPMP tissue are: H&E, PAS, trichrome, and Jones' silver. The light microscopy whole slide images are available for download in the Atlas Repository. See: KPMP Pathology Manual of Procedures for more details on the pathology workflow.

‍

Pathology descriptor scoring

The Kidney Precision Medicine Project (KPMP) tubulointerstitial and vascular (TIV) descriptor scoring parameters were developed based on the NEPTUNE Digital Pathology Scoring System.¹ This form includes 64 unique TIV descriptors, of which 10 are scored as percentages observed across the cortex and medulla, while the remaining descriptors are assessed categorically within the cortex or medulla. Two KPMP pathologists—a primary scorer and a quality control (QC) scorer—review and score all stained sections (H&E, PAS, trichrome, and Jones silver histochemical stains) scanned into whole-slide images and stored in the KPMP Digital Pathology Repository, following the KPMP Manual of Operating Procedures. Scoring discrepancies between the primary and QC pathologists are discussed and resolved through adjudication, with a third pathologist consulted if necessary. These descriptors provide a comprehensive list of non-glomerular structural and cellular abnormalities observed in these regions.

Pathology Descriptor Scoring data can be found in the Atlas Repository and is updated as new scores are made available.

Reference

1. Barisoni L, Troost JP, Nast C, Bagnasco S, Avila-Casado C, Hodgin J, Palmer M, Rosenberg A, Gasim A, Liensziewski C, Merlino L, Chien HP, Chang A, Meehan SM, Gaut J, Song P, Holzman L, Gibson D, Kretzler M, Gillespie BW, Hewitt SM. Reproducibility of the NEPTUNE descriptor-based scoring system on whole-slide images and histologic and ultrastructural digital images. Mod Pathol. 2016 Jul;29(7):671-84. doi: 10.1038/modpathol.2016.58. Epub 2016 Apr 22. PMID: 27102348; PMCID: PMC5515468.

‍

Molecular data

Several tissue interrogation technologies are active in the KPMP. To maximize impact of the limited kidney tissue, participating sites are required to submit their technology for a review of feasibility, reproducibility, rigor, and value of the technology to achieve the goals of the KPMP. The table below lists all of the omics and imaging technologies that are approved and actively analyzing kidney biopsy tissue. The multimodal techniques applied on KPMP biopsies are expected to evolve over time.

To learn more about each tissue interrogation approach, see the Technologies section.

See all available data in KPMP

‍

Approved tissue interrogation technologies

‍

Metadata standards

The Kidney Precision Medicine Project is generating a large amount of data. To enable data accessibility and interoperability, each dataset that is generated must be accompanied by a standard set of metadata. The required metadata properties vary by technology. For the metadata properties being collected for all of the KPMP technologies, refer to the Metadata page to see all of the metadata templates.

‍