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Clinical utility of genetic testing in Indian children with kidney diseases
Anshuman Saha1, Shahenaz F Kapadia2, Kinnari B Vala2
1Department of Pediatric Nephrology, Institute of Kidney Diseases and Research Centre, Gujarat University of Transplantation Sciences, Ahmedabad, India. drasaha1980@gmail.com.
Insights
Genetic testing diagnosed genetic kidney diseases in 46% of children, aiding in new or revised diagnoses for personalized management. This analysis highlights the clinical utility of genetic testing in pediatric nephrology.
Area of Science:
- Pediatric Nephrology
- Clinical Genetics
- Genomic Medicine
Background:
- Genetic kidney diseases in children often present with overlapping symptoms, complicating diagnosis.
- Accurate diagnosis is crucial for effective management and prognosis.
Purpose of the Study:
- To evaluate the clinical utility of genetic testing in diagnosing and managing pediatric kidney diseases with suspected genetic origins.
- To determine the diagnostic yield of genetic testing across various categories of kidney diseases in children.
Main Methods:
- A retrospective study included children (≤18 years) undergoing genetic testing.
- Clinical exome sequencing was the primary method, supplemented by other genetic tests.
- Variants were classified using the American College of Medical Genetics (ACMG) criteria.
Main Results:
- Genetic testing yielded a diagnosis in 46% of the 76 index children.
- Pathogenic or likely pathogenic variants were identified in 46.1% of diagnosed cases.
- Diagnostic yields varied by condition, with nephrolithiasis/nephrocalcinoses showing 81% and glomerular diseases 29.4%.
Conclusions:
- Genetic testing is highly valuable, establishing a genetic diagnosis in nearly half of the pediatric patients evaluated.
- The findings confirmed clinical diagnoses, led to new diagnoses, or revised existing ones, facilitating personalized patient management.
- Genetic testing significantly impacts the diagnostic and therapeutic pathways for children with suspected inherited kidney disorders.
Background:
Kidney diseases with genetic etiology in children present with an overlapping spectrum of manifestations. We aimed to analyze the clinical utility of genetic testing in the diagnosis and management of suspected genetic kidney diseases in children.
Methods:
In this retrospective study, children ≤ 18 years in whom a genetic test was ordered were included. Clinical indications for genetic testing were categorized as Glomerular diseases, nephrolithiasis and/or nephrocalcinoses, tubulopathies, cystic kidney diseases, congenital abnormality of kidney and urinary tract, chronic kidney disease of unknown aetiology and others. Clinical exome sequencing was the test of choice. Other genetic tests ordered were sanger sequencing, gene panel, multiplex ligation-dependent probe amplification and karyotyping. The pathogenicity of the genetic variant was interpreted as per the American College of Medical Genetics classification.
Results:
A total of 86 samples were sent for genetic testing from 76 index children, 8 parents and 2 fetuses. A total of 74 variants were reported in 47 genes. Out of 74 variants, 42 were missense, 9 nonsense, 12 frameshifts, 1 indel, 5 affected the splicing regions and 5 were copy number variants. Thirty-two were homozygous, 36 heterozygous and 6 were hemizygous variants. Twenty-four children (31.6%) had pathogenic and 11 (14.5%) had likely pathogenic variants. Twenty-four children (31.6%) had variants of uncertain significance. No variants were reported in 17 children (22.3%). A genetic diagnosis was made in 35 children with an overall yield of 46%. The diagnostic yield was 29.4% for glomerular diseases, 53.8% for tubular disorders, 81% for nephrolithiasis and/or nephrocalcinoses, 60% for cystic kidney diseases and 50% for chronic kidney disease of unknown etiology. Genetic testing made a new diagnosis or changed the diagnosis in 15 children (19.7%).
Conclusion:
Nearly half (46%) of the children tested for a genetic disease had a genetic diagnosis. Genetic testing confirmed the clinical diagnoses, changed the clinical diagnoses or made a new diagnosis which helped in personalized management.
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