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Hays T, Hernan R, Disco M, Griffin EL, Goldshtrom N, Vargas D, Krishnamurthy G, Bomback M, Rehman AU, Wilson AT, Guha S, Phadke S, Okur V, Robinson D, Felice V, Abhyankar A, Jobanputra V, Chung WK. Implementation of Rapid Genome Sequencing for Critically Ill Infants With Complex Congenital Heart Disease. Circ Genom Precis Med 2023; 16:415-420. [PMID: 37417234 DOI: 10.1161/circgen.122.004050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/16/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Rapid genome sequencing (rGS) has been shown to improve care of critically ill infants. Congenital heart disease (CHD) is a leading cause of infant mortality and is often caused by genetic disorders, yet the utility of rGS has not been prospectively studied in this population. METHODS We conducted a prospective evaluation of rGS to improve the care of infants with complex CHD in our cardiac neonatal intensive care unit. RESULTS In a cohort of 48 infants with complex CHD, rGS diagnosed 14 genetic disorders in 13 (27%) individuals and led to changes in clinical management in 8 (62%) cases with diagnostic results. These included 2 cases in whom genetic diagnoses helped avert intensive, futile interventions before cardiac neonatal intensive care unit discharge, and 3 cases in whom eye disease was diagnosed and treated in early childhood. CONCLUSIONS Our study provides the first prospective evaluation of rGS for infants with complex CHD to our knowledge. We found that rGS diagnosed genetic disorders in 27% of cases and led to changes in management in 62% of cases with diagnostic results. Our model of care depended on coordination between neonatologists, cardiologists, surgeons, geneticists, and genetic counselors. These findings highlight the important role of rGS in CHD and demonstrate the need for expanded study of how to implement this resource to a broader population of infants with CHD.
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Affiliation(s)
- Thomas Hays
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Rebecca Hernan
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Michele Disco
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Emily L Griffin
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
| | - Nimrod Goldshtrom
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Diana Vargas
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Ganga Krishnamurthy
- Division of Neonatology, Department of Pediatrics (T.H., N.G., D.V., G.K.), Columbia University Irving Medical Center, New York, NY
| | - Miles Bomback
- Feinberg School of Medicine, Northwestern University, Chicago, IL (M.B.)
| | - Atteeq U Rehman
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Amanda T Wilson
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Saurav Guha
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Shruti Phadke
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Volkan Okur
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Dino Robinson
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Vanessa Felice
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Avinash Abhyankar
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Vaidehi Jobanputra
- Department of Pathology & Cell Biology (V.J.), Columbia University Irving Medical Center, New York, NY
- New York Genome Center, New York, NY (A.U.R., A.T.W., S.G., S.P., V.O., D.R., V.F., A.A., V.J.)
| | - Wendy K Chung
- Division of Genetics, Department of Pediatrics (R.H., M.D., E.L.G., W.K.C.), Columbia University Irving Medical Center, New York, NY
- Department of Medicine (W.K.C.), Columbia University Irving Medical Center, New York, NY
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2
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Abul-Husn NS, Marathe PN, Kelly NR, Bonini KE, Sebastin M, Odgis JA, Abhyankar A, Brown K, Di Biase M, Gallagher KM, Guha S, Ioele N, Okur V, Ramos MA, Rodriguez JE, Rehman AU, Thomas-Wilson A, Edelmann L, Zinberg RE, Diaz GA, Greally JM, Jobanputra V, Suckiel SA, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD. Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients. Genet Med 2023; 25:100880. [PMID: 37158195 PMCID: PMC10789486 DOI: 10.1016/j.gim.2023.100880] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023] Open
Abstract
PURPOSE Adoption of genome sequencing (GS) as a first-line test requires evaluation of its diagnostic yield. We evaluated the GS and targeted gene panel (TGP) testing in diverse pediatric patients (probands) with suspected genetic conditions. METHODS Probands with neurologic, cardiac, or immunologic conditions were offered GS and TGP testing. Diagnostic yield was compared using a fully paired study design. RESULTS A total of 645 probands (median age 9 years) underwent genetic testing, and 113 (17.5%) received a molecular diagnosis. Among 642 probands with both GS and TGP testing, GS yielded 106 (16.5%) and TGPs yielded 52 (8.1%) diagnoses (P < .001). Yield was greater for GS vs TGPs in Hispanic/Latino(a) (17.2% vs 9.5%, P < .001) and White/European American (19.8% vs 7.9%, P < .001) but not in Black/African American (11.5% vs 7.7%, P = .22) population groups by self-report. A higher rate of inconclusive results was seen in the Black/African American (63.8%) vs White/European American (47.6%; P = .01) population group. Most causal copy number variants (17 of 19) and mosaic variants (6 of 8) were detected only by GS. CONCLUSION GS may yield up to twice as many diagnoses in pediatric patients compared with TGP testing but not yet across all population groups.
