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Ben-Moshe Y, Shlomovitz O, Atias-Varon D, Haskin O, Ben-Shalom E, Shasha Lavsky H, Volovelsky O, Mane S, Ben-Ruby D, Chowers G, Skorecki K, Borovitz Y, Kagan M, Mor N, Khavkin Y, Tzvi-Behr S, Pollack S, Toder MP, Geylis M, Schnapp A, Becker-Cohen R, Weissman I, Schreiber R, Davidovits M, Frishberg Y, Magen D, Barel O, Vivante A. Diagnostic Utility of Exome Sequencing Among Israeli Children With Kidney Failure. Kidney Int Rep 2023; 8:2126-2135. [PMID: 37850020 PMCID: PMC10577315 DOI: 10.1016/j.ekir.2023.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction Genetic etiologies are estimated to account for a large portion of chronic kidney diseases (CKD) in children. However, data are lacking regarding the true prevalence of monogenic etiologies stemming from an unselected population screen of children with advanced CKD. Methods We conducted a national multicenter prospective study of all Israeli pediatric dialysis units to provide comprehensive "real-world" evidence for the genetic basis of childhood kidney failure in Israel. We performed exome sequencing and assessed the genetic diagnostic yield. Results Between 2019 and 2022, we recruited approximately 88% (n = 79) of the children on dialysis from all 6 Israeli pediatric dialysis units. We identified genetic etiologies in 36 of 79 (45%) participants. The most common subgroup of diagnostic variants was in congenital anomalies of the kidney and urinary tract causing genes (e.g., EYA1, HNF1B, PAX2, COL4A1, and NFIA) which together explain 28% of all monogenic etiologies. This was followed by mutations in genes causing renal cystic ciliopathies (e.g., NPHP1, NPHP4, PKHD1, and BBS9), steroid-resistant nephrotic syndrome (e.g., LAGE3, NPHS1, NPHS2, LMX1B, and SMARCAL1) and tubulopathies (e.g., CTNS and AQP2). The genetic diagnostic yield was higher among Arabs compared to Jewish individuals (55% vs. 29%) and in children from consanguineous compared to nonconsanguineous families (63% vs. 29%). In 5 participants (14%) with genetic diagnoses, the molecular diagnosis did not correspond with the pre-exome diagnosis. Genetic diagnosis has a potential influence on clinical management in 27 of 36 participants (75%). Conclusion Exome sequencing in an unbiased Israeli nationwide dialysis-treated kidney failure pediatric cohort resulted in a genetic diagnostic yield of 45% and can often affect clinical decision making.
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Affiliation(s)
- Yishay Ben-Moshe
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Omer Shlomovitz
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Atias-Varon
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Genetic Kidney Disease Research Laboratory, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Orly Haskin
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Nephrology Institute, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel
| | - Efrat Ben-Shalom
- Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hadas Shasha Lavsky
- Pediatric Nephrology Unit, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Oded Volovelsky
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Pediatric Nephrology Unit, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Dror Ben-Ruby
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Genetic Kidney Disease Research Laboratory, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Guy Chowers
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Karl Skorecki
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yael Borovitz
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Nephrology Institute, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel
| | - Maayan Kagan
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Nofar Mor
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yulia Khavkin
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Shimrit Tzvi-Behr
- Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shirley Pollack
- Pediatric Nephrology Institute, Rambam Health Care Campus, Haifa, Israel
- Technion Faculty of Medicine, Ruth Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Moran Plonsky Toder
- Pediatric Nephrology Institute, Rambam Health Care Campus, Haifa, Israel
- Technion Faculty of Medicine, Ruth Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Michael Geylis
- Pediatric Nephrology Clinic, Soroka University Medical Center, Beer Sheva, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Aviad Schnapp
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Pediatric Nephrology Unit, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rachel Becker-Cohen
- Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Irith Weissman
- Pediatric Nephrology Unit, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ruth Schreiber
- Pediatric Nephrology Clinic, Soroka University Medical Center, Beer Sheva, Israel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Miriam Davidovits
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Nephrology Institute, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel
| | - Yaacov Frishberg
- Division of Pediatric Nephrology, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniella Magen
- Pediatric Nephrology Institute, Rambam Health Care Campus, Haifa, Israel
- Technion Faculty of Medicine, Ruth Rappaport Children's Hospital, Rambam Health Care Campus, Haifa, Israel
| | - Ortal Barel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel
| | - Asaf Vivante
- Department of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat-Gan, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Division of Pediatric Nephrology, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel
- Genetic Kidney Disease Research Laboratory, Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
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