1
|
Wang Y, Wang H, Yang W, Guo H, Zhang M, Gao Y, Kang B, Liao S. A novel de novo synonymous variant in GREB1L impacts the mRNA splicing associated with aplasia of the urogenital system. Am J Med Genet A 2024:e63823. [PMID: 39091162 DOI: 10.1002/ajmg.a.63823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/07/2024] [Indexed: 08/04/2024]
Abstract
GREB1-like retinoic acid receptor coactivator (GREB1L) gene is associated with autosomal dominant renal hypodysplasia/aplasia 3 (RHDA3) and deafness, autosomal dominant 80 (DFNA80). Among the GREB1L variants reported, most of them are missense or frameshift, while no pathogenic synonymous variants have been recorded. Classical theory paid little attention to synonymous variants and classified it as nonpathogenic; however, recent studies suggest that the variants might be equally important. Here, we report a 7-year-old girl with new symptoms of clitoromegaly, uterovaginal, and ovarian agenesis as well as right kidney missing. A novel de novo GREB1L synonymous variant (NM_001142966: c.4731C>T, p.G1577=) was identified via whole exome sequencing. The variant was predicted to be disease-causing through in silico analysis and was classified as likely pathogenic. Minigene splicing assays confirmed a 6 bp deletion in mutant cDNA comparing with the wild type, leading to two amino acids lost in GREB1L protein. Secondary and tertiary structure modeling showed alterations in protein structure. Our finding reveals a novel GREB1L variant with a new phenotype of urogenital system and is the first to report a pathogenic synonymous variant in GREB1L which affects mRNA splicing, suggesting synonymous variants cannot be ignored in prenatal diagnosis and genetic counseling.
Collapse
Affiliation(s)
- Yaoping Wang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Hongdan Wang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Wenke Yang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Han Guo
- Department of Pharmacy, Huadong Hospital, Fudan University, Shanghai, China
| | - Mengting Zhang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yue Gao
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Bing Kang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| |
Collapse
|
2
|
Zhao E, Bomback M, Khan A, Murthy SK, Solowiejczyk D, Vora NL, Gilmore KL, Giordano JL, Wapner RJ, Sanna-Cherchi S, Lyford A, Jelin AC, Gharavi AG, Hays T. The expanded spectrum of human disease associated with GREB1L likely includes complex congenital heart disease. Prenat Diagn 2024; 44:343-351. [PMID: 38285371 PMCID: PMC11040453 DOI: 10.1002/pd.6527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
OBJECTIVE GREB1L has been linked prenatally to Potter's sequence, as well as less severe anomalies of the kidney, uterus, inner ear, and heart. The full phenotypic spectrum is unknown. The purpose of this study was to characterize known and novel pre- and postnatal phenotypes associated with GREB1L. METHODS We solicited cases from the Fetal Sequencing Consortium, screened a population-based genomic database, and conducted a comprehensive literature search to identify disease cases associated with GREB1L. We present a detailed phenotypic spectrum and molecular changes. RESULTS One hundred twenty-seven individuals with 51 unique pathogenic or likely pathogenic GREB1L variants were identified. 24 (47%) variants were associated with isolated kidney anomalies, 19 (37%) with anomalies of multiple systems, including one case of hypoplastic left heart syndrome, five (10%) with isolated sensorineural hearing loss, two (4%) with isolated uterine agenesis; and one (2%) with isolated tetralogy of Fallot. CONCLUSION GREB1L may cause complex congenital heart disease (CHD) in humans. Clinicians should consider GREB1L testing in the setting of CHD, and cardiac screening in the setting of GREB1L variants.
Collapse
Affiliation(s)
- Emily Zhao
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Miles Bomback
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Sarath Krishna Murthy
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - David Solowiejczyk
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelly L. Gilmore
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, North Carolina, USA
| | - Jessica L. Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Simone Sanna-Cherchi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Alex Lyford
- Department of Mathematics and Statistics, Middlebury College, Middlebury, Vermont, USA
| | - Angie C. Jelin
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ali G. Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Thomas Hays
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| |
Collapse
|
3
|
Fan L, Shen G, Liu M, Liang Y, Yao J, Ding Z, Li Z, Feng X, Zhang J, Shen X. Renal Hypodysplasia/Aplasia 3 Caused by a Rare Variant of GREB1L With Incomplete Penetrance in a Chinese Family. Urology 2024; 185:49-53. [PMID: 38309594 DOI: 10.1016/j.urology.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/15/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
Renal agenesis represents the most severe form of congenital anomalies of the kidney and urinary tract. Bilateral renal agenesis is almost invariably fatal at birth and has high genetic heterogeneity. Here we report on a Chinese family with two pregnancies affected by a prenatal form of bilateral renal agenesis. Trio-WES was conducted to explore the underlying genetic cause and identified a novel nonsense variant (c .2621G>A: p. Trp874Ter) in the GREB1L gene. Based on previous research, pathogenic mutations in GREB1L can cause renal hypodysplasia/aplasia-3 (RHDA3) with autosomal dominant inheritance. Sanger sequencing performed on the family members revealed that the variant was vertically transmitted from the maternal grandfather through the unaffected mother to the two affected fetuses, fully demonstrating the incomplete dominance of the disease. Our study extends the mutational spectrum associated with RHDA3 and contributes to a more general understanding for the complex genetic inheritance of GREB1L.
Collapse
Affiliation(s)
- Lihong Fan
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Guosong Shen
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Mingsong Liu
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Yufei Liang
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Juan Yao
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Zhongying Ding
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Zhi Li
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Xiangping Feng
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Jinghui Zhang
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Xueping Shen
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China.
| |
Collapse
|
4
|
Kolvenbach CM, Shril S, Hildebrandt F. The genetics and pathogenesis of CAKUT. Nat Rev Nephrol 2023; 19:709-720. [PMID: 37524861 DOI: 10.1038/s41581-023-00742-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2023] [Indexed: 08/02/2023]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) comprise a large variety of malformations that arise from defective kidney or urinary tract development and frequently lead to kidney failure. The clinical spectrum ranges from severe malformations, such as renal agenesis, to potentially milder manifestations, such as vesicoureteral reflux. Almost 50% of cases of chronic kidney disease that manifest within the first three decades of life are caused by CAKUT. Evidence suggests that a large number of CAKUT are genetic in origin. To date, mutations in ~54 genes have been identified as monogenic causes of CAKUT, contributing to 12-20% of the aetiology of the disease. Pathogenic copy number variants have also been shown to cause CAKUT and can be detected in 4-11% of patients. Furthermore, environmental and epigenetic factors can increase the risk of CAKUT. The discovery of novel CAKUT-causing genes is challenging owing to variable expressivity, incomplete penetrance and variable genotype-phenotype correlation. However, such a discovery could ultimately lead to improvements in the accurate molecular genetic diagnosis, assessment of prognosis and multidisciplinary clinical management of patients with CAKUT, potentially including personalized therapeutic approaches.
Collapse
Affiliation(s)
- Caroline M Kolvenbach
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
5
|
Li Y, Zhou Z, Xu Y, Wang ZR. Novel mutation c.2090_2091del in neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities in an 18.5-mo-old boy: A case report. World J Clin Cases 2023; 11:3891-3898. [PMID: 37383123 PMCID: PMC10294165 DOI: 10.12998/wjcc.v11.i16.3891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities (NECRC) is a rare, autosomal, dominant neurological disorder caused by mutations in the ZMYM2 gene. To date, the clinical and functional characteristics of the novel ZMYM2 mutation c.2090_2091del have not yet been reported.
CASE SUMMARY The patient was an 18.5-mo-old Chinese boy with motor and language delay, microcephaly, facial dysmorphism, moderate malnutrition, single palmar crease on the left hand, synpolydactyly of the right foot, hypotonia and feeding problems. The boy who was diagnosed with NECRC was enrolled in the First Affiliated Hospital, Henan University of Chinese Medicine, and his clinical data were collected. From the whole-exon sequencing (WES) data, the pathogenic SNVs/InDels were identified, and the molecular findings were characterized. WES revealed that the heterozygous variant in the ZMYM2 gene was c.2090_2091del, p.Ser697TrpfsTer3, a frameshift mutation, which is a NECRC-related gene mutation.
CONCLUSION We performed a systematic literature review to identify and characterize NECRC. Substantial evidence from the literature indicated that patients with ZMYM2 gene mutation showed different degrees of intellectual disability, motor and language retardation, facial dysmorphism, and a few had congenital heart defects, kidney and urinary tract abnormalities. Early diagnosis and prompt management with comprehensive rehabilitation training are beneficial, but may not improve long-term outcomes.
Collapse
Affiliation(s)
- Yi Li
- College of Pediatrics, Henan University of Chinese Medicine, Zhengzhou 450000, Henan Province, China
| | - Zheng Zhou
- Department of Pediatrics, The First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou 450000, Henan Province, China
| | - Yan Xu
- Department of Pediatrics, The First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou 450000, Henan Province, China
| | - Zhi-Ru Wang
- Department of Pediatrics, The First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou 450000, Henan Province, China
| |
Collapse
|
6
|
Ahram DF, Lim TY, Ke J, Jin G, Verbitsky M, Bodria M, Kil BH, Chatterjee D, Piva SE, Marasa M, Zhang JY, Cocchi E, Caridi G, Gucev Z, Lozanovski VJ, Pisani I, Izzi C, Savoldi G, Gnutti B, Capone VP, Morello W, Guarino S, Esposito P, Lambert S, Radhakrishnan J, Appel GB, Uy NS, Rao MK, Canetta PA, Bomback AS, Nestor JG, Hays T, Cohen DJ, Finale C, van Wijk JA, La Scola C, Baraldi O, Tondolo F, Di Renzo D, Jamry-Dziurla A, Pezzutto A, Manca V, Mitrotti A, Santoro D, Conti G, Martino M, Giordano M, Gesualdo L, Zibar L, Masnata G, Bonomini M, Alberti D, La Manna G, Caliskan Y, Ranghino A, Marzuillo P, Kiryluk K, Krzemień G, Miklaszewska M, Lin F, Montini G, Scolari F, Fiaccadori E, Arapović A, Saraga M, McKiernan J, Alam S, Zaniew M, Szczepańska M, Szmigielska A, Sikora P, Drożdż D, Mizerska-Wasiak M, Mane S, Lifton RP, Tasic V, Latos-Bielenska A, Gharavi AG, Ghiggeri GM, Materna-Kiryluk A, Westland R, Sanna-Cherchi S. Rare Single Nucleotide and Copy Number Variants and the Etiology of Congenital Obstructive Uropathy: Implications for Genetic Diagnosis. J Am Soc Nephrol 2023; 34:1105-1119. [PMID: 36995132 PMCID: PMC10278788 DOI: 10.1681/asn.0000000000000132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/18/2023] [Indexed: 03/31/2023] Open
Abstract
SIGNIFICANCE STATEMENT Congenital obstructive uropathy (COU) is a prevalent human developmental defect with highly heterogeneous clinical presentations and outcomes. Genetics may refine diagnosis, prognosis, and treatment, but the genomic architecture of COU is largely unknown. Comprehensive genomic screening study of 733 cases with three distinct COU subphenotypes revealed disease etiology in 10.0% of them. We detected no significant differences in the overall diagnostic yield among COU subphenotypes, with characteristic variable expressivity of several mutant genes. Our findings therefore may legitimize a genetic first diagnostic approach for COU, especially when burdening clinical and imaging characterization is not complete or available. BACKGROUND Congenital obstructive uropathy (COU) is a common cause of developmental defects of the urinary tract, with heterogeneous clinical presentation and outcome. Genetic analysis has the potential to elucidate the underlying diagnosis and help risk stratification. METHODS We performed a comprehensive genomic screen of 733 independent COU cases, which consisted of individuals with ureteropelvic junction obstruction ( n =321), ureterovesical junction obstruction/congenital megaureter ( n =178), and COU not otherwise specified (COU-NOS; n =234). RESULTS We identified pathogenic single nucleotide variants (SNVs) in 53 (7.2%) cases and genomic disorders (GDs) in 23 (3.1%) cases. We detected no significant differences in the overall diagnostic yield between COU sub-phenotypes, and pathogenic SNVs in several genes were associated to any of the three categories. Hence, although COU may appear phenotypically heterogeneous, COU phenotypes are likely to share common molecular bases. On the other hand, mutations in TNXB were more often identified in COU-NOS cases, demonstrating the diagnostic challenge in discriminating COU from hydronephrosis secondary to vesicoureteral reflux, particularly when diagnostic imaging is incomplete. Pathogenic SNVs in only six genes were found in more than one individual, supporting high genetic heterogeneity. Finally, convergence between data on SNVs and GDs suggest MYH11 as a dosage-sensitive gene possibly correlating with severity of COU. CONCLUSIONS We established a genomic diagnosis in 10.0% of COU individuals. The findings underscore the urgent need to identify novel genetic susceptibility factors to COU to better define the natural history of the remaining 90% of cases without a molecular diagnosis.