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Affiliation(s)
- Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe, Inc., Sunnyvale, CA
| | - Priya N Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Illumina Incorporated, San Diego, CA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katie M Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Invitae Corporation, San Francisco, CA
| | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Nicolette Ioele
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Memorial Sloan Kettering Cancer Center, New York, NY
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Michelle A Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jessica E Rodriguez
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Randi E Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; iECURE Incorporated, Philadelphia, PA
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Sabrina A Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa P Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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3
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Wojcik MH, Lemire G, Zaki MS, Wissman M, Win W, White S, Weisburd B, Waddell LB, Verboon JM, VanNoy GE, Töpf A, Tan TY, Straub V, Stenton SL, Snow H, Singer-Berk M, Silver J, Shril S, Seaby EG, Schneider R, Sankaran VG, Sanchis-Juan A, Russell KA, Reinson K, Ravenscroft G, Pierce EA, Place EM, Pajusalu S, Pais L, Õunap K, Osei-Owusu I, Okur V, Oja KT, O'Leary M, O'Heir E, Morel C, Marchant RG, Mangilog BE, Madden JA, MacArthur D, Lovgren A, Lerner-Ellis JP, Lin J, Laing N, Hildebrandt F, Groopman E, Goodrich J, Gleeson JG, Ghaoui R, Genetti CA, Gazda HT, Ganesh VS, Ganapathy M, Gallacher L, Fu J, Evangelista E, England E, Donkervoort S, DiTroia S, Cooper ST, Chung WK, Christodoulou J, Chao KR, Cato LD, Bujakowska KM, Bryen SJ, Brand H, Bonnemann C, Beggs AH, Baxter SM, Agrawal PB, Talkowski M, Austin-Tse C, Rehm HL, O'Donnell-Luria A. Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis. medRxiv 2023:2023.08.08.23293829. [PMID: 38328047 PMCID: PMC10849673 DOI: 10.1101/2023.08.08.23293829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Background Causal variants underlying rare disorders may remain elusive even after expansive gene panels or exome sequencing (ES). Clinicians and researchers may then turn to genome sequencing (GS), though the added value of this technique and its optimal use remain poorly defined. We therefore investigated the advantages of GS within a phenotypically diverse cohort. Methods GS was performed for 744 individuals with rare disease who were genetically undiagnosed. Analysis included review of single nucleotide, indel, structural, and mitochondrial variants. Results We successfully solved 218/744 (29.3%) cases using GS, with most solves involving established disease genes (157/218, 72.0%). Of all solved cases, 148 (67.9%) had previously had non-diagnostic ES. We systematically evaluated the 218 causal variants for features requiring GS to identify and 61/218 (28.0%) met these criteria, representing 8.2% of the entire cohort. These included small structural variants (13), copy neutral inversions and complex rearrangements (8), tandem repeat expansions (6), deep intronic variants (15), and coding variants that may be more easily found using GS related to uniformity of coverage (19). Conclusion We describe the diagnostic yield of GS in a large and diverse cohort, illustrating several types of pathogenic variation eluding ES or other techniques. Our results reveal a higher diagnostic yield of GS, supporting the utility of a genome-first approach, with consideration of GS as a secondary or tertiary test when higher-resolution structural variant analysis is needed or there is a strong clinical suspicion for a condition and prior targeted genetic testing has been negative.
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Bonini KE, Thomas-Wilson A, Marathe PN, Sebastin M, Odgis JA, Biase MD, Kelly NR, Ramos MA, Insel BJ, Scarimbolo L, Rehman AU, Guha S, Okur V, Abhyankar A, Phadke S, Nava C, Gallagher KM, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Horowitz CR, Kenny EE, Wasserstein M, Gelb BD, Jobanputra V. Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program. Clin Genet 2023; 104:210-225. [PMID: 37334874 PMCID: PMC10505482 DOI: 10.1111/cge.14365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 06/21/2023]
Abstract
Copy number variations (CNVs) play a significant role in human disease. While chromosomal microarray has traditionally been the first-tier test for CNV detection, use of genome sequencing (GS) is increasing. We report the frequency of CNVs detected with GS in a diverse pediatric cohort from the NYCKidSeq program and highlight specific examples of its clinical impact. A total of 1052 children (0-21 years) with neurodevelopmental, cardiac, and/or immunodeficiency phenotypes received GS. Phenotype-driven analysis was used, resulting in 183 (17.4%) participants with a diagnostic result. CNVs accounted for 20.2% of participants with a diagnostic result (37/183) and ranged from 0.5 kb to 16 Mb. Of participants with a diagnostic result (n = 183) and phenotypes in more than one category, 5/17 (29.4%) were solved by a CNV finding, suggesting a high prevalence of diagnostic CNVs in participants with complex phenotypes. Thirteen participants with a diagnostic CNV (35.1%) had previously uninformative genetic testing, of which nine included a chromosomal microarray. This study demonstrates the benefits of GS for reliable detection of CNVs in a pediatric cohort with variable phenotypes.
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Affiliation(s)
- Katherine E. Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Priya N. Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A. Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beverly J. Insel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Laura Scarimbolo
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY
| | | | - Shruti Phadke
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Caroline Nava
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A. Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Sabrina A. Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
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5
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Abul-Husn NS, Marathe PN, Kelly NR, Bonini KE, Sebastin M, Odgis JA, Abhyankar A, Brown K, Di Biase M, Gallagher KM, Guha S, Ioele N, Okur V, Ramos MA, Rodriguez JE, Rehman AU, Thomas-Wilson A, Edelmann L, Zinberg RE, Diaz GA, Greally JM, Jobanputra V, Suckiel SA, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD. Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients. medRxiv 2023:2023.03.18.23286992. [PMID: 36993157 PMCID: PMC10055570 DOI: 10.1101/2023.03.18.23286992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Purpose Adoption of genome sequencing (GS) as a first-line test requires evaluation of its diagnostic yield. We evaluated the GS and targeted gene panel (TGP) testing in diverse pediatric patients (probands) with suspected genetic conditions. Methods Probands with neurologic, cardiac, or immunologic conditions were offered GS and TGP testing. Diagnostic yield was compared using a fully paired study design. Results 645 probands (median age 9 years) underwent genetic testing, and 113 (17.5%) received a molecular diagnosis. Among 642 probands with both GS and TGP testing, GS yielded 106 (16.5%) and TGPs yielded 52 (8.1%) diagnoses ( P < .001). Yield was greater for GS vs . TGPs in Hispanic/Latino(a) (17.2% vs . 9.5%, P < .001) and White/European American (19.8% vs . 7.9%, P < .001), but not in Black/African American (11.5% vs . 7.7%, P = .22) population groups by self-report. A higher rate of inconclusive results was seen in the Black/African American (63.8%) vs . White/European American (47.6%; P = .01) population group. Most causal copy number variants (17 of 19) and mosaic variants (6 of 8) were detected only by GS. Conclusion GS may yield up to twice as many diagnoses in pediatric patients compared to TGP testing, but not yet across all population groups.
