Nephrotic Syndrome Phenotyping Project
Overview
This is a specialized data request by Matt Sampson of Boston Children's Hospital (BCH).
The request is search for specific data that are not mapped to current GIC concept paths, such as ICD 9 codes, hence the regular GIC workflow via the web portal is not currently ideal for this request.
The original redcap request form that was filled out in June for this project included patients with ICD-10 code N04, N02.2, N03.3, N05.2, or protein in urine lab result.
Eligibility (any of the following):
- Protein [Mass/Volume] in 24 hour Urine
- Protein in Urine
- Protein in Urine by Test strip / dipstick test
- Creatinine in Urine
- Protein-Creatinine ratio
- 582.1 Chronic GN with lesion of MN or FSGS
- 583.1 Nephritis and nephropathy; acute/chronic unspecific, with lesion of MN or FSGS
- N02.0 Recurrent and persistent hematuria with minor glomerular abnormality
- N03.3 Chronic nephritic syndrome with diffuse mesangial proliferative GN
- N05.2 Unspecified nephritic syndrome with diffuse membranous GN
- any N04 code Nephrotic syndrome
- any 581 code Nephrotic syndrome
See the associated google doc (Google Drive Path: NCATS GIC > GIC Researchers > Matt Sampson, BCH) for the latest details, both technical and non-technical, for this request.
Danielle led a discussion with the BMI working group on Wednesday, October 9, 2024 to prep everyone for the request and what is being asked each institution's local data warehouses.
Specialized SDAC Approval
The data being requested is not in the site's local PIC-SURE, each team will need to pull a list of patients that meet the criteria. That list of patient IDs will need to be provided to your local SDAC. Based on SDAC approval, the sites will manually load the data into the S3 bucket, as described in the [google doc][0].
Note
The WashU SDAC reviewed and approved this request on October 24, 2024.
The SDAC approved this request as it didn't involve any genomic data.
Deliverables
Note
Based on the discussions at GIC BMI Meeting on November 6, 2024.
The researchers have confirmed that they want all of the patients in the cohort criteria and all demographics (including age, race, sex), labs, medications, diagnoses (ICD9 and ICD10), and procedures.
Digital Landmarks
- WUSM Box folder: 2024-10-14-bch-nephrotic-data-request"
- Google Doc: Nephrotic Syndrome Phenotyping Project: Manual data upload to S3
- Microsoft Word edition of the "Nephrotic Syndrome Phenotype Project: Manual data upload to S3" Google Doc - (circa 2024-10-14)
- REDCap / SDAC data request document:
GenomicInformationCommonsGICSa_2024-10-10_1610.pdf
Useful Email Threads
- Subject: "GIC Request for NS data" / Date: 2024-10-14
Technical Notes & Details
Git Repositories
Databricks Notebooks
Useful External Links
- athena.ohdsi.org
- Azure DevOps: GIC EHR Data Quality Study
- Nephrotic Syndrome Lab Codes (Google Spreadsheet)
- Nephrotic Syndrome Phenotyping Project: GIC Processes (Google Document)
Contact Info
For additional details about request please reach out to the following:
Danielle Pillion <Danielle_Pillion@hms.harvard.edu>- for overall project requests. She's the main project manager.Simran Makwana <Simran_Makwana@hms.harvard.edu>- for data questions. She's the primary data analyst/scientist involved.Luke Sikina <Luke_Sikina@hms.harvard.edu>- for data transfer AWS S3 details