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Ma BM, Elefant N, Tedesco M, Bogyo K, Vena N, Murthy SK, Bheda SA, Yang S, Tomar N, Zhang JY, Husain SA, Mohan S, Kiryluk K, Rasouly HM, Gharavi AG. Developing a genetic testing panel for evaluation of morbidities in kidney transplant recipients. Kidney Int 2024; 106:115-125. [PMID: 38521406 DOI: 10.1016/j.kint.2024.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/18/2024] [Accepted: 02/13/2024] [Indexed: 03/25/2024]
Abstract
Cardiovascular disease, infection, malignancy, and thromboembolism are major causes of morbidity and mortality in kidney transplant recipients (KTR). Prospectively identifying monogenic conditions associated with post-transplant complications may enable personalized management. Therefore, we developed a transplant morbidity panel (355 genes) associated with major post-transplant complications including cardiometabolic disorders, immunodeficiency, malignancy, and thrombophilia. This gene panel was then evaluated using exome sequencing data from 1590 KTR. Additionally, genes associated with monogenic kidney and genitourinary disorders along with American College of Medical Genetics (ACMG) secondary findings v3.2 were annotated. Altogether, diagnostic variants in 37 genes associated with Mendelian kidney and genitourinary disorders were detected in 9.9% (158/1590) of KTR; 25.9% (41/158) had not been clinically diagnosed. Moreover, the transplant morbidity gene panel detected diagnostic variants for 56 monogenic disorders in 9.1% KTRs (144/1590). Cardiovascular disease, malignancy, immunodeficiency, and thrombophilia variants were detected in 5.1% (81), 2.1% (34), 1.8% (29) and 0.2% (3) among 1590 KTRs, respectively. Concordant phenotypes were present in half of these cases. Reviewing implications for transplant care, these genetic findings would have allowed physicians to set specific risk factor targets in 6.3% (9/144), arrange intensive surveillance in 97.2% (140/144), utilize preventive measures in 13.2% (19/144), guide disease-specific therapy in 63.9% (92/144), initiate specialty referral in 90.3% (130/144) and alter immunosuppression in 56.9% (82/144). Thus, beyond diagnostic testing for kidney disorders, sequence annotation identified monogenic disorders associated with common post-transplant complications in 9.1% of KTR, with important clinical implications. Incorporating genetic diagnostics for transplant morbidities would enable personalized management in pre- and post-transplant care.
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Affiliation(s)
- Becky M Ma
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA; Division of Nephrology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, China
| | - Naama Elefant
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Martina Tedesco
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA; Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Kelsie Bogyo
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Natalie Vena
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Sarath K Murthy
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Shiraz A Bheda
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Sandy Yang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Nikita Tomar
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Jun Y Zhang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Syed Ali Husain
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Sumit Mohan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.
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Auwerx C, Jõeloo M, Sadler MC, Tesio N, Ojavee S, Clark CJ, Mägi R, Reymond A, Kutalik Z. Rare copy-number variants as modulators of common disease susceptibility. Genome Med 2024; 16:5. [PMID: 38185688 PMCID: PMC10773105 DOI: 10.1186/s13073-023-01265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described. METHODS Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank. RESULTS We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS. CONCLUSIONS Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
| | - Maarja Jõeloo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland
| | - Nicolò Tesio
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Sven Ojavee
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Charlie J Clark
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
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Münch J, Goodyer PR, Wagner CA. Tubular Diseases and Stones Seen From Pediatric and Adult Nephrology Perspectives. Semin Nephrol 2023; 43:151437. [PMID: 37968178 DOI: 10.1016/j.semnephrol.2023.151437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The tubular system of the kidneys is a complex series of morphologic and functional units orchestrating the content of tubular fluid as it flows along the nephron and collecting ducts. Renal tubules maintain body water, regulate electrolytes and acid-base balance, reabsorb precious organic solutes, and eliminate specific metabolites, toxins, and drugs. In addition, decisive mechanisms to adjust blood pressure are governed by the renal tubules. Genetic as well as acquired disorders of these tubular functions may cause serious diseases that manifest both in childhood and adulthood. This article addresses a selection of tubulopathies and the underlying pathomechanisms, while highlighting the important differences in pediatric and adult nephrology care. These range from rare monogenic conditions such as nephrogenic diabetes insipidus, cystinosis, and Bartter syndrome that present in childhood, to the genetic and acquired tubular pathologies causing hypertension or nephrolithiasis that are more prevalent in adults. Both pediatric and adult nephrologists must be aware of these conditions and the age-dependent manifestations that warrant close interaction between the two subspecialties.
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Affiliation(s)
- Johannes Münch
- Institute of Physiology, University of Zurich, Zurich, Switzerland; Institute of Human Genetics, University of Zurich, Zurich, Switzerland; National Center of Competence in Research, NCCR Kidney.CH, Switzerland
| | - Paul R Goodyer
- McGill University Health Centre, Montreal, Quebec, Canada
| | - Carsten A Wagner
- Institute of Physiology, University of Zurich, Zurich, Switzerland; National Center of Competence in Research, NCCR Kidney.CH, Switzerland.
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