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6
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Odgis JA, Gallagher KM, Rehman AU, Marathe P, Bonini KE, Sebastin M, Di Biase M, Brown K, Kelly NR, Ramos MA, Thomas-Wilson A, Guha S, Okur V, Ganapathi M, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Jobanputra V, Horowitz CR, Kenny EE, Wasserstein MP, Gelb BD. Detection of mosaic variants using genome sequencing in a large pediatric cohort. Am J Med Genet A 2023; 191:699-710. [PMID: 36563179 PMCID: PMC10266700 DOI: 10.1002/ajmg.a.63062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
The increased use of next-generation sequencing has expanded our understanding of the involvement and prevalence of mosaicism in genetic disorders. We describe a total of eleven cases: nine in which mosaic variants detected by genome sequencing (GS) and/or targeted gene panels (TGPs) were considered to be causative for the proband's phenotype, and two of apparent parental mosaicism. Variants were identified in the following genes: PHACTR1, SCN8A, KCNT1, CDKL5, NEXMIF, CUX1, TSC2, GABRB2, and SMARCB1. In addition, we identified one large duplication including three genes, UBE3A, GABRB3, and MAGEL2, and one large deletion including deletion of ARFGAP1, EEF1A2, CHRNA4, and KCNQ2. All patients were enrolled in the NYCKidSeq study, a research program studying the communication of genomic information in clinical care, as well as the clinical utility and diagnostic yield of GS for children with suspected genetic disorders in diverse populations in New York City. We observed variability in the correlation between reported variant allele fraction and the severity of the patient's phenotype, although we were not able to determine the mosaicism percentage in clinically relevant tissue(s). Although our study was not sufficiently powered to assess differences in mosaicism detection between the two testing modalities, we saw a trend toward better detection by GS as compared with TGP testing. This case series supports the importance of mosaicism in childhood-onset genetic conditions and informs guidelines for laboratory and clinical interpretation of mosaic variants detected by GS.
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Affiliation(s)
- Jacqueline A. Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Atteeq U. Rehman
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Priya Marathe
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine E. Bonini
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | | | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noura S. Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George A. Diaz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sabrina A. Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E. Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P. Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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7
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Unni P, Friend J, Weinberg J, Okur V, Hochscherf J, Dominguez I. Predictive functional, statistical and structural analysis of CSNK2A1 and CSNK2B variants linked to neurodevelopmental diseases. Front Mol Biosci 2022; 9:851547. [PMID: 36310603 PMCID: PMC9608649 DOI: 10.3389/fmolb.2022.851547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/29/2022] [Indexed: 12/02/2022] Open
Abstract
Okur-Chung Neurodevelopmental Syndrome (OCNDS) and Poirier-Bienvenu Neurodevelopmental Syndrome (POBINDS) were recently identified as rare neurodevelopmental disorders. OCNDS and POBINDS are associated with heterozygous mutations in the CSNK2A1 and CSNK2B genes which encode CK2α, a serine/threonine protein kinase, and CK2β, a regulatory protein, respectively, which together can form a tetrameric enzyme called protein kinase CK2. A challenge in OCNDS and POBINDS is to understand the genetic basis of these diseases and the effect of the various CK2⍺ and CK2β mutations. In this study we have collected all variants available to date in CSNK2A1 and CSNK2B, and identified hotspots. We have investigated CK2⍺ and CK2β missense mutations through prediction programs which consider the evolutionary conservation, functionality and structure or these two proteins, compared these results with published experimental data on CK2α and CK2β mutants, and suggested prediction programs that could help predict changes in functionality of CK2α mutants. We also investigated the potential effect of CK2α and CK2β mutations on the 3D structure of the proteins and in their binding to each other. These results indicate that there are functional and structural consequences of mutation of CK2α and CK2β, and provide a rationale for further study of OCNDS and POBINDS-associated mutations. These data contribute to understanding the genetic and functional basis of these diseases, which is needed to identify their underlying mechanisms.
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Affiliation(s)
- Prasida Unni
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Jack Friend
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston University, Boston, MA, United States
| | - Volkan Okur
- New York Genome Center, New York, NY, United States
| | - Jennifer Hochscherf
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Isabel Dominguez
- Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston University, Boston, MA, United States
- *Correspondence: Isabel Dominguez,
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8
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Ganapathi M, Friocourt G, Gueguen N, Friederich MW, Le Gac G, Okur V, Loaëc N, Ludwig T, Ka C, Tanji K, Marcorelles P, Theodorou E, Lignelli-Dipple A, Voisset C, Walker MA, Briere LC, Bourhis A, Blondel M, LeDuc C, Hagen J, Cooper C, Muraresku C, Ferec C, Garenne A, Lelez-Soquet S, Rogers CA, Shen Y, Strode DK, Bizargity P, Iglesias A, Goldstein A, High FA, Network UD, Sweetser DA, Ganetzky R, Van Hove JLK, Procaccio V, Le Marechal C, Chung WK. A homozygous splice variant in ATP5PO, disrupts mitochondrial complex V function and causes Leigh syndrome in two unrelated families. J Inherit Metab Dis 2022; 45:996-1012. [PMID: 35621276 PMCID: PMC9474623 DOI: 10.1002/jimd.12526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 11/10/2022]
Abstract
Mitochondrial complex V plays an important role in oxidative phosphorylation by catalyzing the generation of ATP. Most complex V subunits are nuclear encoded and not yet associated with recognized Mendelian disorders. Using exome sequencing, we identified a rare homozygous splice variant (c.87+3A>G) in ATP5PO, the complex V subunit which encodes the oligomycin sensitivity conferring protein, in three individuals from two unrelated families, with clinical suspicion of a mitochondrial disorder. These individuals had a similar, severe infantile and often lethal multi-systemic disorder that included hypotonia, developmental delay, hypertrophic cardiomyopathy, progressive epileptic encephalopathy, progressive cerebral atrophy, and white matter abnormalities on brain MRI consistent with Leigh syndrome. cDNA studies showed a predominant shortened transcript with skipping of exon 2 and low levels of the normal full-length transcript. Fibroblasts from the affected individuals demonstrated decreased ATP5PO protein, defective assembly of complex V with markedly reduced amounts of peripheral stalk proteins, and complex V hydrolytic activity. Further, expression of human ATP5PO cDNA without exon 2 (hATP5PO-∆ex2) in yeast cells deleted for yATP5 (ATP5PO homolog) was unable to rescue growth on media which requires oxidative phosphorylation when compared to the wild type construct (hATP5PO-WT), indicating that exon 2 deletion leads to a non-functional protein. Collectively, our findings support the pathogenicity of the ATP5PO c.87+3A>G variant, which significantly reduces but does not eliminate complex V activity. These data along with the recent report of an affected individual with ATP5PO variants, add to the evidence that rare biallelic variants in ATP5PO result in defective complex V assembly, function and are associated with Leigh syndrome.