Collapse
Affiliation(s)
- Dina F. Ahram
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Tze Y. Lim
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Juntao Ke
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Gina Jin
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Miguel Verbitsky
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Monica Bodria
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Byum Hee Kil
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Debanjana Chatterjee
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Stacy E. Piva
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Maddalena Marasa
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Jun Y. Zhang
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Enrico Cocchi
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Gianluca Caridi
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Zoran Gucev
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
| | - Vladimir J. Lozanovski
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
- Department of General, Visceral and Transplant Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Isabella Pisani
- Unità Operativa Nefrologia, Azienda Ospedaliero-Universitaria di Parma, Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Claudia Izzi
- Division of Nephrology, Department of Obstetrics and Gynecology, ASST Spedali Civili of Brescia, Brescia, Italy
| | | | - Barbara Gnutti
- Medical Genetics Laboratory, ASST-Spedali Civili, Brescia, Italy
| | - Valentina P. Capone
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - William Morello
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Guarino
- Department of Woman and Child and of General and Specialized Surgery, Università degli Studi della Campania “Luigi Vanvitelli,” Naples, Italy
| | - Pasquale Esposito
- Department of Internal Medicine, University of Genoa, Genova, Italy
- Unit of Nephrology, IRCCS San Martino Polyclinic Hospital, Genoa, Italy
| | - Sarah Lambert
- Yale School of Medicine/Yale New Haven Health System, New Haven, Connecticut
| | - Jai Radhakrishnan
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Gerald B. Appel
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Natalie S. Uy
- Division of Pediatric Nephrology, Department of Pediatric, NewYork-Presbyterian Morgan Stanley Children's Hospital, Columbia University Irving Medical Center, New York, New York
| | - Maya K. Rao
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Pietro A. Canetta
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Andrew S. Bomback
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Jordan G. Nestor
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Thomas Hays
- Department of Pediatrics, Division of Neonatology, Columbia University, New York, New York
| | - David J. Cohen
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Carolina Finale
- Nephrology, Dialysis and Renal Transplantation Unit, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I, Lancisi, Salesi of Ancona, Ancona, Italy
| | - Joanna A.E. van Wijk
- Department of Pediatric Nephrology, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Claudio La Scola
- Nephrology and Dialysis Unit, Department of Pediatrics, Azienda Ospedaliero Universitaria Sant'Orsola-Malpighi, Bologna, Italy
| | - Olga Baraldi
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Francesco Tondolo
- Nephrology, Dialysis and Renal Transplant Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Dacia Di Renzo
- “Spirito Santo” Hospital of Pescara, Pediatric Surgery of “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Anna Jamry-Dziurla
- Polish Registry of Congenital Malformations, Chair and Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Alessandro Pezzutto
- Nephrology and Dialysis Unit, Department of Medicine, SS Annunziata Hospital, “G. d'Annunzio” University, Chieti, Italy
| | - Valeria Manca
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Adele Mitrotti
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Domenico Santoro
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria “G. Martino,” Messina, Italy
| | - Marida Martino
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital “Giovanni XXIII,” Bari, Italy
| | - Mario Giordano
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital “Giovanni XXIII,” Bari, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Lada Zibar
- Department of Nephrology, University Hospital Merkur, Zagreb, Croatia
- Faculty of Medicine, University Josip Juraj Strossmayer in Osijek, Osijek, Croatia
| | - Giuseppe Masnata
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Mario Bonomini
- Nephrology and Dialysis Unit, Department of Medicine, SS Annunziata Hospital, “G. d'Annunzio” University, Chieti, Italy
| | | | - Gaetano La Manna
- IRCCS Azienda Ospedaliera di Bologna, Nephrology, Dialysis and Kidney Transplant Unit, St. Orsola University Hospital, Bologna, Italy
| | - Yasar Caliskan
- Division of Nephrology, Saint Louis University School of Medicine, Saint Louis, Missouri
| | - Andrea Ranghino
- Nephrology, Dialysis and Renal Transplantation Unit, Azienda Ospedaliera Universitaria Ospedali Riuniti Umberto I, Lancisi, Salesi of Ancona, Ancona, Italy
| | - Pierluigi Marzuillo
- Department of Woman and Child and of General and Specialized Surgery, Università degli Studi della Campania “Luigi Vanvitelli,” Naples, Italy
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Grażyna Krzemień
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatric, NewYork-Presbyterian Morgan Stanley Children's Hospital, Columbia University Irving Medical Center, New York, New York
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, Giuliana and Bernardo Caprotti Chair of Pediatrics, University of Milano, Milano, Italy
| | - Francesco Scolari
- Division of Nephrology and Dialysis, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia and ASST Spedali Civili of Brescia, Brescia, Italy
| | - Enrico Fiaccadori
- Unità Operativa Nefrologia, Azienda Ospedaliero-Universitaria di Parma, Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy
| | - Adela Arapović
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - James McKiernan
- Department of Urology, Columbia University Irving Medical Center, New York, New York
| | - Shumyle Alam
- Department of Urology, Columbia University Irving Medical Center, New York, New York
- Division of Pediatric Urology, MUSC Health-University Medical Center, Charleston, South Carolina
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Maria Szczepańska
- Department of Pediatrics, FMS in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Przemysław Sikora
- Department of Pediatric Nephrology, Medical University of Lublin, Lublin, Poland
| | - Dorota Drożdż
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Krakow, Poland
| | | | - Shrikant Mane
- Yale Center for Mendelian Genomics (YCMG), New Haven, Connecticut
| | | | - Velibor Tasic
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
| | - Anna Latos-Bielenska
- Polish Registry of Congenital Malformations, Chair and Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Ali G. Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| | - Gian Marco Ghiggeri
- Division of Nephrology and Renal Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Laboratory on Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Anna Materna-Kiryluk
- Polish Registry of Congenital Malformations, Chair and Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Rik Westland
- Department of Pediatric Nephrology, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University, New York, New York
| |
Collapse
|
7
|
Riedhammer KM, Ćomić J, Tasic V, Putnik J, Abazi-Emini N, Paripovic A, Stajic N, Meitinger T, Nushi-Stavileci V, Berutti R, Braunisch MC, Hoefele J. Exome sequencing in individuals with congenital anomalies of the kidney and urinary tract (CAKUT): a single-center experience. Eur J Hum Genet 2023; 31:674-680. [PMID: 36922632 PMCID: PMC10250376 DOI: 10.1038/s41431-023-01331-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Individuals with congenital anomalies of the kidney and urinary tract (CAKUT) show a broad spectrum of malformations. CAKUT can occur in an isolated fashion or as part of a syndromic disorder and can lead to end-stage kidney failure. A monogenic cause can be identified in ~12% of affected individuals. This study investigated a single-center CAKUT cohort analyzed by exome sequencing (ES). Emphasis was placed on the question whether diagnostic yield differs between certain CAKUT phenotypes (e.g., bilateral kidney affection, unilateral kidney affection or only urinary tract affection). 86 unrelated individuals with CAKUT were categorized according to their phenotype and analyzed by ES to identify a monogenic cause. Prioritized variants were rated according to the recommendations of the American College of Medical Genetics and Genomics and the Association for Clinical Genomic Science. Diagnostic yields of different phenotypic categories were compared. Clinical data were collected using a standardized questionnaire. In the study cohort, 7/86 individuals had a (likely) pathogenic variant in the genes PAX2, PBX1, EYA1, or SALL1. Additionally, in one individual, a 17q12 deletion syndrome (including HNF1B) was detected. 64 individuals had a kidney affection, which was bilateral in 36. All solved cases (8/86, 9%) had bilateral kidney affection (diagnostic yield in subcohort: 8/36, 22%). Although the diagnostic yield in CAKUT cohorts is low, our single-center experience argues, that, in individuals with bilateral kidney affection, monogenic burden is higher than in those with unilateral kidney or only urinary tract affection.
Collapse
Affiliation(s)
- Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Jasmina Ćomić
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Velibor Tasic
- University Children's Hospital, Medical Faculty of Skopje, Skopje, North Macedonia
| | - Jovana Putnik
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Nora Abazi-Emini
- University Children's Hospital, Medical Faculty of Skopje, Skopje, North Macedonia
| | - Aleksandra Paripovic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Natasa Stajic
- Institute for Mother and Child Health Care of Serbia "Dr Vukan Čupić", Department of Nephrology, University of Belgrade, Faculty of Medicine, Belgrade, Serbia
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | | | - Riccardo Berutti
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Matthias C Braunisch
- Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany.
| |
Collapse
|
8
|
Shao YF, Wang H, Wang YX, Shao LP, Wang S. Prenatal diagnosis of congenital chloride diarrhea by whole exome sequencing in four Chinese families and prenatal genotype-phenotype association study. World J Pediatr 2023; 19:200-207. [PMID: 36417080 DOI: 10.1007/s12519-022-00634-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 10/06/2022] [Indexed: 11/24/2022]
Affiliation(s)
- Ying-Fei Shao
- Renji College of Wenzhou Medical University, Wenzhou, China
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
- Laboratory of Renal Disease, Qingdao, China
| | - Hong Wang
- Department of Nephrology, Eighth People's Hospital of Qingdao, Qingdao, China
| | - Yi-Xiu Wang
- Darpartment of Hepatic Surgery, Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Le-Ping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China.
- Laboratory of Renal Disease, Qingdao, China.
| | - Sai Wang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China.
- Department of Dermatology, Peking University First Hospital, Beijing, China.
| |
Collapse
|
9
|
Connaughton DM, Hildebrandt F. Disease mechanisms of monogenic congenital anomalies of the kidney and urinary tract American Journal of Medical Genetics Part C. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:325-343. [PMID: 36208064 PMCID: PMC9618346 DOI: 10.1002/ajmg.c.32006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/14/2022] [Accepted: 09/16/2022] [Indexed: 11/05/2022]
Abstract
Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is a developmental disorder of the kidney and/or genito-urinary tract that results in end stage kidney disease (ESKD) in up to 50% of children. Despite the congenital nature of the disease, CAKUT accounts for almost 10% of adult onset ESKD. Multiple lines of evidence suggest that CAKUT is a Mendelian disorder, including the observation of familial clustering of CAKUT. Pathogenesis in CAKUT is embryonic in origin, with disturbances of kidney and urinary tract development resulting in a heterogeneous range of disease phenotypes. Despite polygenic and environmental factors being implicated, a significant proportion of CAKUT is monogenic in origin, with studies demonstrating single gene defects in 10%-20% of patients with CAKUT. Here, we review monogenic disease causation with emphasis on the etiological role of gene developmental pathways in CAKUT.
