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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Next-Generation Sequencing in Diagnosis of Monogenic Cholestatic Liver Disorders: A Single-Center Experience
Engin Demir1, Fatma Derya Bulut2, Berrak Bilginer-Gürbüz3
1Division of Pediatric Gastroenterology, Department of Pediatrics, Mersin City Training and Research Hospital, Mersin, Turkey.
Insights
Next-generation sequencing (NGS) accurately diagnosed pediatric cholestasis when traditional methods failed. This genetic testing identified new gene variants, improving diagnosis for rare liver diseases in children.
Area of Science:
- Pediatric Gastroenterology
- Clinical Genetics
- Molecular Diagnostics
Background:
- Childhood cholestasis is a rare but serious condition requiring prompt diagnosis for effective treatment.
- Biliary atresia, monogenic, and metabolic diseases are common causes, but diagnosis can be challenging.
- Conventional diagnostic methods may not always elucidate the etiology of cholestasis.
Purpose of the Study:
- To assess the clinical utility of next-generation sequencing (NGS) panels in diagnosing pediatric cholestasis.
- To evaluate the effectiveness of clinical exome sequencing and whole exome sequencing when conventional methods are insufficient.
- To identify novel genetic variants associated with cholestatic liver diseases.
Main Methods:
- Retrospective analysis of 36 pediatric cholestasis patients from August 2020 to March 2022.
- Exclusion of patients diagnosed via traditional investigations, with 14 undergoing NGS (whole exome or targeted).
- Comprehensive exclusion of infectious, toxic, metabolic, structural, chromosomal, and endocrine causes.
Main Results:
- NGS achieved a definitive diagnosis in 12 out of 14 patients (85.7% diagnostic accuracy).
- Commonly identified conditions included progressive familial intrahepatic cholestasis (PFIC) and Dubin-Johnson syndrome.
- Three novel variants were discovered in the ABCB11 and ABCC2 genes.
Conclusions:
- NGS is a valuable tool for diagnosing pediatric cholestasis when conventional methods are inconclusive.
- Genetic sequencing aids in identifying specific monogenic causes, guiding treatment and prognosis.
- The discovery of new variants expands the understanding of genetic cholestatic diseases.
Introduction:
Cholestasis in childhood is a rare clinical condition, yet a definitive diagnosis is crucial for initiating treatment of these curable diseases and preventing related morbidity and mortality. The most common cause of infant cholestasis is biliary atresia (25-40%), followed by monogenic cholestatic diseases (25%), metabolic diseases (20%), and cryptogenic cholestasis. This study focuses on assessing the clinical utility of next-generation sequencing (NGS) panels, including clinical exome sequencing and whole exome sequencing, in diagnosing cholestatic diseases when the etiology cannot be elucidated through conventional methods.
Materials And Methods:
We conducted a retrospective examination of pediatric patients who sought care at a single-center pediatric gastroenterology department between August 2020 and March 2022 and were diagnosed with cholestasis. A total of 36 patients underwent a thorough investigation to rule out infectious, toxic, metabolic, structural, chromosomal, and endocrine causes. Patients whose diagnoses were established through traditional investigations were excluded from the study. The remaining 14 patients underwent either whole exome sequencing or targeted NGS methods.
Results:
A definitive diagnosis was achieved for 12 patients, while 2 patients remained undiagnosed despite comprehensive genetic examinations. The most commonly encountered diseases in this cohort were progressive familial intrahepatic cholestasis, linked to mutations in the ABCB11, ATP8B1, and TJP2 genes, as well as Dubin-Johnson syndrome associated with ABCC2 mutations. NGS demonstrated a diagnostic accuracy of 85.7% in patients for whom a diagnosis could not be established through extensive traditional workup.
Conclusion:
NGS emerges as a valuable diagnostic tool in cases of cholestasis where traditional methods fall short in providing a definitive diagnosis. Moreover, our study unveiled three previously undocumented variants in the ABCB11 [c.1165G>C; p.(Ala389Pro) and c.783 + 1G>A] and ABCC2 [c.4246_4247del; p.(Lys1416ValfsTer46)] genes.
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