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Frequently Asked Questions: KPMP Kidney Tissue Atlas Coordinating Center (KTACC)

  1. What is a Kidney Tissue Atlas?
  2. What is a Digital Pathology Bank?
  3. What types of people are expected to use the Kidney Tissue Atlas and Digital Pathology Bank?
  4. What types of data will the KTACC deal with?

What is a Kidney Tissue Atlas?

The KTACC will create and enhance an interactive Kidney Tissue Atlas to visualize all of the various KPMP data types and support efforts from the community to retrieve, explore, interrogate, and perform novel analyses. The atlas is expected to contain a set of 2- and 3-D maps representing health (e.g., healthy living donor, healthy volunteer) and disease (e.g., KPMP AKI and CKD biopsies) across a diverse population (accounting for sex, age, race, and ethnicity). Maps will be used to classify and locate ('paint') different cell types, cell states (healthy, injured, dying, recovering, undergoing adaptive/maladaptive repair, etc.) and interstitial components (collagens, proteoglycans, signaling molecules, etc.). The maps will include specific genes, proteins, RNAs, metabolites, and/or epigenetic landmarks that are visualized by advanced imaging and are expected to facilitate identification of cell, structural, and regional heterogeneity throughout the kidney, and allow for interrogation of compartments that are currently difficult to visualize (interstitium, glomerulus, etc.). The atlas will ultimately be used to improve the diagnosis, staging, grading, prognosis, subgroup stratification, and drug effect prediction in AKI and CKD.

What is a Digital Pathology Bank?

The KPMP Digital Pathology Bank houses all existing and new biopsy whole slide images and develops tools for accessing and analyzing image data, including the ability to perform comparisons and searches, and curation or quality control tasks such as de-identification and artifact detection.

What types of people are expected to use the Kidney Tissue Atlas and Digital Pathology Bank?

The KTACC will develop potential user personas for the Kidney Tissue Atlas and Digital Pathology Bank. These may include, but are not limited to: a bioinformatic super-user familiar with large and complex datasets; a basic scientist seeking discovery data to generate or support a hypothesis; a clinical researcher trying to link histopathologic structures to disease pathways; a student trying to visualize renal physiology; a KPMP patient participant hoping to better understand kidney disease.

Based on these user personas, the KTACC will build and manage a suite of visualization and analysis tools to facilitate computational access, navigation and downloading data to maximize broad usability and incentivize public interrogation and discovery.

The KTACC is also expected to harmonize with complementary datasets to maximize discovery (e.g., Chronic Renal Insufficiency Cohort (CRIC), Human BioMolecular Atlas Program (HuBMAP), Human Cell Atlas (HCA), GenitoUrinary Development Molecular Anatomy Project (GUDMAP), ReBuilding a Kidney (RBK)).

What types of data will the KTACC deal with?

At a minimum, the KTACC is expected to integrate the clinical phenotypic, physiologic, and digital pathological data generated by the RS and the molecular data generated by the TIS. For more information visit KPMP's for Researchers page.

The KTACC is also expected to harmonize with complementary datasets to maximize discovery (e.g., Chronic Renal Insufficiency Cohort (CRIC), Human BioMolecular Atlas Program (HuBMAP), Human Cell Atlas (HCA), GenitoUrinary Development Molecular Anatomy Project (GUDMAP), ReBuilding a Kidney (RBK)).

With the data, the KTACC will use state-of-the-art computational approaches to identify key molecular pathways, gene targets, diagnostic markers to redefine and sub-stratify AKI and CKD and to identify possible targets for intervention.