Collapse
Affiliation(s)
- Dervla M Connaughton
- Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, Canada
- Department of Medicine, Division of Nephrology, London Health Sciences Centre, London, Ontario, Canada
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
10
|
Claus LR, Snoek R, Knoers NVAM, van Eerde AM. Review of genetic testing in kidney disease patients: Diagnostic yield of single nucleotide variants and copy number variations evaluated across and within kidney phenotype groups. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:358-376. [PMID: 36161467 PMCID: PMC9828643 DOI: 10.1002/ajmg.c.31995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/02/2022] [Accepted: 08/18/2022] [Indexed: 01/29/2023]
Abstract
Genetic kidney disease comprises a diverse group of disorders. These can roughly be divided in the phenotype groups congenital anomalies of the kidney and urinary tract, ciliopathies, glomerulopathies, stone disorders, tubulointerstitial kidney disease, and tubulopathies. Many etiologies can lead to chronic kidney disease that can progress to end-stage kidney disease. Despite each individual disease being rare, together these genetic disorders account for a large proportion of kidney disease cases. With the introduction of massively parallel sequencing, genetic testing has become more accessible, but a comprehensive analysis of the diagnostic yield is lacking. This review gives an overview of the diagnostic yield of genetic testing across and within the full range of kidney disease phenotypes through a systematic literature search that resulted in 115 included articles. Patient, test, and cohort characteristics that can influence the diagnostic yield are highlighted. Detection of copy number variations and their contribution to the diagnostic yield is described for all phenotype groups. Also, the impact of a genetic diagnosis for a patient and family members, which can be diagnostic, therapeutic, and prognostic, is shown through the included articles. This review will allow clinicians to estimate an a priori probability of finding a genetic cause for the kidney disease in their patients.
Collapse
Affiliation(s)
- Laura R. Claus
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Rozemarijn Snoek
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nine V. A. M. Knoers
- Department of GeneticsUniversity Medical Center GroningenGroningenThe Netherlands
| | | |
Collapse
|
11
|
A single center experience of prenatal parent‐fetus trio exome sequencing for pregnancies with congenital anomalies. Prenat Diagn 2022; 42:901-910. [DOI: 10.1002/pd.6170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/07/2022]
|
12
|
Münch J, Engesser M, Schönauer R, Hamm JA, Hartig C, Hantmann E, Akay G, Pehlivan D, Mitani T, Coban Akdemir Z, Tüysüz B, Shirakawa T, Dateki S, Claus LR, van Eerde AM, Smol T, Devisme L, Franquet H, Attié-Bitach T, Wagner T, Bergmann C, Höhn AK, Shril S, Pollack A, Wenger T, Scott AA, Paolucci S, Buchan J, Gabriel GC, Posey JE, Lupski JR, Petit F, McCarthy AA, Pazour GJ, Lo CW, Popp B, Halbritter J. Biallelic pathogenic variants in roundabout guidance receptor 1 associate with syndromic congenital anomalies of the kidney and urinary tract. Kidney Int 2022; 101:1039-1053. [PMID: 35227688 PMCID: PMC10010616 DOI: 10.1016/j.kint.2022.01.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) represent the most common cause of chronic kidney failure in children. Despite growing knowledge of the genetic causes of CAKUT, the majority of cases remain etiologically unsolved. Genetic alterations in roundabout guidance receptor 1 (ROBO1) have been associated with neuronal and cardiac developmental defects in living individuals. Although Slit-Robo signaling is pivotal for kidney development, diagnostic ROBO1 variants have not been reported in viable CAKUT to date. By next-generation-sequencing methods, we identified six unrelated individuals and two non-viable fetuses with biallelic truncating or combined missense and truncating variants in ROBO1. Kidney and genitourinary manifestation included unilateral or bilateral kidney agenesis, vesicoureteral junction obstruction, vesicoureteral reflux, posterior urethral valve, genital malformation, and increased kidney echogenicity. Further clinical characteristics were remarkably heterogeneous, including neurodevelopmental defects, intellectual impairment, cerebral malformations, eye anomalies, and cardiac defects. By in silico analysis, we determined the functional significance of identified missense variants and observed absence of kidney ROBO1 expression in both human and murine mutant tissues. While its expression in multiple tissues may explain heterogeneous organ involvement, variability of the kidney disease suggests gene dosage effects due to a combination of null alleles with mild hypomorphic alleles. Thus, comprehensive genetic analysis in CAKUT should include ROBO1 as a new cause of recessively inherited disease. Hence, in patients with already established ROBO1-associated cardiac or neuronal disorders, screening for kidney involvement is indicated.
Collapse
Affiliation(s)
- Johannes Münch
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Marie Engesser
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Ria Schönauer
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - J Austin Hamm
- East Tennessee Children's Hospital, Genetic Center, Knoxville, Tennessee, USA
| | - Christin Hartig
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Elena Hantmann
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Pediatrics, University of Utah, Salt Lake, Utah, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA; Texas Children's Hospital, Houston, Texas, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University Cerrahpasa Medical Faculty, Istanbul, Turkey
| | | | - Sumito Dateki
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Thomas Smol
- Centre Hospitalier Universitaire de Lille, Institut de Génétique Médicale, Lille, France
| | - Louise Devisme
- Centre Hospitalier Universitaire de Lille, Institut de Pathologie, Lille, France
| | - Hélène Franquet
- Centre Hospitalier Universitaire de Lille, Institut de Pathologie, Lille, France
| | - Tania Attié-Bitach
- Laboratoire de biologie médicale multisites SeqOIA, Paris, France; Service de Médecine Génomique des Maladies Rares, APHP.Centre, Université de Paris, Paris, France
| | - Timo Wagner
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany; Department of Medicine, Nephrology, University Hospital Freiburg, Freiburg, Germany
| | - Anne Kathrin Höhn
- Division of Pathology, University of Leipzig Medical Center, Leipzig, Germany
| | - Shirlee Shril
- Division of Nephrology, Boston Children's Hospital, Boston, USA
| | - Ari Pollack
- Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Tara Wenger
- Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Abbey A Scott
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - Sarah Paolucci
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jillian Buchan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Texas Children's Hospital, Houston, Texas, USA; Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Florence Petit
- Centre Hospitalier Universitaire de Lille, Clinique de Génétique Guy Fontaine, Lille, France
| | | | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Worcester, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
| | - Bernt Popp
- Institute for Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
| | - Jan Halbritter
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany.
| |
Collapse
|
13
|
Xiong HY, Shi YQ, Zhong C, Yang Q, Zhang G, Yang H, Wu D, Chen Y, Li Q, Wang M. Detection of De Novo PAX2 Variants and Phenotypes in Chinese Population: A Single-Center Study. Front Genet 2022; 13:799562. [PMID: 35444690 PMCID: PMC9014304 DOI: 10.3389/fgene.2022.799562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background:PAX2 is a nuclear transcription factor gene that is highly conserved among species. Variants within PAX2 could result in optic nerve colobomas and kidney hypoplasia. However, little clinical and genetic information is currently available about PAX2 variants in Chinese children. Objective: This study aims to further understand the clinical manifestations and genetic characteristics of PAX2 variants in Chinese population. Methods: In this single-center retrospective study, we analyzed the clinical data of 10 children identified as carriers of PAX2 variants by gene sequencing. All the variants found in this study were analyzed using in silico prediction and American College of Medical Genetics and Genomics (ACMG) standards and guidelines. Results: The mean age for developing the first symptom in 10 unrelated children was 7.2 years old. Proteinuria and bilateral kidney dysplasia were found in every patient. Two children underwent kidney histological examination; one child showed high-intensity C1q deposition in the kidney, and the other child showed focal segmental glomerular sclerosis (FSGS). Three children had PAX2-related ocular abnormalities, including nystagmus, retinal exudation, amblyopia, microphthalmia, microcornea, and total blindness. In addition, one patient had the comorbidity of oculocutaneous albinism (OCA). Eight different PAX2 variants were found in ten patients, three of which were reported for the first time. Conclusion: We reported some patients with unique manifestations and comorbidities, and we reported three variants that have not been previously identified. The PAX2 gene is prone to spontaneous variants, and the outcome of patients is unfavorable. Because of the lack of specific therapy, genetic testing should be recommended for individuals with obvious evidence of kidney dysplasia and eye abnormalities, and kidney protective treatment should be initiated early.
Collapse
Affiliation(s)
- Hua-Ying Xiong
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
| | - Yong-Qi Shi
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
| | - Cheng Zhong
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
| | - Qin Yang
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
| | - Gaofu Zhang
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
| | - Haiping Yang
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
| | - Daoqi Wu
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
| | - Yaxi Chen
- Key Laboratory of Molecular Biology for Infectious Diseases, Department of Infectious Diseases, Ministry of Education, Centre for Lipid Research, The Second Affiliated Hospital, Institute for Viral Hepatitis, Chongqing Medical University, Chongqing, China
| | - Qiu Li
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
- *Correspondence: Qiu Li, ; Mo Wang,
| | - Mo Wang
- Department of Nephrology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Pediatric Research Institute, Chongqing, China
- *Correspondence: Qiu Li, ; Mo Wang,
| |
Collapse
|
14
|
Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
Collapse
Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
| | | | | | | | | | | |
Collapse
|
15
|
Seltzsam S, Wang C, Zheng B, Mann N, Connaughton DM, Wu CHW, Schneider S, Schierbaum L, Kause F, Kolvenbach CM, Nakayama M, Dai R, Ottlewski I, Schneider R, Deutsch K, Buerger F, Klämbt V, Mao Y, Onuchic-Whitford AC, Nicolas-Frank C, Yousef K, Pantel D, Lai EW, Salmanullah D, Majmundar AJ, Bauer SB, Rodig NM, Somers MJG, Traum AZ, Stein DR, Daga A, Baum MA, Daouk GH, Tasic V, Awad HS, Eid LA, El Desoky S, Shalaby M, Kari JA, Fathy HM, Soliman NA, Mane SM, Shril S, Ferguson MA, Hildebrandt F. Reverse phenotyping facilitates disease allele calling in exome sequencing of patients with CAKUT. Genet Med 2022; 24:307-318. [PMID: 34906515 PMCID: PMC8876311 DOI: 10.1016/j.gim.2021.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/08/2021] [Accepted: 09/14/2021] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the leading cause of chronic kidney disease in children. In total, 174 monogenic causes of isolated or syndromic CAKUT are known. However, syndromic features may be overlooked when the initial clinical diagnosis of CAKUT is made. We hypothesized that the yield of a molecular genetic diagnosis by exome sequencing (ES) can be increased by applying reverse phenotyping, by re-examining the case for signs/symptoms of the suspected clinical syndrome that results from the genetic variant detected by ES. METHODS We conducted ES in an international cohort of 731 unrelated families with CAKUT. We evaluated ES data for variants in 174 genes, in which variants are known to cause isolated or syndromic CAKUT. In cases in which ES suggested a previously unreported syndromic phenotype, we conducted reverse phenotyping. RESULTS In 83 of 731 (11.4%) families, we detected a likely CAKUT-causing genetic variant consistent with an isolated or syndromic CAKUT phenotype. In 19 of these 83 families (22.9%), reverse phenotyping yielded syndromic clinical findings, thereby strengthening the genotype-phenotype correlation. CONCLUSION We conclude that employing reverse phenotyping in the evaluation of syndromic CAKUT genes by ES provides an important tool to facilitate molecular genetic diagnostics in CAKUT.