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Affiliation(s)
- Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Naig Gueguen
- MitoLab, UMR CNRS 6015 - INSERM U1083, MitoVasc Institute, Angers University Hospital, Angers, France
| | - Marisa W Friederich
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Volkan Okur
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Thomas Ludwig
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Kurenai Tanji
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Pascale Marcorelles
- CHRU de Brest, Service d'anatomie cytologie pathologie, CHU et centre de référence des maladies neuromusculaires, Brest, France
| | - Evangelos Theodorou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Angela Lignelli-Dipple
- Department of Radiology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Melissa A Walker
- Division of Neurogenetics, Child Neurology, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Amélie Bourhis
- CHRU de Brest, Service d'anatomie cytologie pathologie, CHU et centre de référence des maladies neuromusculaires, Brest, France
| | | | - Charles LeDuc
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Jacob Hagen
- Department of Biomedical Sciences, Columbia University Irving Medical Center, New York, New York, USA
| | - Cathleen Cooper
- Department of Radiology, Columbia University Irving Medical Center, New York, New York, USA
| | - Colleen Muraresku
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Cassandra A Rogers
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yufeng Shen
- Department of Biomedical Sciences, Columbia University Irving Medical Center, New York, New York, USA
| | - Dana K Strode
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
| | - Peyman Bizargity
- Division of Medical Genetics, Cohen Children's Medical Center, New York, New York, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, New York, USA
| | - Alejandro Iglesias
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Amy Goldstein
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frances A High
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rebecca Ganetzky
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Johan L K Van Hove
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015 - INSERM U1083, MitoVasc Institute, Angers University Hospital, Angers, France
| | - Cedric Le Marechal
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
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9
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Abul-Husn N, Kelly N, Rodriguez J, Abhyankar A, Donohue K, Brown K, DiBiase M, Gallagher K, Guha S, Ioele N, Marathe P, Odgis J, Okur V, Ramos M, Rehman A, Sebastin M, Thomas-Wilson A, Zinberg R, Diaz G, Suckiel S, Greally J, Jobanputra V, Horowitz C, Wasserstein M, Kenny E, Gelb B. eP067: Diagnostic yield of genome sequencing versus targeted gene panel testing in diverse pediatric patients in the NYCKidSeq study. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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10
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Owen N, Okur V, Anderson S, Smith J, Bacino C, Ward P, Cheung S, Breman A, Van Den Veyver I, Bi W. eP462: Detection of clinically relevant exonic copy number changes in fetuses by chromosomal microarray analysis. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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11
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Okur V, Chen Z, Vossaert L, Peacock S, Rosenfeld J, Zhao L, Du H, Calamaro E, Gerard A, Zhao S, Kelsay J, Lahr A, Mighton C, Porter HM, Siemon A, Silver J, Svihovec S, Fong CT, Grant CL, Lerner-Ellis J, Manickam K, Madan-Khetarpal S, McCandless SE, Morel CF, Schaefer GB, Berry-Kravis EM, Gates R, Gomez-Ospina N, Qiu G, Zhang TJ, Wu Z, Meng L, Liu P, Scott DA, Lupski JR, Eng CM, Wu N, Yuan B. De novo variants in H3-3A and H3-3B are associated with neurodevelopmental delay, dysmorphic features, and structural brain abnormalities. NPJ Genom Med 2021; 6:104. [PMID: 34876591 PMCID: PMC8651650 DOI: 10.1038/s41525-021-00268-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/28/2021] [Indexed: 11/26/2022] Open
Abstract
The histone H3 variant H3.3, encoded by two genes H3-3A and H3-3B, can replace canonical isoforms H3.1 and H3.2. H3.3 is important in chromatin compaction, early embryonic development, and lineage commitment. The role of H3.3 in somatic cancers has been studied extensively, but its association with a congenital disorder has emerged just recently. Here we report eleven de novo missense variants and one de novo stop-loss variant in H3-3A (n = 6) and H3-3B (n = 6) from Baylor Genetics exome cohort (n = 11) and Matchmaker Exchange (n = 1), of which detailed phenotyping was conducted for 10 individuals (H3-3A = 4 and H3-3B = 6) that showed major phenotypes including global developmental delay, short stature, failure to thrive, dysmorphic facial features, structural brain abnormalities, hypotonia, and visual impairment. Three variant constructs (p.R129H, p.M121I, and p.I52N) showed significant decrease in protein expression, while one variant (p.R41C) accumulated at greater levels than wild-type control. One H3.3 variant construct (p.R129H) was found to have stronger interaction with the chaperone death domain-associated protein 6.
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Affiliation(s)
- Volkan Okur
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Zefu Chen
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
- Graduate School of Peking Union Medical College, 100005, Beijing, China
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Sandra Peacock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lina Zhao
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Emily Calamaro
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - Sen Zhao
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Jill Kelsay
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, 72701, USA
| | - Ashley Lahr
- Department of Medical Genetics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, 15224, USA
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, M5T 3M6, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, M5B 1A6, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
| | - Hillary M Porter
- Rare Disease Institute, Children's National Hospital, Washington, DC, 20010, USA
| | - Amy Siemon
- Nationwide Children's Hospital (NCH) and The Ohio State University College of Medicine Section of Genetic and Genomic Medicine, Columbus, OH, 43205, USA
| | - Josh Silver
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, ON, M5T 3L9, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Shayna Svihovec
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, and Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Christina L Grant
- Rare Disease Institute, Children's National Hospital, Washington, DC, 20010, USA
| | - Jordan Lerner-Ellis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, M5G 1X5, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kandamurugu Manickam
- Nationwide Children's Hospital (NCH) and The Ohio State University College of Medicine Section of Genetic and Genomic Medicine, Columbus, OH, 43205, USA
| | - Suneeta Madan-Khetarpal
- Department of Medical Genetics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, 15224, USA
| | - Shawn E McCandless
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, and Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - Chantal F Morel
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, ON, M5T 3L9, Canada
- Department of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - G Bradley Schaefer
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, 72701, USA
| | - Elizabeth M Berry-Kravis
- Departments of Pediatrics, Neurological Sciences, and Biochemistry, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Ryan Gates
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratories, Houston, TX, 77021, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Nan Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 100730, Beijing, China.
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Baylor Genetics Laboratories, Houston, TX, 77021, USA.
- Seattle Children's Hospital, Seattle, WA, 98105, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, UW, 98105, USA.
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12
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Dworschak GC, Punetha J, Kalanithy JC, Mingardo E, Erdem HB, Akdemir ZC, Karaca E, Mitani T, Marafi D, Fatih JM, Jhangiani SN, Hunter JV, Dakal TC, Dhabhai B, Dabbagh O, Alsaif HS, Alkuraya FS, Maroofian R, Houlden H, Efthymiou S, Dominik N, Salpietro V, Sultan T, Haider S, Bibi F, Thiele H, Hoefele J, Riedhammer KM, Wagner M, Guella I, Demos M, Keren B, Buratti J, Charles P, Nava C, Héron D, Heide S, Valkanas E, Waddell LB, Jones KJ, Oates EC, Cooper ST, MacArthur D, Syrbe S, Ziegler A, Platzer K, Okur V, Chung WK, O'Shea SA, Alcalay R, Fahn S, Mark PR, Guerrini R, Vetro A, Hudson B, Schnur RE, Hoganson GE, Burton JE, McEntagart M, Lindenberg T, Yilmaz Ö, Odermatt B, Pehlivan D, Posey JE, Lupski JR, Reutter H. Biallelic and monoallelic variants in PLXNA1 are implicated in a novel neurodevelopmental disorder with variable cerebral and eye anomalies. Genet Med 2021; 23:1715-1725. [PMID: 34054129 PMCID: PMC8460429 DOI: 10.1038/s41436-021-01196-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To investigate the effect of PLXNA1 variants on the phenotype of patients with autosomal dominant and recessive inheritance patterns and to functionally characterize the zebrafish homologs plxna1a and plxna1b during development. METHODS We assembled ten patients from seven families with biallelic or de novo PLXNA1 variants. We describe genotype-phenotype correlations, investigated the variants by structural modeling, and used Morpholino knockdown experiments in zebrafish to characterize the embryonic role of plxna1a and plxna1b. RESULTS Shared phenotypic features among patients include global developmental delay (9/10), brain anomalies (6/10), and eye anomalies (7/10). Notably, seizures were predominantly reported in patients with monoallelic variants. Structural modeling of missense variants in PLXNA1 suggests distortion in the native protein. Our zebrafish studies enforce an embryonic role of plxna1a and plxna1b in the development of the central nervous system and the eye. CONCLUSION We propose that different biallelic and monoallelic variants in PLXNA1 result in a novel neurodevelopmental syndrome mainly comprising developmental delay, brain, and eye anomalies. We hypothesize that biallelic variants in the extracellular Plexin-A1 domains lead to impaired dimerization or lack of receptor molecules, whereas monoallelic variants in the intracellular Plexin-A1 domains might impair downstream signaling through a dominant-negative effect.
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Affiliation(s)
- Gabriel C Dworschak
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany.
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany.
- Department of Pediatrics, University Hospital Bonn, Bonn, Germany.
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeshurun C Kalanithy
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Enrico Mingardo
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Haktan B Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, TX, USA
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Bhanupriya Dhabhai
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Omar Dabbagh
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Tipu Sultan
- Department of Pediatric Neurology, Institute of Child Health, The Children's Hospital Lahore, Lahore, Pakistan
| | - Shahzad Haider
- Department of Paediatric Medicine, Wah Medical College, Rawalpindi, Pakistan
| | - Farah Bibi
- University Institute of Biochemistry & Biotechnology, PMAS - Arid Agriculture University, Rawalpindi, Pakistan
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ilaria Guella
- Department of Medical Genetics, Centre for Applied Neurogenetics, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Boris Keren
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Julien Buratti
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Perrine Charles
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Caroline Nava
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
- Institut du Cerveau et de la Moelle épinière, Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, Paris, France
| | - Delphine Héron
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Solveig Heide
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Elise Valkanas
- Center for Mendelian Genomics, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Leigh B Waddell
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Kristi J Jones
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Emily C Oates
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, The University of New South Wales, Sydney, NSW, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Children's Medical Research Institute, Westmead, NSW, Australia
| | - Daniel MacArthur
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steffen Syrbe
- Division of Pediatric Epileptology, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Ziegler
- Division of Pediatric Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Volkan Okur
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Sarah A O'Shea
- Department of Neurology, Columbia University, New York, NY, USA
| | - Roy Alcalay
- Department of Neurology, Columbia University, New York, NY, USA
| | - Stanley Fahn
- Department of Neurology, Columbia University, New York, NY, USA
| | - Paul R Mark
- Division of Medical Genetics, Helen DeVos Children's Hospital Grand Rapids, New York, MI, USA
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Annalisa Vetro
- Neuroscience Department, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | | | | | - George E Hoganson
- Department of Pediatrics, University of Illinois, College of Medicine, Chicago, IL, USA
| | - Jennifer E Burton
- Department of Pediatrics, University of Illinois, College of Medicine, Peoria, IL, USA
| | - Meriel McEntagart
- South West Thames Regional Genetics Centre, St. George's Healthcare NHS Trust, St. George's, University of London, London, United Kingdom
| | - Tobias Lindenberg
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, Germany
| | - Öznur Yilmaz
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin Odermatt
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, Germany
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Heiko Reutter
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Department of Neonatology and Pediatric Intensive Care, University Hospital Bonn, Bonn, Germany
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13
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O'Shea SA, Hickman RA, Cortes E, Vonsattel JP, Fahn S, Okur V, Alcalay RN, Chung WK. Neuropathological Findings in a Case of Parkinsonism and Developmental Delay Associated with a Monoallelic Variant in PLXNA1. Mov Disord 2021; 36:2681-2687. [PMID: 34415653 DOI: 10.1002/mds.28756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/02/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND PLXNA1 encodes for Plexin-A, a transmembrane protein expressed in the developing nervous system. Mutations in this gene have been associated with developmental delay but have not been previously associated with the development of parkinsonism. OBJECTIVES To describe the case of a 38-year-old patient with developmental delay who developed parkinsonism later in life. METHODS Post-mortem exome sequencing was performed with confirmation by Sanger sequencing. Brain autopsy was also performed. RESULTS Post-mortem exome sequencing on the proband identified a heterozygous predicted nonsense PLXNA1 variant (c.G3361T:p.Glu1121Ter). Pathology demonstrated arhinencephaly with brainstem heterotopia, diffuse Lewy body disease, and frontotemporal lobar dementia-tau. CONCLUSIONS This case of a patient with developmental delay and parkinsonism with PLXNA1 mutation highlights a need for assessing long-term outcomes of individuals with neurodevelopmental disorders, as well as the need for genetic testing in adults. It also suggests that the link between PLXNA1 and α-synuclein should be explored in the future. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Sarah A O'Shea
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA.,Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Richard A Hickman
- Department of Pathology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Etty Cortes
- Department of Pathology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jean Paul Vonsattel
- Department of Pathology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Stanley Fahn
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Volkan Okur
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Roy N Alcalay
- Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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14
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Okur V, Hamm L, Kavus H, Mebane C, Robinson S, Levy B, Chung WK. Clinical and genomic characterization of 8p cytogenomic disorders. Genet Med 2021; 23:2342-2351. [PMID: 34282301 DOI: 10.1038/s41436-021-01270-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To provide a detailed clinical and cytogenomic summary of individuals with chromosome 8p rearrangements of invdupdel(8p), del(8p), and dup(8p). METHODS We enrolled 97 individuals with invdupdel(8p), del(8p), and dup(8p). Clinical and molecular data were collected to delineate and compare the clinical findings and rearrangement breakpoints. We included additional 5 individuals with dup(8p) from the literature for a total of 102 individuals. RESULTS Eighty-one individuals had recurrent rearrangements of invdupdel(8p) (n = 49), del(8p)_distal (n = 4), del(8p)_proximal (n = 9), del(8p)_proximal&distal (n = 12), and dup(8p)_proximal (n = 7). Twenty-one individuals had nonrecurrent rearrangements. While all individuals had neurodevelopmental features, the frequency and severity of clinical findings were higher in individuals with invdupdel(8p), and with larger duplications. All individuals with GATA4 deletion had structural congenital heart defects; however, the presence of structural heart defects in some individuals with normal GATA4 copy number suggests there are other potentially contributing gene(s) on 8p. CONCLUSION Our study may inform families and health-care providers about the associated clinical findings and severity in individuals with chromosome 8p rearrangements, and guide researchers in investigating the underlying molecular and biological mechanisms by providing detailed clinical and cytogenomic information about individuals with distinct 8p rearrangements.
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Affiliation(s)
- Volkan Okur
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Laura Hamm
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Haluk Kavus
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Caroline Mebane
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Scott Robinson
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Wendy K Chung
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA. .,Department of Medicine, Columbia University Medical Center, New York, NY, USA.
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15
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Kim CY, Wirth T, Hubsch C, Németh AH, Okur V, Anheim M, Drouot N, Tranchant C, Rudolf G, Chelly J, Tatton-Brown K, Blauwendraat C, Vonsattel JPG, Cortes E, Alcalay RN, Chung WK. Reply to "PPP2R5D Genetic Mutations and Early Onset Parkinsonism". Ann Neurol 2020; 89:195-196. [PMID: 33098324 DOI: 10.1002/ana.25945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Christine Y Kim
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, USA.,Center for Neuroepidemiology and Clinical Neurological Research, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Thomas Wirth
- Unit of Functional Neurosurgery, National Hospital for Neurology and Neurosurgery, University College London Hospital, London, UK.,Neurology Department, Strasbourg University Hospitals, Strasbourg, France.,Institute of Genetics and Molecular and Cellular Biology, INSERM-U964/CNRS-UMR7104/University of Strasbourg, Illkirch-Graffenstaden, France
| | - Cécile Hubsch
- A. de Rothschild Ophthalmological Foundation, Paris, France
| | - Andrea H Németh
- Oxford University Hospitals National Health Service Trust and University of Oxford, Oxford, UK
| | - Volkan Okur
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mathieu Anheim
- Neurology Department, Strasbourg University Hospitals, Strasbourg, France.,Institute of Genetics and Molecular and Cellular Biology, INSERM-U964/CNRS-UMR7104/University of Strasbourg, Illkirch-Graffenstaden, France.,Strasbourg Federation of Translational Medicine, Strasbourg, France
| | - Nathalie Drouot
- Institute of Genetics and Molecular and Cellular Biology, INSERM-U964/CNRS-UMR7104/University of Strasbourg, Illkirch-Graffenstaden, France
| | - Christine Tranchant
- Neurology Department, Strasbourg University Hospitals, Strasbourg, France.,Institute of Genetics and Molecular and Cellular Biology, INSERM-U964/CNRS-UMR7104/University of Strasbourg, Illkirch-Graffenstaden, France.,Strasbourg Federation of Translational Medicine, Strasbourg, France
| | - Gabrielle Rudolf
- Neurology Department, Strasbourg University Hospitals, Strasbourg, France.,Institute of Genetics and Molecular and Cellular Biology, INSERM-U964/CNRS-UMR7104/University of Strasbourg, Illkirch-Graffenstaden, France.,Strasbourg Federation of Translational Medicine, Strasbourg, France
| | - Jamel Chelly
- Neurology Department, Strasbourg University Hospitals, Strasbourg, France.,Institute of Genetics and Molecular and Cellular Biology, INSERM-U964/CNRS-UMR7104/University of Strasbourg, Illkirch-Graffenstaden, France.,Genetic Diagnostic Laboratory, Strasbourg University Hospitals, Strasbourg, France
| | - Katrina Tatton-Brown
- St George's University Hospitals National Health Service Foundation Trust, London, UK
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jean Paul G Vonsattel
- Department of Pathology and Cell Biology, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY, USA
| | - Etty Cortes
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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16
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Al-Deri N, Okur V, Ahimaz P, Milev M, Valivullah Z, Hagen J, Sheng Y, Chung W, Sacher M, Ganapathi M. A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function. J Med Genet 2020; 58:592-601. [PMID: 32843486 DOI: 10.1136/jmedgenet-2020-107016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/25/2020] [Accepted: 06/26/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Next-generation sequencing has facilitated the diagnosis of neurodevelopmental disorders with variable and non-specific clinical findings. Recently, a homozygous missense p.(Asp37Tyr) variant in TRAPPC2L, a core subunit of TRAPP complexes which function as tethering factors during membrane trafficking, was reported in two unrelated individuals with neurodevelopmental delay, post-infectious encephalopathy-associated developmental arrest, tetraplegia and accompanying rhabdomyolysis. METHODS We performed whole genome sequencing on members of an Ashkenazi Jewish pedigree to identify the underlying genetic aetiology of global developmental delay/intellectual disability in three affected siblings. To assess the effect of the identified TRAPPC2L variant, we performed biochemical and cell biological functional studies on the TRAPPC2L protein. RESULTS A rare homozygous predicted deleterious missense variant, p.(Ala2Gly), in TRAPPC2L was identified in the affected siblings and it segregated with the neurodevelopmental phenotype within the family. Using a yeast two-hybrid assay and in vitro binding, we demonstrate that the p.(Ala2Gly) variant, but not the p.(Asp37Tyr) variant, disrupted the interaction between TRAPPC2L and another core TRAPP protein, TRAPPC6a. Size exclusion chromatography suggested that this variant affects the assembly of TRAPP complexes. Employing two different membrane trafficking assays using fibroblasts from one of the affected siblings, we found a delay in traffic into and out of the Golgi. Similar to the p.(Asp37Tyr) variant, the p.(Ala2Gly) variant resulted in an increase in the levels of active RAB11. CONCLUSION Our data fill in a gap in the knowledge of TRAPP architecture with TRAPPC2L interacting with TRAPPC6a, positioning it as a putative adaptor for other TRAPP subunits. Collectively, our findings support the pathogenicity of the TRAPPC2L p.(Ala2Gly) variant.
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Affiliation(s)
- Noraldin Al-Deri
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Volkan Okur
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | - Miroslav Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Zaheer Valivullah
- Center for Mendelian Genomics, Broad Institute Harvard, Cambridge, Massachusetts, USA
| | - Jacob Hagen
- Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
| | - Yufeng Sheng
- Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
| | - Wendy Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA.,Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada .,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
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17
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Kim CY, Wirth T, Hubsch C, Németh AH, Okur V, Anheim M, Drouot N, Tranchant C, Rudolf G, Chelly J, Tatton-Brown K, Blauwendraat C, Vonsattel JPG, Cortes E, Alcalay RN, Chung WK. Early-Onset Parkinsonism Is a Manifestation of the PPP2R5D p.E200K Mutation. Ann Neurol 2020; 88:1028-1033. [PMID: 32743835 DOI: 10.1002/ana.25863] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022]
Abstract
PPP2R5D-related neurodevelopmental disorder is characterized by a range of neurodevelopmental and behavioral manifestations. We report the association of early-onset parkinsonism with the PPP2R5D p.E200K mutation. Clinical characterization and exome sequencing were performed on three patients, with postmortem neuropathologic examination for one patient. All patients had mild developmental delay and developed levodopa-responsive parkinsonism between the ages of 25 and 40 years. The PPP2R5D c.598G>A (p.E200K) mutation was identified in all patients. Neuropathologic examination demonstrated uneven, focally severe neuronal loss and gliosis in the substantia nigra pars compacta, without Lewy bodies. Our findings suggest the PPP2R5D p.E200K mutation to be a possible new cause of early-onset parkinsonism. ANN NEUROL 2020;88:1028-1033.
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Affiliation(s)
- Christine Y Kim
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, USA.,Center for Neuroepidemiology and Clinical Neurological Research, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Thomas Wirth
- Unit of Functional Neurosurgery, National Hospital for Neurology and Neurosurgery, University College London Hospital, London, UK.,Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Cécile Hubsch
- Fondation Ophtalmologique A. de Rothschild, Paris, France
| | - Andrea H Németh
- Oxford University Hospitals NHS Trust and University of Oxford, Oxford, UK
| | - Volkan Okur
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Mathieu Anheim
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France.,Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Nathalie Drouot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Christine Tranchant
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France.,Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Gabrielle Rudolf
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France.,Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Jamel Chelly
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, Illkirch-Graffenstaden, France.,Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | | | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jean Paul G Vonsattel
- Department of Pathology and Cell Biology, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY, USA
| | - Etty Cortes
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY, USA.,Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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18
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Chilton I, Okur V, Vitiello G, Selicorni A, Mariani M, Goldenberg A, Husson T, Campion D, Lichtenbelt KD, van Gassen K, Steinraths M, Rice J, Roeder ER, Littlejohn RO, Srour M, Sebire G, Accogli A, Héron D, Heide S, Nava C, Depienne C, Larson A, Niyazov D, Azage M, Hoganson G, Burton J, Rush ET, Jenkins JL, Saunders CJ, Thiffault I, Alaimo JT, Fleischer J, Groepper D, Gripp KW, Chung WK. De novo heterozygous missense and loss-of-function variants in CDC42BPB are associated with a neurodevelopmental phenotype. Am J Med Genet A 2020; 182:962-973. [PMID: 32031333 DOI: 10.1002/ajmg.a.61505] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/30/2019] [Accepted: 01/12/2020] [Indexed: 11/08/2022]
Abstract
CDC42BPB encodes MRCKβ (myotonic dystrophy-related Cdc42-binding kinase beta), a serine/threonine protein kinase, and a downstream effector of CDC42, which has recently been associated with Takenouchi-Kosaki syndrome, an autosomal dominant neurodevelopmental disorder. We identified 12 heterozygous predicted deleterious variants in CDC42BPB (9 missense, 2 frameshift, and 1 nonsense) in 14 unrelated individuals (confirmed de novo in 11/14) with neurodevelopmental disorders including developmental delay/intellectual disability, autism, hypotonia, and structural brain abnormalities including cerebellar vermis hypoplasia and agenesis/hypoplasia of the corpus callosum. The frameshift and nonsense variants in CDC42BPB are expected to be gene-disrupting and lead to haploinsufficiency via nonsense-mediated decay. All missense variants are located in highly conserved and functionally important protein domains/regions: 3 are found in the protein kinase domain, 2 are in the citron homology domain, and 4 in a 20-amino acid sequence between 2 coiled-coil regions, 2 of which are recurrent. Future studies will help to delineate the natural history and to elucidate the underlying biological mechanisms of the missense variants leading to the neurodevelopmental and behavioral phenotypes.
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Affiliation(s)
- Ilana Chilton
- Department of Pediatrics, Columbia University, New York, New York
| | - Volkan Okur
- Department of Pediatrics, Columbia University, New York, New York
| | | | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna Hospital, Como, Italy
| | - Milena Mariani
- Pediatric Department, ASST Lariana, Sant'Anna Hospital, Como, Italy
| | - Alice Goldenberg
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Thomas Husson
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Dominique Campion
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
| | - Klaske D Lichtenbelt
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jennifer Rice
- Department of Medical Genetics, University of British Columbia, Canada
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | | | - Myriam Srour
- McGill University Health Center, Montreal Children's Hospital, Canada
| | - Guillaume Sebire
- McGill University Health Center, Montreal Children's Hospital, Canada
| | - Andrea Accogli
- Medical Genetics Unit, IRCCS Ospedale Policlinico San Martino and DINOGMI-Università degli Studi di Genova, Genoa, Italy
| | - Delphine Héron
- Département de Génétique et de Cytogénétique; Centre de Référence Déficiences Intellectuelles de Causes Rares; GRC UPMC, Déficience Intellectuelle et Autisme, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Solveig Heide
- Département de Génétique et de Cytogénétique; Centre de Référence Déficiences Intellectuelles de Causes Rares; GRC UPMC, Déficience Intellectuelle et Autisme, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Caroline Nava
- Département de Génétique et de Cytogénétique; Centre de Référence Déficiences Intellectuelles de Causes Rares; GRC UPMC, Déficience Intellectuelle et Autisme, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.,INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, Paris, France
| | - Christel Depienne
- INSERM U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, Paris, France.,Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Austin Larson
- Department of Pediatrics-Clinical Genetics and Metabolism, University of Colorado, Colorado, USA
| | | | - Meron Azage
- Department of Genetics, Ochsner Health System, Louisiana
| | - George Hoganson
- Department of Pediatrics, University of Illinois, Chicago, Illinois, 60612, USA
| | - Jennifer Burton
- Department of Pediatrics, University of Illinois, Chicago, Illinois, 60612, USA
| | - Eric T Rush
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri
| | - Janda L Jenkins
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Joseph T Alaimo
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, Illinois, 62702, USA
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, Illinois, 62702, USA
| | - Karen W Gripp
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware, 19803, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York.,Department of Medicine, Columbia University, New York, New York
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Okur V, Watschinger K, