Sherley Cohort — CysC / Creatinine Ratio – Project Summary

Author

Tianqi Ouyang

Published

March 31, 2026

Project Overview

  • Primary exposure: cr_cys_7 — binary indicator for creatinine / cystatin C ratio < 0.7
  • Follow-up: 90 days from baseline sample date
  • Framework: Competing risks (death as competing event for non-fatal outcomes)

Study Design

Details
Data sources REDCap export + RPDR (Dia, Lab, Med)
REDCap export CystatinCInPatientsO_DATA_2026-04-27_0819.csv
Patient list Patient IDS_Tianqi_20May2026.xlsx (Sheet3, Sherley sub-cohort N=169; EMPI filter applied to REDCap)
RPDR pull Carboplatin Paper/RPDR 2026-03-19/mes98_03182614492143216
RPDR lab groups ALB, CRE, HGB, PLT, GHBA1C
Platinum types Cisplatin and Carboplatin
High dose Cisplatin >= 75 mg/m² or Carboplatin AUC >= 5
CKD staging Cockcroft-Gault eGFR from pre-baseline creatinine

Cohort Definition

Inclusion

  • Patients in REDCap export whose EMPI appears in Patient IDS_Tianqi_20May2026.xlsx (Sherley sub-cohort, N=169)
  • Received cisplatin or carboplatin (platin_group non-missing)
  • Baseline cystatin C value available (cys_c_baseline non-missing)

Exclusion

  1. EMPI not in list: REDCap records filtered to only EMPIs present in Patient IDS_Tianqi_20May2026.xlsx (Sherley sub-cohort, N=169)
  2. No RPDR labs: Patients with no matching RPDR lab records excluded
  3. Missing baseline cystatin C: Patients with cys_c_baseline = NA excluded
  4. Missing platinum group: Patients with platin_group = NA excluded

Final cohort: Determined at render time (see data_management output for exact counts)

Outcomes

Grade 2/3 Adverse Events (within 90 days)

Outcome Definition
Anemia grade 2 HGB < 10 g/dL
Anemia grade 3 HGB < 8 g/dL
Thrombocytopenia grade 2 PLT < 75 x10^9/L
Thrombocytopenia grade 3 PLT < 50 x10^9/L
AKI grade 2 Post-baseline CRE > 1.5x pre-baseline CRE (KDIGO)
AKI grade 3 Post-baseline CRE > 3.0x pre-baseline CRE (KDIGO)
Composite grade 2 Any of anemia/thrombocytopenia/AKI grade 2
Composite grade 3 Any of anemia/thrombocytopenia/AKI grade 3

Hospitalizations & ED Visits

  • Hospitalizations: 11 reason categories; reasons 1-7 define side_effect (platinum-related)
  • ED visits: 7 reason categories
  • All censored at 90 days

Mortality

  • 90-day mortality (death_90): derived from pt_status and days_last_follow_up

Input Files

File Description
CystatinCInPatientsO_DATA_2026-04-27_0819.csv REDCap export
Patient IDS_Tianqi_20May2026.xlsx EMPI inclusion list (Sherley sub-cohort, N=169)
mes98_03182614492143216_Dia.txt RPDR Diagnoses
mes98_03182614492143216_Lab.txt RPDR Labs (ALB, CRE, HGB, PLT, GHBA1C)
mes98_03182614492143216_Med.txt RPDR Medications

Key Variables

Exposure

Variable Description
cr_cys Raw ratio: baseline creatinine / cystatin C
cr_cys_7 Primary exposure: 1 if ratio < 0.7
cr_cys_cat Categorical: <0.5 / 0.5-0.7 / 0.7-0.9 / >=0.9

eGFR & Kidney Function

Variable Description
baseline_cre_egfr CKD-EPI eGFR from creatinine
baseline_cys_c_egfr CKD-EPI eGFR from cystatin C
ckd_epi_gfr_cre_cys CKD-EPI combined creatinine-cystatin C eGFR
cockcroft Cockcroft-Gault creatinine clearance
ckd_stage_cg CKD stage from Cockcroft-Gault

Pre-baseline Labs (closest value within 45 days before baseline)

Variable RPDR Group_Id
pre_CRE_45days CRE
pre_HGB_45days HGB
pre_PLT_45days PLT
pre_ALB_45days ALB
pre_GHBA1C_45days GHBA1C

Comorbidities & Treatment

Variable Description
score / cci Charlson comorbidity index (from RPDR ICD codes)
thyroid Thyroid disease (RPDR diagnosis + medication)
hiv_rpdr HIV from RPDR diagnoses + medications
high_dose High-dose platinum flag
cancer_type_cat_7 Cancer type (7 categories)
ici Immune checkpoint inhibitor use

Competing Risk Variables

Pattern Description
cmp_time_<outcome> Time for competing risk model
cmp_status_<outcome> 0 = censored, 1 = event, 2 = death

Key Conventions

  • Time anchor: All outcomes measured from baseline_sample_date
  • Competing risks: Death coded as event = 2; tidycmprsk::crr() used instead of standard Cox
  • Pre-baseline labs: Closest value within 45 days before baseline
  • eGFR formulas: CKD-EPI 2021 (creatinine, cystatin C, combined) and Cockcroft-Gault
  • RPDR lab groups: ALB, CRE, HGB, PLT, GHBA1C (electrolyte labs K/MG/NA and WBC not included)