Collapse
Affiliation(s)
- Steve Seltzsam
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Chunyan Wang
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bixia Zheng
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Nina Mann
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dervla M Connaughton
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Chen-Han Wilfred Wu
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sophia Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Luca Schierbaum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Franziska Kause
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Caroline M Kolvenbach
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Makiko Nakayama
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Rufeng Dai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Isabel Ottlewski
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ronen Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Konstantin Deutsch
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Florian Buerger
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Verena Klämbt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Youying Mao
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ana C Onuchic-Whitford
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Camille Nicolas-Frank
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Kirollos Yousef
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dalia Pantel
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ethan W Lai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Daanya Salmanullah
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Amar J Majmundar
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Nancy M Rodig
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michael J G Somers
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Avram Z Traum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Deborah R Stein
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ankana Daga
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michelle A Baum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ghaleb H Daouk
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Sherif El Desoky
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Mohammed Shalaby
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Jameela A Kari
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michael A Ferguson
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
| |
Collapse
|
16
|
Harris M, Schuh MP, McKinney D, Kaufman K, Erkan E. Whole Exome Sequencing in a Population With Severe Congenital Anomalies of Kidney and Urinary Tract. Front Pediatr 2022; 10:898773. [PMID: 35990004 PMCID: PMC9386178 DOI: 10.3389/fped.2022.898773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022] Open
Abstract
Fetal and neonatal interventions (e.g., amnioinfusions, amniotic shunting, and infant dialysis) have increased survival of infants with severe Congenital Anomalies of the Kidney and Urinary Tract (CAKUT), however, outcomes vary dramatically. Our aim was to perform Whole Exome Sequencing (WES) in a unique severe CAKUT population with the goal to identify new variants that will enhance prediction of postnatal outcomes. We performed trio WES on five infants with severe CAKUT (undergoing fetal interventions and/or those who initiated renal replacement therapy (RRT) within 1 month of life) and their parents as well as three singletons. We identified three potential candidate gene variants (NSUN7, MTMR3, CEP162) and validated two variants in known CAKUT genes (GATA3 and FRAS1) showing strong enrichment in this severe phenotype population. Based on our small pilot study of a unique severe CAKUT population, WES appears to be a potential tool to help predict the course of infants with severe CAKUT prenatally.
Collapse
Affiliation(s)
- Meredith Harris
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Nephrology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Meredith P Schuh
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - David McKinney
- University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Kenneth Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Elif Erkan
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,University of Cincinnati College of Medicine, Cincinnati, OH, United States
| |
Collapse
|
17
|
Li L, Chu C, Li S, Lu D, Zheng P, Sheng J, Luo LJ, Wu X, Zhang YD, Yin C, Duan AH. Renal agenesis-related genes are associated with Herlyn-Werner-Wunderlich syndrome. Fertil Steril 2021; 116:1360-1369. [PMID: 34311961 DOI: 10.1016/j.fertnstert.2021.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To explore the genetic causes of Herlyn-Werner-Wunderlich syndrome (HWWS) using whole-exome sequencing. DESIGN Retrospective genetic study. SETTING Academic medical center. PATIENT(S) Twelve patients with HWWS. INTERVENTION(S) Whole-exome sequencing was performed for each patient. Sanger sequencing was used to confirm the potential causative genetic variants. In silico analysis and American College of Medical Genetics and Genomics guidelines were used to classify the pathogenicity of each variant. MAIN OUTCOME MEASURE(S) Rare sequence variants associated with müllerian duct development and renal agenesis were identified and included in subsequent analyses. RESULT(S) A total of 11 variants were identified in 10 of 12 patients (83.3%) and were considered to constitute a molecular genetic diagnosis of HWWS. These 11 variants were related to 9 genes: CHD1L, TRIM32, TGFBR3, WNT4, RET, FRAS1, FAT1, FOXF1, and PCSK5. All variants were heterozygous and confirmed by Sanger sequencing. The changes included one frameshift variant, one splice-site variant, and eight missense variants. All of the identified variants were absent or rare in Genome Aggregation Database East Asian populations. One of the 11 variants (9.1%) was classified as a pathogenic variant according to the American College of Medical Genetics and Genomics guidelines, and 8 of the 11 variants (72.7%) were classified as variants of uncertain significance. CONCLUSION(S) To our knowledge, this is the first report of the genetic causes of HWWS. Renal agenesis-related genes, such as CHD1L, TRIM32, RET, and WNT4, may be associated with HWWS. Identification of these variants can not only help us understand the etiology of HWWS and the relationship between reproductive tract development and urinary system development, but additionally improve the level of genetic counseling for HWWS.
Collapse
Affiliation(s)
- Lin Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Chunfang Chu
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Shenghui Li
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Dan Lu
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Ping Zheng
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Jie Sheng
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Li-Jing Luo
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Xia Wu
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Yu-Di Zhang
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Chenghong Yin
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China
| | - Ai-Hong Duan
- Department of Gynecology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, Beijing, People's Republic of China; Beijing Maternal and Child Health Care Hospital, Chaoyang, Beijing, People's Republic of China.
| |
Collapse
|
18
|
Woodring TS, Mirza MH, Benavides V, Ellsworth KA, Wright MS, Javed MJ, Ramiro S. Uncertain, Not Unimportant: Callosal Dysgenesis and Variants of Uncertain Significance in ROBO1. Pediatrics 2021; 148:e2020019000. [PMID: 34193621 DOI: 10.1542/peds.2020-019000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Congenital anomalies affect 3% to 5% of births and remain the leading cause of infant death in the United States. As whole exome and genome sequencing are increasingly used to diagnose underlying genetic disease, the patient's clinical presentation remains the most important context for interpreting sequencing results, including frequently reported variants of uncertain significance (VUS). Classification of a variant as VUS acknowledges limits on evidence to establish whether a variant can be classified as pathogenic or benign according to the American College of Medical Genetics guidelines. Importantly, the VUS designation reflects limits on the breadth of evidence linking the genetic variant to a disease. However, available evidence, although limited, may be surprisingly relevant in an individual patient's case. Accordingly, a VUS result should be approached neither as nondiagnostic genetic result nor as automatically "uncertain" in its potential to guide clinical decision-making. In this article, we discuss a case of an infant born at 29 weeks 4 days without a corpus callosum, whose whole genome sequencing yielded compound heterozygous variants both classified as VUS in ROBO1, a gene encoding for a receptor involved in a canonical signaling mechanism that guides axons across midline. Approaching the VUS result as potentially pathogenic, we found the infant ultimately had pituitary dysfunction and renal anomalies consistent with other reported ROBO1 variants and basic science literature. Accordingly, we highlight resources for variant interpretation available to clinicians to evaluate VUS results, particularly as they inform the diagnosis of individually rare but collectively common rare diseases.
Collapse
Affiliation(s)
- Therese S Woodring
- University of Wisconsin Hospital and Clinics, Madison, Wisconsin
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
| | - Mohammed H Mirza
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
| | | | | | | | - M Jawad Javed
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
- NICU, Children's Hospital of Illinois, Peoria, Illinois
| | - Susan Ramiro
- College of Medicine Peoria, University of Illinois, Peoria, Illinois
- NICU, Children's Hospital of Illinois, Peoria, Illinois
| |
Collapse
|
19
|
Kyei Barffour I, Kyei Baah Kwarkoh R. GREB1L as a candidate gene of Mayer-Rokitansky-Küster-Hauser Syndrome. Eur J Med Genet 2021; 64:104158. [PMID: 33548512 DOI: 10.1016/j.ejmg.2021.104158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/10/2020] [Accepted: 01/30/2021] [Indexed: 01/14/2023]
Abstract
Mayer-Rokitansky-Küster-Hauser (MRKH) Syndrome is a sex development disorder that affects 1 in every 4500 46, XX live births. At least a subset of MRKH syndrome is genetically related to which various candidate genes have been identified. The growth regulation by estrogen in breast cancer 1-like gene (GREB1L) is an androgen-regulated gene reported to be a co-activator of the retinoic acid receptor gene (RAR). Thus expression levels of GREB1L have implications on renal system cellular differentiation, morphogenesis, and homeostasis in vertebrates. Variants of GREB1L have been reported in familial and sporadic MRKH Syndrome and more importantly, in a three-generation family ofMRKH syndrome propositae. Much the same way, Mutants of GREB1L have also been identified in isolated bilateral renal agenesis and deafness both of which are extra-genital tract anomalies in MRKH type 2. Again, renal agenesis transgenic mice have been produced from an E13.5 CRISPR/cas9 GREB1L mutagenesis. Though no GREB1L mutation has been reported in cardiac malformation, there is evidence that GREB1L is involved in ventricular development. Here, we intorigate evidence that projects GREB1L as a candidate gene of Mayer-Rokitansky-Küster-Hauser Syndrome and propose that functional validation analysis to that effect is imparative.
Collapse
Affiliation(s)
- Isaac Kyei Barffour
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Ghana.
| | - Roselind Kyei Baah Kwarkoh
- Department of Physician Assistant Studies, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Ghana
| |
Collapse
|
20
|
Guadagnolo D, Mastromoro G, Di Palma F, Pizzuti A, Marchionni E. Prenatal Exome Sequencing: Background, Current Practice and Future Perspectives-A Systematic Review. Diagnostics (Basel) 2021; 11:diagnostics11020224. [PMID: 33540854 PMCID: PMC7913004 DOI: 10.3390/diagnostics11020224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/16/2022] Open
Abstract
The introduction of Next Generation Sequencing (NGS) technologies has exerted a significant impact on prenatal diagnosis. Prenatal Exome Sequencing (pES) is performed with increasing frequency in fetuses with structural anomalies and negative chromosomal analysis. The actual diagnostic value varies extensively, and the role of incidental/secondary or inconclusive findings and negative results has not been fully ascertained. We performed a systematic literature review to evaluate the diagnostic yield, as well as inconclusive and negative-result rates of pES. Papers were divided in two groups. The former includes fetuses presenting structural anomalies, regardless the involved organ; the latter focuses on specific class anomalies. Available findings on non-informative or negative results were gathered as well. In the first group, the weighted average diagnostic yield resulted 19%, and inconclusive finding rate 12%. In the second group, the percentages were extremely variable due to differences in sample sizes and inclusion criteria, which constitute major determinants of pES efficiency. Diagnostic pES availability and its application have a pivotal role in prenatal diagnosis, though more homogeneity in access criteria and a consensus on clinical management of controversial information management is envisageable to reach widespread use in the near future.
Collapse
Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Francesca Di Palma
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Clinical Genomics Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Correspondence:
| |
Collapse
|
21
|
Lasić V, Kosović I, Jurić M, Racetin A, Čurčić J, Šolić I, Lozić M, Filipović N, Šoljić V, Martinović V, Saraga-Babić M, Vukojević K. GREB1L, CRELD2 and ITGA10 expression in the human developmental and postnatal kidneys: an immunohistochemical study. Acta Histochem 2021; 123:151679. [PMID: 33460985 DOI: 10.1016/j.acthis.2021.151679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/19/2020] [Accepted: 01/01/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Aim of our study is to provide an insight into the genetic expression landscape of GREB1L, ITGA10 and CRELD2 which are important in human genitourinary tract development which might help elucidate the critical stages for the onset of kidney anomalies. METHODS Morphological parameters were analyzed using immunohistochemistry on human foetal (13-38 w) and postnatal (1.5 and 7.5y) human kidney samples. RESULTS GREB1L marker had a strong intensity and the highest rate in proximal tubules (PTC) of 1.5 years' kidney (90.25%). In the distal tubules (DCT) there were statistically significant differences in 13 w, 15 w, 16 w, 21 w, 38 w and 7.5y regarding 1.5y (Kruskal-Wallis test, p < 0.001). There was significantly more GREB1L in the glomeruli at 21 w and 38 w in regard to all other stages (Kruskal-Wallis test, p < 0.01). ITGA10 staining intensity was strongest in PCT with the highest rate in 13 w (92.75%), while the lowest rate was found in glomeruli and DCT (Kruskal-Wallis test, p < 0.001). CRELD2 had the strongest staining intensity in PCT with the highest rate in 13 w and 1.5y (92.25%) and lowest in the glomeruli of 7.5 years (24.3 %). In DCT there were statistically significant differences in CRELD2 positive cells in 13 w, 15 w, 16 w, 21 w, 38 w and 7.5y regarding 1.5y (Kruskal-Wallis test, p < 0.01). ITGA10 and CRELD2 co-localised in the postnatal period in DCT. CONCLUSION High kidney expressions of GREB1L, ITGA10 and CRELD2 even in the postnatal period implicate their importance not only for the onset of CAKUT in the case of their mutation but also for maintenance of kidney homeostasis.
