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Diagnostic yield and novel candidate genes by next generation sequencing in 166 children with intrahepatic cholestasis

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Abstract

Background and aims

Cholestatic liver disease is a leading referral to pediatric liver transplant centers. Inherited disorders are the second most frequent cause of cholestasis in the first month of life.

Methods

We retrospectively characterized the genotype and phenotype of 166 participants with intrahepatic cholestasis, and re-analyzed phenotype and whole-exome sequencing (WES) data from patients with previously undetermined genetic etiology for newly published genes and novel candidates. Functional validations of selected variants were conducted in cultured cells.

Results

Overall, we identified disease-causing variants in 31% (52/166) of our study participants. Of the 52 individuals, 18 (35%) had metabolic liver diseases, 9 (17%) had syndromic cholestasis, 9 (17%) had progressive familial intrahepatic cholestasis, 3 (6%) had bile acid synthesis defects, 3(6%) had infantile liver failure and 10 (19%) had a phenocopy of intrahepatic cholestasis. By reverse phenotyping, we identified a de novo variant c.1883G > A in FAM111B of a case with high glutamyl transpeptidase (GGT) cholestasis. By re-analyzing WES data, two patients were newly solved, who had compound heterozygous variants in recently published genes KIF12 and USP53, respectively. Our additional search for novel candidates in unsolved WES families revealed four potential novel candidate genes (NCOA6, CCDC88B, USP24 and ATP11C), among which the patients with variants in NCOA6 and ATP11C recapitulate the cholestasis phenotype in mice models.

Conclusions

In a single-center pediatric cohort, we identified monogenic variants in 22 known human intrahepatic cholestasis or phenocopy genes, explaining up to 31% of the intrahepatic cholestasis patients. Our findings suggest that re-evaluating existing WES data from well-phenotyped patients on a regular basis can increase the diagnostic yield for cholestatic liver disease in children.

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Funding

This work was supported by grants from the National Natural Science Foundation of China (no. 81873542) and Nanjing Medical Science and technique Development Foundation, Nanjing Department of Health (no. YKK19107).

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Author notes

  1. Bixia Zheng and Zhifeng Liu share last authorship.

Authors and Affiliations

  1. Department of Gastroenterology, Children’s Hospital of Nanjing Medical University, Nanjing, China

    Yucan Zheng, Hongmei Guo, Leilei Chen, Weixia Cheng, Kunlong Yan, Zhihua Zhang, Mei Li, Yu Jin, Guorui Hu & Zhifeng Liu

  2. Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China

    Chunli Wang, Wei Zhou, Zhanjun Jia & Bixia Zheng

  3. Department of Pathology, Children’s Hospital of Nanjing Medical University, Nanjing, China

    Chunlei Zhou

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  1. Yucan Zheng
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Correspondence to Bixia Zheng or Zhifeng Liu.

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Conflict of interest

Yucan Zheng, Hongmei Guo, Leilei Chen, Weixia Cheng, Kunlong Yan, Zhihua Zhang, Mei Li, Yu Jin, Guorui Hu, Chunli Wang, Chunlei Zhou, Wei Zhou, Zhanjun Jia, Bixia Zheng, and Zhifeng Liu disclose no conflicts.

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The study was approved by the Ethics Committee of Children’s Hospital of Nanjing Medical University (no.202012090-1). A written informed consent was obtained from all patients or their guardians.

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Zheng, Y., Guo, H., Chen, L. et al. Diagnostic yield and novel candidate genes by next generation sequencing in 166 children with intrahepatic cholestasis. Hepatol Int 18, 661–672 (2024). https://doi.org/10.1007/s12072-023-10553-6

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