Decoding the Genetic Landscape of Chronic Kidney Disease: Insights from a Prospective Indian CohortFunding

 

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Decoding the Genetic Landscape of Chronic Kidney Disease: Insights from a Prospective Indian CohortFunding

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Manish
Lalwani
Manish Lalwani Manishmedicine1308@gmail.com Christian Medical College Vellore Department of Nephrology Vellore India *
Rajanbabu Franklin annalfrank2905@gmail.com Christian Medical College Vellore Department of Nephrology Vellore India -
Likhita Vuyuru likhita1994@gmail.com Christian Medical College Vellore Department of Nephrology Vellore India -
Santosh Varughese santosh.vellore@gmail.com Christian Medical College Vellore Department of Nephrology Vellore India -
Suceena Alexander suceena@gmail.com Christian Medical College Vellore Department of Nephrology Vellore India -
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Funding- ICMR Extramural Adhoc grant (No. 5/4/7-10/Nephro/2022-NCD-II)

Background: Monogenic causes of chronic kidney disease (CKD) are increasingly recognized in adolescents and adults with early-onset, syndromic, or familial disease. Genetic testing can clarify diagnosis, guide management, and inform family counselling; however, data from India remain scarce.

Study Design: Prospective observational cohort study.

Setting & Participants: 155 adolescents and adults with clinically suspected monogenic CKD evaluated at a tertiary nephrology centre in India between January 2023 and April 2025.

Predictors: Clinical, laboratory, imaging, and histopathological features.

Outcomes: Diagnostic yield of genetic testing, genotype–phenotype correlations, and impact on clinical management.

Measurements: Whole exome sequencing ± MLPA; classification of variants as pathogenic, likely pathogenic, or negative. Patients were grouped as genetically positive or negative. Logistic regression identified predictors of genetic positivity.

Results: Median age at symptom onset was 22 years (IQR 17–32); 69% were male. Family history of CKD was reported in 41%, and consanguinity in 2.6%. Genetic testing identified a monogenic aetiology in 109 patients (70%), most frequently COL4A5, PKD1, NPHP4, and GRHPR. Syndromic features, particularly hearing loss, were the strongest independent predictor of a positive genetic result (OR 4.74; 95% CI 1.11–20.14; p=0.035), followed by renal cysts and positive family history. Genotype–phenotype correlations included PKD1 with bilateral cystic kidneys, GRHPR with nephrocalcinosis, and COL4A5 with hematuria and CKD. Histopathological diagnoses such as focal segmental glomerulosclerosis and thrombotic microangiopathy were enriched in genetically positive patients. Genetic results prompted changes in clinical management in 8.4% of patients, including therapy modification and family counselling.

Limitations: Single-centre study; incomplete biopsy and EM data in some cases; potential referral bias.

Conclusions: In this Indian cohort, genomic testing demonstrated high diagnostic yield and meaningful clinical impact in adolescents and adults with suspected monogenic CKD. Syndromic features, family history, and imaging abnormalities are key predictors of genetic positivity. Integration of genomic diagnostics can enhance precision nephrology, particularly in settings with high consanguinity and limited resources.


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