Challenges associated with diagnostic exome sequencing in liver diseases

Exome sequencing (ES) has been used in a variety of clinical settings but there are limited data on its utility for diagnosis and/or prediction of monogenic liver diseases. We analyzed ES data in 758 patients with liver diseases., We developed a curated list of 502 genes for monogenic disorders associated with liver phenotypes and analyzed ES data for these genes in 758 patients with chronic liver diseases (CLD). For comparison, we examined ES data in 7,856 self-declared healthy controls (HC), and 2,187 patients with chronic kidney disease (CKD). Candidate pathogenic (P) or likely pathogenic (LP) variants were initially identified in 19.9% of participants, most of which were attributable to previously reported pathogenic variants with implausibly high allele frequencies. After variant annotation and stringent filtering based on population minor allele frequency, we detected a significant enrichment of P/LP variants in the CLD cohort compared to the HC cohort ( X 2 test OR: 5.00, 95% CI:3.06-8.18,, p-value=4.5 e-12). A second-level manual annotation was necessary to capture true pathogenic variants that were removed by stringent allele frequency filters. After these sequential steps, the diagnostic rate of monogenic disorders was 5.7% in the CLD cohort, attributable to P/LP variants in 25 genes. We also identified concordant liver disease phenotypes for 15/22 kidney disease patients with P/LP variants in liver genes, mostly associated with cystic liver disease phenotypes. Clinically confirmed sequencing results had many implications for clinical management, including familial testing for early diagnosis and management, preventative screening for associated comorbidities, and in some cases for therapy. Exome sequencing provided a 5.7% diagnostic rate in CLD patients and required multiple rounds of review to reduce both false positive and false negative findings. The identification of concordant phenotypes in many patients with P/LP variants and no known liver disease also indicates a potential for predictive testing for selected monogenic liver disorders. ### Competing Interest Statement Dr. Gharavi has received research funding from the Renal Research Institute and Natera and has served as a consultant for Goldfinch Bio. All other authors declare no conflicts of interest. ### Funding Statement Research reported in this publication was supported by the National Institute Of Diabetes And Digestive And Kidney Diseases of the National Institutes of Health under Award Number K08DK128631. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: I attest that the research included in this report was conducted in a manner consistent with the principles of research ethics, such as those described in the Declaration of Helsinki and/or the Belmont Report. In particular, this research was conducted with the voluntary, informed consent of all research participants, free of coercion or coercive circumstances, and received Columbia University Irving Medical Center Institutional Review Board (IRB) approval consistent with the principles of research ethics and the legal requirements of the lead authors' jurisdictions. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The data sets supporting this study are available at the following publicly accessible websites: [igmdx.org][1] and [atavdb.org][2]. All data produced in the present study are available upon reasonable request to the authors. * ES : whole-exome sequencing CLD : chronic liver disease CKD : chronic kidney disease HGMD : Human Gene Mutation Database PTV : protein truncating variants MAF : minor allele frequency GWAS : next-generation sequencing: NGS, genome-wide association studies ACMG-AMP : American College of Medical Genetics and Genomics and the Association for Molecular Pathology OMIM : Online Mendelian Inheritance in Man database HPO : Human Phenotype Ontology gnomAD : Genome Aggregation Database ExAC : Exome Aggregation Consortium AD : autosomal dominant AR : autosomal recessive XLD : X-linked dominant XLR : X-linked recessive disorders DM : disease-causing mutation P/LP : pathogenic/likely pathogenic CADD : Combined Annotation Dependent Depletion QC : quality control [1]: http://igmdx.org [2]: http://atavdb.org