Collapse
|
22
|
Digby EL, Liauw J, Dionne J, Langlois S, Nikkel SM. Etiologies and outcomes of prenatally diagnosed hyperechogenic kidneys. Prenat Diagn 2021; 41:465-477. [PMID: 33337554 DOI: 10.1002/pd.5883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To determine etiologies and outcomes of fetal hyperechogenic kidneys (HEK). METHODS We conducted a retrospective chart review of HEK in British Columbia (January 2013-December 2019) and literature review. RESULTS We identified 20 cases of HEK without other anomalies (isolated) in our provincial cohort, one was lost to follow-up. Eight had testable genetic etiologies (autosomal dominant polycystic kidney disease [ADPKD], autosomal recessive polycystic kidney disease [ARPKD], Bardet-Biedl syndrome [BBS], and HNF1B-related disorder). The remaining seven did not have an identifiable genetic etiology. Of cases without a genetic etiology with postnatal follow-up (n = 6) there were no abnormalities of blood pressure, creatinine/estimated glomerular filtration rate or urinalysis identified with follow-up from 2-71 months. We report 11 cases with extrarenal anomalies (nonisolated), with outcomes and etiologies. We identified 224 reported cases of isolated HEK in the literature. A potentially testable genetic etiology was found in 128/224 (57.1%). The neonatal death rate in those with testable etiologies was 17/128 (13.3%) compared to 2/96 (2.1%) when testable etiologies were excluded. CONCLUSIONS Genetic etiologies (ARPKD, ADPKD, BBS, HNF1B-related disorder, Beckwith-Wiedemann syndrome, tubular dysgenesis, familial nephroblastoma, and cytogenetic abnormalities) account for approximately half of prenatally isolated HEK; once excluded there are few neonatal deaths and short-term renal outcomes may be normal. There remains a paucity of knowledge about long-term renal outcomes.
Collapse
Affiliation(s)
- Elizabeth L Digby
- Provincial Medical Genetics Program, BC Women's Hospital, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica Liauw
- Division of Maternal-Fetal-Medicine, Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janis Dionne
- University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics, Division of Nephrology, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Sylvie Langlois
- Provincial Medical Genetics Program, BC Women's Hospital, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah M Nikkel
- Provincial Medical Genetics Program, BC Women's Hospital, Vancouver, British Columbia, Canada.,University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
23
|
Diderich KEM, Romijn K, Joosten M, Govaerts LCP, Polak M, Bruggenwirth HT, Wilke M, van Slegtenhorst MA, van Bever Y, Brooks AS, Mancini GMS, van de Laar IMBH, Kromosoeto JNR, Knapen MFCM, Go ATJI, Van Opstal D, Hoefsloot LH, Galjaard RJH, Srebniak MI. The potential diagnostic yield of whole exome sequencing in pregnancies complicated by fetal ultrasound anomalies. Acta Obstet Gynecol Scand 2020; 100:1106-1115. [PMID: 33249554 PMCID: PMC8247008 DOI: 10.1111/aogs.14053] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/30/2020] [Accepted: 11/22/2020] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The aim of this retrospective cohort study was to determine the potential diagnostic yield of prenatal whole exome sequencing in fetuses with structural anomalies on expert ultrasound scans and normal chromosomal microarray results. MATERIAL AND METHODS In the period 2013-2016, 391 pregnant women with fetal ultrasound anomalies who received normal chromosomal microarray results, were referred for additional genetic counseling and opted for additional molecular testing pre- and/or postnatally. Most of the couples received only a targeted molecular test and in 159 cases (40.7%) whole exome sequencing (broad gene panels or open exome) was performed. The results of these molecular tests were evaluated retrospectively, regardless of the time of the genetic diagnosis (prenatal or postnatal). RESULTS In 76 of 391 fetuses (19.4%, 95% CI 15.8%-23.6%) molecular testing provided a genetic diagnosis with identification of (likely) pathogenic variants. In the majority of cases (91.1%, 73/76) the (likely) pathogenic variant would be detected by prenatal whole exome sequencing analysis. CONCLUSIONS Our retrospective cohort study shows that prenatal whole exome sequencing, if offered by a clinical geneticist, in addition to chromosomal microarray, would notably increase the diagnostic yield in fetuses with ultrasound anomalies and would allow early diagnosis of a genetic disorder irrespective of the (incomplete) fetal phenotype.
Collapse
Affiliation(s)
- Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Kathleen Romijn
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Marike Polak
- Department of Psychology, Education & Child Studies (DPECS), Erasmus University Rotterdam, Rotterdam, the Netherlands
| | | | - Martina Wilke
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Yolande van Bever
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Joan N R Kromosoeto
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Maarten F C M Knapen
- Department of Obstetrics and Prenatal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands.,Foundation Prenatal Screening Southwest Region of the Netherlands, Rotterdam, The Netherlands
| | - Attie T J I Go
- Department of Obstetrics and Prenatal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | | |
Collapse
|
24
|
Zhou X, Wang Y, Shao B, Wang C, Hu P, Qiao F, Xu Z. Molecular diagnostic in fetuses with isolated congenital anomalies of the kidney and urinary tract by whole-exome sequencing. J Clin Lab Anal 2020; 34:e23480. [PMID: 32779812 PMCID: PMC7676188 DOI: 10.1002/jcla.23480] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In prenatal care, accumulating evidences has demonstrated that whole-exome sequencing (WES) expedites the genetic diagnosis of fetal structural anomalies. However, the clinical value of WES in the diagnosis of prenatal isolated congenital anomalies of the kidney and urinary tract (CAKUT) is unknown. METHODS Forty-one fetuses with unexplained isolated CAKUT, normal karyotype and negative chromosomal microarray analysis (CMA) results, underwent WES and were accordingly grouped as (a) Group 1: complex cases with bilateral renal abnormalities (N = 19); and (b) Group 2: cases with isolated unilateral fetal renal abnormalities (N = 22). RESULTS The detection rate of WES for pathogenic variants and incidental variants was 7.32% (3/41) and 2.4% (1/41), respectively. The three pathogenic variants were identified in the genes ACTA2 (multisystem smooth muscle dysfunction syndrome), PKHD1 (autosomal recessive form of polycystic kidney disease), and PKD1 (autosomal dominant polycystic kidney disease type 1). The incidental variants were detected in genes PPM1D (syndromic neurodevelopmental disorders). Furthermore, all above fetuses carrying pathogenic variants came from bilateral kidney anomalies. Thus, the detection rate was 0 for fetuses with unilateral fetal renal abnormalities and 15.7% (3/19) for bilateral renal abnormalities. CONCLUSION This cohort shows that prenatal WES is a supplementary approach for the etiologic diagnosis of unexplained isolated CAKUT with negative CMA, especially for fetuses with bilateral renal abnormality.
Collapse
Affiliation(s)
- Xiaoyan Zhou
- State Key Laboratory of Reproductive MedicineDepartment of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjingChina
- Department of ObstetricsThe Affiliated Huai an No. 1 People's Hospital of NanjingMedical UniversityHuai anChina
| | - Yan Wang
- State Key Laboratory of Reproductive MedicineDepartment of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjingChina
| | - Binbin Shao
- State Key Laboratory of Reproductive MedicineDepartment of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjingChina
| | - Chen Wang
- State Key Laboratory of Reproductive MedicineDepartment of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjingChina
| | - Ping Hu
- State Key Laboratory of Reproductive MedicineDepartment of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjingChina
| | - Fengchang Qiao
- State Key Laboratory of Reproductive MedicineDepartment of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjingChina
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive MedicineDepartment of Prenatal DiagnosisWomen's Hospital of Nanjing Medical UniversityNanjingChina
| |
Collapse
|
25
|
Cocchi E, Nestor JG, Gharavi AG. Clinical Genetic Screening in Adult Patients with Kidney Disease. Clin J Am Soc Nephrol 2020; 15:1497-1510. [PMID: 32646915 PMCID: PMC7536756 DOI: 10.2215/cjn.15141219] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Expanded accessibility of genetic sequencing technologies, such as chromosomal microarray and massively parallel sequencing approaches, is changing the management of hereditary kidney diseases. Genetic causes account for a substantial proportion of pediatric kidney disease cases, and with increased utilization of diagnostic genetic testing in nephrology, they are now also detected at appreciable frequencies in adult populations. Establishing a molecular diagnosis can have many potential benefits for patient care, such as guiding treatment, familial testing, and providing deeper insights on the molecular pathogenesis of kidney diseases. Today, with wider clinical use of genetic testing as part of the diagnostic evaluation, nephrologists have the challenging task of selecting the most suitable genetic test for each patient, and then applying the results into the appropriate clinical contexts. This review is intended to familiarize nephrologists with the various technical, logistical, and ethical considerations accompanying the increasing utilization of genetic testing in nephrology care.
Collapse
Affiliation(s)
- Enrico Cocchi
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
- Department of Pediatrics, Universita' degli Studi di Torino, Torino, Italy
| | - Jordan Gabriela Nestor
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
| | - Ali G Gharavi
- Division of Nephrology and Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, New York
- Insititute of Genomic Medicine, Columbia University, New York, New York
| |
Collapse
|
26
|
Connaughton DM, Dai R, Owen DJ, Marquez J, Mann N, Graham-Paquin AL, Nakayama M, Coyaud E, Laurent EMN, St-Germain JR, Blok LS, Vino A, Klämbt V, Deutsch K, Wu CHW, Kolvenbach CM, Kause F, Ottlewski I, Schneider R, Kitzler TM, Majmundar AJ, Buerger F, Onuchic-Whitford AC, Youying M, Kolb A, Salmanullah D, Chen E, van der Ven AT, Rao J, Ityel H, Seltzsam S, Rieke JM, Chen J, Vivante A, Hwang DY, Kohl S, Dworschak GC, Hermle T, Alders M, Bartolomaeus T, Bauer SB, Baum MA, Brilstra EH, Challman TD, Zyskind J, Costin CE, Dipple KM, Duijkers FA, Ferguson M, Fitzpatrick DR, Fick R, Glass IA, Hulick PJ, Kline AD, Krey I, Kumar S, Lu W, Marco EJ, Wentzensen IM, Mefford HC, Platzer K, Povolotskaya IS, Savatt JM, Shcherbakova NV, Senguttuvan P, Squire AE, Stein DR, Thiffault I, Voinova VY, Somers MJG, Ferguson MA, Traum AZ, Daouk GH, Daga A, Rodig NM, Terhal PA, van Binsbergen E, Eid LA, Tasic V, Rasouly HM, Lim TY, Ahram DF, Gharavi AG, Reutter HM, Rehm HL, MacArthur DG, Lek M, Laricchia KM, Lifton RP, Xu H, Mane SM, Sanna-Cherchi S, Sharrocks AD, Raught B, Fisher SE, Bouchard M, Khokha MK, Shril S, Hildebrandt F. Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations. Am J Hum Genet 2020; 107:727-742. [PMID: 32891193 PMCID: PMC7536580 DOI: 10.1016/j.ajhg.2020.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/14/2020] [Indexed: 01/10/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) constitute one of the most frequent birth defects and represent the most common cause of chronic kidney disease in the first three decades of life. Despite the discovery of dozens of monogenic causes of CAKUT, most pathogenic pathways remain elusive. We performed whole-exome sequencing (WES) in 551 individuals with CAKUT and identified a heterozygous de novo stop-gain variant in ZMYM2 in two different families with CAKUT. Through collaboration, we identified in total 14 different heterozygous loss-of-function mutations in ZMYM2 in 15 unrelated families. Most mutations occurred de novo, indicating possible interference with reproductive function. Human disease features are replicated in X. tropicalis larvae with morpholino knockdowns, in which expression of truncated ZMYM2 proteins, based on individual mutations, failed to rescue renal and craniofacial defects. Moreover, heterozygous Zmym2-deficient mice recapitulated features of CAKUT with high penetrance. The ZMYM2 protein is a component of a transcriptional corepressor complex recently linked to the silencing of developmentally regulated endogenous retrovirus elements. Using protein-protein interaction assays, we show that ZMYM2 interacts with additional epigenetic silencing complexes, as well as confirming that it binds to FOXP1, a transcription factor that has also been linked to CAKUT. In summary, our findings establish that loss-of-function mutations of ZMYM2, and potentially that of other proteins in its interactome, as causes of human CAKUT, offering new routes for studying the pathogenesis of the disorder.
Collapse
Affiliation(s)
- Dervla M Connaughton
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Nephrology, Department of Medicine, University Hospital - London Health Sciences Centre, Schulich School of Medicine & Dentistry, Western University, 339 Windermere Road, London, ON N6A 5A5, Canada
| | - Rufeng Dai
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Danielle J Owen
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adda L Graham-Paquin
- Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Makiko Nakayama
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Jonathan R St-Germain
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Lot Snijders Blok
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands; Human Genetics Department, Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Arianna Vino
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands
| | - Verena Klämbt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantin Deutsch
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chen-Han Wilfred Wu
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Caroline M Kolvenbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Franziska Kause
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Ottlewski
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ronen Schneider
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas M Kitzler
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amar J Majmundar
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Florian Buerger
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ana C Onuchic-Whitford
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mao Youying
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amy Kolb
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daanya Salmanullah
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Evan Chen
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amelie T van der Ven
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Hadas Ityel
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Steve Seltzsam
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Johanna M Rieke
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Chen
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Asaf Vivante
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Tel Aviv University, Faculty of Medicine, Tel Aviv-Yafo 6997801, Israel
| | - Daw-Yang Hwang
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Kohl
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriel C Dworschak
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Tobias Hermle
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mariëlle Alders
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Meibergdreef 9, 1105 Amsterdam, Netherlands
| | - Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle A Baum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Thomas D Challman
- Geisinger, Autism & Developmental Medicine Institute, 100 N Academy Avenue, Danville, PA 17822, USA
| | - Jacob Zyskind
- Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA
| | - Carrie E Costin
- Department of Clinical Genetics, Akron Children's Hospital, One Perkins Square, Akron, OH 44308, USA
| | - Katrina M Dipple
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Floor A Duijkers
- Department of Clinical Genetics, University of Amsterdam, 1012 WX Amsterdam, the Netherlands
| | - Marcia Ferguson
- Department of Clinical Genetics, Harvey Institute for Human Genetics, 6701 Charles St, Towson, MD 21204, USA
| | - David R Fitzpatrick
- MRC Institute of Genetics & Molecular Medicine, Royal Hospital for Sick Children, The University of Edinburgh, 2XU, Crewe Rd S, Edinburgh EH4 2XU, UK
| | - Roger Fick
- Mary Bridge Childrens Hospital, 316 Martin Luther King JR Way, Tacoma, WA 98405, USA
| | - Ian A Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, 1000 Central Street, Suite 610, Evanston, IL 60201, USA
| | - Antonie D Kline
- Department of Clinical Genetics, Harvey Institute for Human Genetics, 6701 Charles St, Towson, MD 21204, USA
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany; Swiss Epilepsy Center, Klinik Lengg, Bleulerstrasse 60, 8000 Zürich, Switzerland
| | - Selvin Kumar
- Department of Pediatric Nephrology, Institute of Child Health and Hospital for Children, Tamil Salai, Egmore, Chennai, Tamil Nadu 600008, India
| | - Weining Lu
- Renal Section, Department of Medicine, Boston University Medical Center, 650 Albany Street, Boston, MA 02118, USA
| | - Elysa J Marco
- Cortica Healthcare, 4000 Civic Center Drive, Ste 100, San Rafael, CA 94939, USA
| | - Ingrid M Wentzensen
- Department of Clinical Genomics, GeneDx, 207 Perry Pkwy, Gaithersburg, MD 20877, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Philipp-Rosenthal- Straße 55, 04103 Leipzig, Germany
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Juliann M Savatt
- Geisinger, Autism & Developmental Medicine Institute, 100 N Academy Avenue, Danville, PA 17822, USA
| | - Natalia V Shcherbakova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Prabha Senguttuvan
- Department of Pediatric Nephrology, Dr. Mehta's Multi-Specialty Hospital, No.2, Mc Nichols Rd, Chetpet, Chennai, Tamil Nadu 600031, India
| | - Audrey E Squire
- Seattle Children's Hospital, Department of Genetic Medicine, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Deborah R Stein
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, 2401 Gillham Rd, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO 64108, USA; University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, 5000 Holmes St, Kansas City, MO 64110, USA
| | - Victoria Y Voinova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow 117997, Russia
| | - Michael J G Somers
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael A Ferguson
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Avram Z Traum
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ghaleb H Daouk
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ankana Daga
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nancy M Rodig
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje 1000, North Macedonia
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Tze Y Lim
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Dina F Ahram
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Heiko M Reutter
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany; Section of Neonatology and Pediatric Intensive Care, Clinic for Pediatrics, University Hospital Bonn, Adenauerallee 119, 53313 Bonn, Germany
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Kristen M Laricchia
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Richard P Lifton
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06510, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Columbia University, 630 W 168th St, New York, NY 10032, USA
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network & Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 XD Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6500HE Nijmegen, the Netherlands
| | - Maxime Bouchard
- Rosalind & Morris Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shirlee Shril
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
27
|
Connaughton DM, Hildebrandt F. Personalized medicine in chronic kidney disease by detection of monogenic mutations. Nephrol Dial Transplant 2020; 35:390-397. [PMID: 30809662 DOI: 10.1093/ndt/gfz028] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/08/2019] [Indexed: 12/18/2022] Open
Abstract
A large fraction of early-onset chronic kidney disease (CKD) is known to be monogenic in origin. To date, ∼450 monogenic (synonymous with single-gene disorders) genes, if mutated, are known to cause CKD, explaining ∼30% of cases in pediatric cohorts and ∼5-30% in adult cohorts. However, there are likely hundreds of additional monogenic nephropathy genes that may be revealed by whole-exome or -genome sequencing. Although the discovery of novel CKD-causing genes has accelerated, significant challenges in adult populations remain due to broad phenotypic heterogeneity together with variable expressivity, incomplete penetrance or age-related penetrance of these genes. Here we give an overview of the currently known monogenic causes for human CKD. We also describe how next-generation sequencing facilitates rapid molecular genetic diagnostics in individuals with suspected genetic kidney disease. In an era of precision medicine, understanding the utility of genetic testing in individuals with a suspected inherited nephropathy has important diagnostic and prognostic implications. Detection of monogenic causes of CKD permits molecular genetic diagnosis for patients and families and opens avenues for personalized treatment strategies for CKD. As an example, detection of a pathogenic mutation in the gene HNF1B not only allows for the formal diagnosis of CKD, but can also facilitate screening for additional extrarenal manifestations of disease, such as maturity-onset diabetes of youth, subclinical abnormal liver function tests, neonatal cholestasis and pancreatic hypoplasia. It also provides the driving force towards a better understanding of disease pathogenesis, potentially facilitating targeted new therapies for individuals with CKD.
Collapse
Affiliation(s)
- Dervla M Connaughton
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Boston, MA, USA
| |
Collapse
|
28
|
Tan H, Xie Y, Chen F, Chen M, Yu L, Chen D, Chen J. Novel and recurrent variants identified in fetuses with central nervous system abnormalities by trios-medical exome sequencing. Clin Chim Acta 2020; 510:599-604. [PMID: 32798513 DOI: 10.1016/j.cca.2020.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/12/2020] [Accepted: 08/10/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Fetal central nervous system abnormalities often associated with infant death or severe disability. The etiology in fetuses with CNS abnormalities who have normal karyotypes and copy number variants (CNVs) remains unclear, which increases the difficulty in following management and the assessment of prognosis. METHOD 11 unrelated fetuses with CNS abnormalities and their parents were enrolled. Genomic DNA was obtained and then trios-medical exome sequencing (trios-MES) including 4000 genes (fetuses and their parents) was performed after both karyotyping and chromosome microarray showed negative results. RESULTS Pathogenic and likely pathogenic variants were identified in five of 11 cases (5/11, 45.5%), including five novel mutations and two recurrent mutations in ISPD, L1CAM, and GRIN2B genes. Most cases (4/5, 80%) carried one or two recessive mutations, indicating a high recurrent risk. CONCLUSION Exome sequencing should be considered for fetuses with CNS abnormalities following negative results of karyotyping and chromosome array. Trios-MES as one of exome sequencing is a potential method for the diagnosis of these fetuses.
Collapse
Affiliation(s)
- Hu Tan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou 510150, China
| | - Yinong Xie
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Fei Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Li Yu
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong, China
| | - Dunjin Chen
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou 510150, China.
| | - Jingsi Chen
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, Guangdong, China; Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou 510150, China; Obstetrics & Gynecology Institute of Guangzhou, Guangzhou 510150, China.
| |
Collapse
|
29
|
Wang A, Ji B, Wu F, Zhao X. Clinical Exome Sequencing Identifies a Novel Mutation of the GREB1L Gene in a Chinese Family with Renal Agenesis. Genet Test Mol Biomarkers 2020; 24:520-526. [PMID: 32598191 DOI: 10.1089/gtmb.2020.0036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Renal agenesis (RA) is one of the most severe congenital anomalies of the kidney and urinary tract; it is known to be highly genetically heterogeneous. The purpose of this study was to explore the clinical significance of genetic diagnostics in a Chinese RA family. Methods: Five members of an RA family and 100 healthy people were recruited. Clinical exome sequencing was conducted to explore the underlying genetic cause in the affected family. Results: Exome sequencing identified a novel missense mutation (c.2333T>A, p.Val778Asp) in the GREB1L gene. This GREB1L variant was not detected in controls and was predicted to be highly damaging to the physiological function of the GREB1L protein. Conclusion: We identified a novel c.2333T>A variant in the GREB1L gene that extends the mutational spectrum associated with renal agenesis.
Collapse
Affiliation(s)
- Ancong Wang
- Department of Reproductive Medicine, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
- Department of Obstetrics and Gynecology, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
| | - Baoju Ji
- Department of Clinical Laboratory, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
| | - Fengxia Wu
- Department of Anatomy, School of Basic Medical Sciences, Shandong University, Jinan, Shandong Province, P.R. China
| | - Xiangyu Zhao
- Department of Clinical Laboratory, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
- Department of Medical Genetics, Linyi People's Hospital, Linyi, Shandong Province, P.R. China
| |
Collapse
|
30
|
Autosomal Dominantly Inherited GREB1L Variants in Individuals with Profound Sensorineural Hearing Impairment. Genes (Basel) 2020; 11:genes11060687. [PMID: 32585897 PMCID: PMC7349314 DOI: 10.3390/genes11060687] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/16/2020] [Accepted: 06/20/2020] [Indexed: 01/15/2023] Open
Abstract
Congenital hearing impairment is a sensory disorder that is genetically highly heterogeneous. By performing exome sequencing in two families with congenital nonsyndromic profound sensorineural hearing loss (SNHL), we identified autosomal dominantly inherited missense variants [p.(Asn283Ser); p.(Thr116Ile)] in GREB1L, a neural crest regulatory molecule. The p.(Thr116Ile) variant was also associated with bilateral cochlear aplasia and cochlear nerve aplasia upon temporal bone imaging, an ultra-rare phenotype previously seen in patients with de novo GREB1L variants. An important role of GREB1L in normal ear development has also been demonstrated by greb1l-/- zebrafish, which show an abnormal sensory epithelia innervation. Last, we performed a review of all disease-associated variation described in GREB1L, as it has also been implicated in renal, bladder and genital malformations. We show that the spectrum of features associated with GREB1L is broad, variable and with a high level of reduced penetrance, which is typically characteristic of neurocristopathies. So far, seven GREB1L variants (14%) have been associated with ear-related abnormalities. In conclusion, these results show that autosomal dominantly inherited variants in GREB1L cause profound SNHL. Furthermore, we provide an overview of the phenotypic spectrum associated with GREB1L variants and strengthen the evidence of the involvement of GREB1L in human hearing.
Collapse
|
31
|
Jacquinet A, Boujemla B, Fasquelle C, Thiry J, Josse C, Lumaka A, Brischoux-Boucher E, Dubourg C, David V, Pasquier L, Lehman A, Morcel K, Guerrier D, Bours V. GREB1L variants in familial and sporadic hereditary urogenital adysplasia and Mayer-Rokitansky-Kuster-Hauser syndrome. Clin Genet 2020; 98:126-137. [PMID: 32378186 DOI: 10.1111/cge.13769] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/22/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022]
Abstract
Congenital uterine anomalies (CUA) may have major impacts on the health and social well-being of affected individuals. Their expressivity is variable, with the most severe end of the spectrum being the absence of any fully or unilaterally developed uterus (aplastic uterus), which is a major feature in Mayer-Rokitansky-Kuster-Hauser syndrome (MRKH). So far, etiologies of CUA remain largely unknown. As reports of familial occurrences argue for strong genetic contributors in some cases, we performed whole exome sequencing in nine multiplex families with recurrence of uterine and kidney malformations, a condition called hereditary urogenital adysplasia. Heterozygous likely causative variants in the gene GREB1L were identified in four of these families, confirming GREB1L as an important gene for proper uterine and kidney development. The apparent mode of inheritance was autosomal dominant with incomplete penetrance. The four families included fetuses with uterovaginal aplasia and bilateral renal agenesis, highlighting the importance to investigate GREB1L in such phenotypes. Subsequent sequencing of the gene in a cohort of 68 individuals with MRKH syndrome or uterine malformation (mostly sporadic cases) identified six additional variants of unknown significance. We therefore conclude that heterozygous GREB1L variants contribute to MRKH syndrome and this probably requires additional genetic or environmental factors for full penetrance.
Collapse
Affiliation(s)
- Adeline Jacquinet
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.,Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Bouchra Boujemla
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Corinne Fasquelle
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium
| | - Jerôme Thiry
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | - Claire Josse
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium.,Medical Oncology, Centre Hospitalier Universitaire CHU Liege, Liège, Belgium
| | - Aimé Lumaka
- Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Christèle Dubourg
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France.,Department of Molecular Genetics and Genomics, Université de Rennes, CHU Rennes, Rennes, France
| | - Véronique David
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France.,Department of Molecular Genetics and Genomics, Université de Rennes, CHU Rennes, Rennes, France
| | - Laurent Pasquier
- Department of Medical Genetics, CLAD Ouest, Université de Rennes, CHU Rennes, Rennes, France
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, BC Children's Hospital and BC Women's Hospital, Vancouver, British Columbia, Canada
| | - Karine Morcel
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France
| | - Daniel Guerrier
- Univ. Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, Rennes, France
| | - Vincent Bours
- Center for Human Genetics, Centre Hospitalier Universitaire, Liège, Belgium.,Human Genetic Laboratory, GIGA Institute, University of Liège, Liège, Belgium
| |
Collapse
|
32
|
Tang J, Zhou C, Shi H, Mo Y, Tan W, Sun T, Zhu J, Li Q, Li H, Li Y, Wang S, Hong Y, Li N, Zeng Q, Tan J, Ma W, Luo L. Prenatal diagnosis of skeletal dysplasias using whole exome sequencing in China. Clin Chim Acta 2020; 507:187-193. [PMID: 32360156 DOI: 10.1016/j.cca.2020.04.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/04/2020] [Accepted: 04/27/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Skeletal dysplasias account for nearly 10% of fetal structural malformations detected by ultrasonography. This clinically heterogeneous group of genetic anomaly includes at least 461 genetic skeletal disorders with extreme clinical, phenotypic, and genetic heterogeneities, thus, significantly complicates accurate diagnosis. Researches have used whole exome sequencing (WES) for prenatal molecular diagnoses of skeletal dysplasias, however, data are still limited. METHODS DNA extracted from umbilical cord blood or amniocytes from fetuses suspected of skeletal dysplasias based on ultrasound evaluations were analyzed by WES. Blood samples were taken from the parents of the positive fetuses for co-segregation analysis using Sanger sequencing. RESULT Definitive molecular diagnosis was made in 6/8 (75%) cases, comprised of 5 de novo disease-causing changes in 3 genes (FGFR3, COL2A1, and COL1A2) and one proband with a biallelic deficiency for Lamin B Receptor(LBR),and including 3 novel variants. All fetuses had no detectable copy number variation (CNV) from sequencing results. CONCLUSIONS Our study suggests that WES is an efficient approach for prenatal diagnosis of fetuses suspected of skeletal abnormalities and contributes to parental genetics counseling and pregnancy management.
Collapse
Affiliation(s)
- Jia Tang
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China; Department of Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510080, China.
| | - Chenglong Zhou
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China; Halo Genetics, Guangzhou, Guangdong 510000, China
| | - Haihong Shi
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China; Halo Genetics, Guangzhou, Guangdong 510000, China
| | - Yuying Mo
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Weilan Tan
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Tielan Sun
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Jinling Zhu
- Department of Biology, School of Basic Medicine, Jiamusi University, Jiamusi, Heilongjiang 154007, China
| | - Qing Li
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Hui Li
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Yuping Li
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Songbai Wang
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Yan Hong
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Ning Li
- Halo Genetics, Guangzhou, Guangdong 510000, China
| | - Qinlong Zeng
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Jieliang Tan
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, Guangdong 529000, China
| | - Wei Ma
- Department of Biology, School of Basic Medicine, Jiamusi University, Jiamusi, Heilongjiang 154007, China
| | - Liangping Luo
- Department of Medical Imaging Center, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510080, China.
| |
Collapse
|
33
|
Darlow JM, Dobson MG, Green AJ, Puri P, Barton DE. Investigation of DNA variants specific to ROBO2 Isoform 'a' in Irish vesicoureteric reflux patients reveals marked CpG island variation. Sci Rep 2020; 10:2265. [PMID: 32041992 PMCID: PMC7010700 DOI: 10.1038/s41598-020-58818-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/29/2019] [Indexed: 11/09/2022] Open
Abstract
ROBO2 gene disruption causes vesicoureteric reflux (VUR) amongst other congenital anomalies. Several VUR patient cohorts have been screened for variants in the ubiquitously expressed transcript, ROBO2b, but, apart from low levels in a few adult tissues, ROBO2a expression is confined to the embryo, and might be more relevant to VUR, a developmental disorder. ROBO2a has an alternative promoter and two alternative exons which replace the first exon of ROBO2b. We screened probands from 251 Irish VUR families for DNA variants in these. The CpG island of ROBO2a, which includes the non-coding first exon, was found to contain a run of six variants abolishing/creating CpG dinucleotides, including a novel variant, present in the VUR cases in one family, that was not present in 592 healthy Irish controls. In three of these positions, the CpG was created by the non-reference allele, and the reference allele was not the nucleotide that would result from spontaneous deamination of methylcytosine to thymine, suggesting that there might have been selection for variability in number of CpGs in this island. This is in marked contrast to the CpG island at the start of ROBO2b, which only contained a single variant that abolishes a CpG.
Collapse
Affiliation(s)
- John M Darlow
- Department of Clinical Genetics, Dublin, Ireland. .,National Children's Research Centre, Dublin, Ireland.
| | - Mark G Dobson
- Department of Clinical Genetics, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Andrew J Green
- Department of Clinical Genetics, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin - all at Our Lady's Children's Hospital, Crumlin, (now renamed 'Children's Health Ireland at Crumlin'), Crumlin, Dublin, D12 N512, Ireland
| | - Prem Puri
- National Children's Research Centre, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin - all at Our Lady's Children's Hospital, Crumlin, (now renamed 'Children's Health Ireland at Crumlin'), Crumlin, Dublin, D12 N512, Ireland.,Beacon Hospital, Beacon Court, Sandyford, Dublin, D18 AK68, Ireland
| | - David E Barton
- Department of Clinical Genetics, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin - all at Our Lady's Children's Hospital, Crumlin, (now renamed 'Children's Health Ireland at Crumlin'), Crumlin, Dublin, D12 N512, Ireland
| |
Collapse
|
34
|
Bui TPH, Nguyen NT, Ngo VD, Nguyen HN, Ly TTH, Do HD, Huynh MT. Novel compound heterozygous TMEM67 variants in a Vietnamese family with Joubert syndrome: a case report. BMC MEDICAL GENETICS 2020; 21:18. [PMID: 32000717 PMCID: PMC6993522 DOI: 10.1186/s12881-020-0962-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/24/2020] [Indexed: 11/10/2022]
Abstract
Background Joubert syndrome is a genetically heterogeneous autosomal recessive ciliopathy characterized by the combination of hypoplasia/aplasia of the cerebellar vermis, thickened and elongated superior cerebellar peduncles and a deep interpeduncular fossa, known as “molar tooth sign” associated with hypotonia, respiratory control disturbances and abnormal eye movements. To date, pathogenic variants in over 35 genes are known to cause autosomal recessive Joubert Syndrome, while one gene is associated with X-linked recessive inheritance. Case presentation We describe here a non-consanguineous Vietnamese family with Joubert syndrome, a fetus and 10-year-old developmentally delayed boy. Ultrasonography showed ventriculomegaly at 26 + 6 weeks of gestation in the fetus. The 10-year-old-boy was diagnosed with cerebral palsy of unknown origin. Clinical physical examination at the age of 10, he showed clinical features of Joubert syndrome including typical facial dysmorphism, ataxia, severe psychomotor delay, oculomotor apraxia and molar tooth sign on brain MRI. Whole exome sequencing analysis identified a novel compound heterozygous c.725A > G p.Asn242Ser and c.313-3 T > G p.Lys105Valfs*16 TMEM67 variant in the proband and the affected fetus. These two variants were inherited from each parent and confirmed by Sanger sequencing. The variant c.725A > G p.Asn242Ser was previously documented in patients with JS, the novel splice-site c.313-3 T > G p.Lys105Valfs*16 TMEM67 variant produced an aberrant transcript with the loss of four nucleotides of exon 03. Conclusion This study confirms the diagnosis of Joubert syndrome in a Vietnamese family and expands the mutational spectrum of TMEM67 sequence variations. We also highlight the importance of molecular approaches to unravel underlying mechanisms of human genetic disorders. Early precise diagnosis could help provide further accurate genetic counseling for recurrence-risk assessment, future diagnostic option, management as well as treatment guidance for rare disorders.
Collapse
Affiliation(s)
- Thi Phuong Hoa Bui
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Ngoc Tu Nguyen
- Fetal Medicine Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Van Doan Ngo
- Diagnostic Imaging Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Hoai-Nghia Nguyen
- Center for Molecular Medicine, University of Medicine and Pharmacy, Ho Chi Minh city, Vietnam
| | - Thi Thanh Ha Ly
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Huy Duong Do
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam
| | - Minh-Tuan Huynh
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Vietnam.
| |
Collapse
|
35
|
Aggarwal S, Vineeth VS, Das Bhowmik A, Tandon A, Kulkarni A, Narayanan DL, Bhattacherjee A, Dalal A. Exome sequencing for perinatal phenotypes: The significance of deep phenotyping. Prenat Diagn 2019; 40:260-273. [PMID: 31742715 DOI: 10.1002/pd.5616] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To ascertain the performance of exome sequencing (ES) technology for determining the etiological basis of abnormal perinatal phenotypes and to study the impact of comprehensive phenotyping on variant prioritization. METHODS A carefully selected cohort of 32/204 fetuses with abnormal perinatal phenotypes following postmortem/postnatal deep phenotyping underwent ES to identify a causative variant for the fetal phenotype. A retrospective comparative analysis of the prenatal versus postmortem/postnatal phenotype-based variant prioritization was performed with aid of Phenolyzer software. A review of selected literature reports was done to examine the completeness of phenotypic information for cases in those reports and how it impacted the performance of fetal ES. RESULTS In 18/32 (56%) fetuses, a pathogenic/likely pathogenic variant was identified. This included novel genotype-phenotype associations, expanded prenatal phenotypes of known Mendelian disorders and dual Mendelian diagnoses. The retrospective analysis revealed that the putative diagnostic variant could not be identified on basis of prenatal findings alone in 15/22 (68%) cases, indicating the importance of comprehensive postmortem/postnatal phenotype information. Literature review was supportive of these findings but could not be conclusive due to marked heterogeneity of involved studies. CONCLUSION Comprehensive phenotyping is essential for improving diagnostic performance and facilitating identification of novel genotype-phenotype associations in perinatal cohorts undergoing ES.
Collapse
Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | - Aneek Das Bhowmik
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwani Tandon
- Department of Pathology, All India Institute of Medical Sciences, Bhopal, India
| | | | - Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Amrita Bhattacherjee
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India.,Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
36
|
Talati AN, Webster CM, Vora NL. Prenatal genetic considerations of congenital anomalies of the kidney and urinary tract (CAKUT). Prenat Diagn 2019; 39:679-692. [PMID: 31343747 DOI: 10.1002/pd.5536] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 12/20/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) constitute 20% of all congenital malformations occurring in one in 500 live births. Worldwide, CAKUT are responsible for 40% to 50% of pediatric and 7% of adult end-stage renal disease. Pathogenic variants in genes causing CAKUT include monogenic diseases such as polycystic kidney disease and ciliopathies, as well as syndromes that include isolated kidney disease in conjunction with other abnormalities. Prenatal diagnosis most often occurs using ultrasonography; however, further genetic diagnosis may be made using a variety of testing strategies. Family history and pathologic examination can also provide information to improve the ability to make a prenatal diagnosis of CAKUT. Here, we provide a comprehensive overview of genetic considerations in the prenatal diagnosis of CAKUT disorders. Specifically, we discuss monogenic causes of CAKUT, associated ultrasound characteristics, and considerations for genetic diagnosis, antenatal care, and postnatal care.
Collapse
Affiliation(s)
- Asha N Talati
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Carolyn M Webster
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, DRAFT, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
37
|
de Koning MA, Haak MC, Adama van Scheltema PN, Peeters-Scholte CMPCD, Koopmann TT, Nibbeling EAR, Aten E, den Hollander NS, Ruivenkamp CAL, Hoffer MJV, Santen GWE. From diagnostic yield to clinical impact: a pilot study on the implementation of prenatal exome sequencing in routine care. Genet Med 2019; 21:2303-2310. [PMID: 30918357 DOI: 10.1038/s41436-019-0499-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/14/2019] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Exome sequencing (ES) is an efficient tool to diagnose genetic disorders postnatally. Recent studies show that it may have a considerable diagnostic yield in fetuses with structural anomalies on ultrasound. We report on the clinical impact of the implementation of prenatal ES (pES) for ongoing pregnancies in routine care. METHODS We retrospectively analyzed the impact of pES on pregnancy outcome and pre- or perinatal management in the first 22 patients counseled for pES because of one or more structural anomalies on fetal ultrasound. RESULTS In two cases, a diagnosis was made by chromosomal microarray analysis after ES counseling. The remaining 20 cases were divided in three groups: (1) pES to aid parental decision making (n = 12), (2) pES in the context of late pregnancy termination requests (n = 5), and (3) pES to guide pre- or perinatal management (n = 3). pES had a clinical impact in 75% (9/12), 40% (2/5), and 100% (3/3) respectively, showing an overall clinical impact of pES of 70% (14/20). CONCLUSION We show that clinical implementation of pES is feasible and affects parental decision making or pre- and perinatal management supporting further implementation of ES in the prenatal setting.
Collapse
Affiliation(s)
- Maayke A de Koning
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique C Haak
- Department of Obstetrics and Fetal Medicine, Leiden University Medical Centre, Leiden, the Netherlands
| | | | | | - Tamara T Koopmann
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands.
| |
Collapse
|
38
|
Kosfeld A, Martens H, Hennies I, Haffner D, Weber RG. Kongenitale Anomalien der Nieren und ableitenden Harnwege (CA KUT). MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-018-0226-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Zusammenfassung
Der Begriff CAKUT (Congenital Anomalies of the Kidney and Urinary Tract) bezeichnet diverse angeborene Fehlbildungen der Nieren und ableitenden Harnwege. Da alle CAKUT-Phänotypen zusammengenommen etwa 15–30 % aller pränatal diagnostizierten Fehlbildungen ausmachen und etwa 40 % der Fälle mit terminalem Nierenversagen bei Kindern und Jugendlichen verursachen, sind diese Anomalien epidemiologisch hochrelevant. Die Diagnosestellung erfolgt mit radiologischen Verfahren, insbesondere mit Ultraschall, wobei bei vielen Patienten eine Kombination verschiedener CAKUT-Phänotypen nachgewiesen wird. CAKUT tritt zu etwa 85 % sporadisch auf, zu etwa 15 % familiär. Das Vererbungsmuster ist häufig dominant, kann aber auch rezessiv sein. CAKUT kann isoliert auftreten, aber auch als Teil einer syndromalen Erkrankung. Variable Expressivität und inkomplette Penetranz sind bei CAKUT häufig. CAKUT ist genetisch sehr heterogen. Im Mausmodell wurden bislang über 180 CAKUT-assoziierte Gene beschrieben. Da Mutationen in den etwa 50 bisher bekannten humanen CAKUT-Genen nur ca. 20 % der CAKUT-Fälle erklären und sich verschiedene chromosomale Aberrationen wie Mikrodeletionen in weiteren ca. 15 % der Patienten insbesondere mit syndromalen CAKUT finden, sind exom-/genomweite Screeningverfahren für die Aufklärung genetischer CAKUT-Ursachen besonders geeignet. Bei sporadischen Fällen ist eine Trio-basierte Analyse der Exome/Genome von Patienten-Eltern-Trios zur Identifizierung von De-novo-Aberrationen und biallelischen Varianten vielversprechend. Eine Abklärung der genetischen Ursache ist für die Präzisierung von Wiederholungsrisiken sowie eine gezielte Untersuchung von CAKUT-Patienten im Hinblick auf extrarenale Phänotypen von klinischer Bedeutung.
Collapse
Affiliation(s)
- Anne Kosfeld
- Aff1 0000 0000 9529 9877 grid.10423.34 Institut für Humangenetik Medizinische Hochschule Hannover Carl-Neuberg-Straße 1 30625 Hannover Deutschland
| | - Helge Martens
- Aff1 0000 0000 9529 9877 grid.10423.34 Institut für Humangenetik Medizinische Hochschule Hannover Carl-Neuberg-Straße 1 30625 Hannover Deutschland
| | - Imke Hennies
- Aff2 0000 0000 9529 9877 grid.10423.34 Klinik für Pädiatrische Nieren-, Leber- und Stoffwechselerkrankungen Medizinische Hochschule Hannover Hannover Deutschland
| | - Dieter Haffner
- Aff2 0000 0000 9529 9877 grid.10423.34 Klinik für Pädiatrische Nieren-, Leber- und Stoffwechselerkrankungen Medizinische Hochschule Hannover Hannover Deutschland
| | - Ruthild G. Weber
- Aff1 0000 0000 9529 9877 grid.10423.34 Institut für Humangenetik Medizinische Hochschule Hannover Carl-Neuberg-Straße 1 30625 Hannover Deutschland
| |
Collapse
|
39
|
Normand EA, Braxton A, Nassef S, Ward PA, Vetrini F, He W, Patel V, Qu C, Westerfield LE, Stover S, Dharmadhikari AV, Muzny DM, Gibbs RA, Dai H, Meng L, Wang X, Xiao R, Liu P, Bi W, Xia F, Walkiewicz M, Van den Veyver IB, Eng CM, Yang Y. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Med 2018; 10:74. [PMID: 30266093 PMCID: PMC6162951 DOI: 10.1186/s13073-018-0582-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background Exome sequencing is now being incorporated into clinical care for pediatric and adult populations, but its integration into prenatal diagnosis has been more limited. One reason for this is the paucity of information about the clinical utility of exome sequencing in the prenatal setting. Methods We retrospectively reviewed indications, results, time to results (turnaround time, TAT), and impact of exome results for 146 consecutive “fetal exomes” performed in a clinical diagnostic laboratory between March 2012 and November 2017. We define a fetal exome as one performed on a sample obtained from a fetus or a product of conception with at least one structural anomaly detected by prenatal imaging or autopsy. Statistical comparisons were performed using Fisher’s exact test. Results Prenatal exome yielded an overall molecular diagnostic rate of 32% (n = 46/146). Of the 46 molecular diagnoses, 50% were autosomal dominant disorders (n = 23/46), 41% were autosomal recessive disorders (n = 19/46), and 9% were X-linked disorders (n = 4/46). The molecular diagnostic rate was highest for fetuses with anomalies affecting multiple organ systems and for fetuses with craniofacial anomalies. Out of 146 cases, a prenatal trio exome option designed for ongoing pregnancies was performed on 62 fetal specimens, resulting in a diagnostic yield of 35% with an average TAT of 14 days for initial reporting (excluding tissue culture time). The molecular diagnoses led to refined recurrence risk estimates, altered medical management, and informed reproductive planning for families. Conclusion Exome sequencing is a useful diagnostic tool when fetal structural anomalies suggest a genetic etiology, but other standard prenatal genetic tests did not provide a diagnosis. Electronic supplementary material The online version of this article (10.1186/s13073-018-0582-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Salma Nassef
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Lauren E Westerfield
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Stover
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Present address: The National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
| |
Collapse
|
40
|
Impact of next generation sequencing on our understanding of CAKUT. Semin Cell Dev Biol 2018; 91:104-110. [PMID: 30172048 DOI: 10.1016/j.semcdb.2018.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 08/16/2018] [Accepted: 08/28/2018] [Indexed: 12/29/2022]
Abstract
Congenital abnormalities of the kidney and urinary tract (CAKUT) form the leading cause of pediatric end-stage renal disease. Knowledge on the molecular mechanisms that underlie CAKUT leads to the improvement of DNA diagnostics and counseling regarding prognosis and recurrence risk estimation for CAKUT patients and their relatives. Implementation of next generation sequencing in research and diagnostic settings has led to the identification of the molecular basis of many developmental diseases. In this review, we summarize the efforts on next generation sequencing in CAKUT research and we discuss how next generation sequencing added to our understanding of CAKUT genetics. Although next generation sequencing has certainly proven to be a game changer in the field of disease gene identification and novel CAKUT-causing gene variants have been identified, most CAKUT cases still remain unsolved. Occurring with genetic and phenotypic heterogeneity along with incomplete penetrance, the identification of CAKUT etiology poses many challenges. We see great potential for combined -omics approaches that include next generation sequencing in the identification of CAKUT-specific biomarkers, which is necessary to optimize the care for CAKUT patients.
Collapse
|
41
|
Vora NL, Hui L. Next-generation sequencing and prenatal 'omics: advanced diagnostics and new insights into human development. Genet Med 2018; 20:791-799. [PMID: 30032162 PMCID: PMC6123255 DOI: 10.1038/s41436-018-0087-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/01/2018] [Indexed: 12/16/2022] Open
Abstract
Prenatal genetics has evolved over the last decade to include application of new 'omics technologies to improve perinatal care. The clinical utility of these technologies when applied to direct fetal specimens from amniocentesis or chorionic villus sampling is being explored. In this review, we provide an overview of use of prenatal exome sequencing and role in evaluation of the structurally abnormal fetus, potential applications of genome sequencing, and finally, use of transcriptomics to assess placental and fetal well-being.
Collapse
Affiliation(s)
- Neeta L Vora
- Department of Obstetrics & Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Lisa Hui
- Department of Obstetrics & Gynaecology, University of Melbourne, Heidelberg, Victoria, Australia
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia
- Murdoch Children's Research Institute, Public Health Genetics Group, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, The Northern Hospital, Epping, Victoria, Australia
| |
Collapse
|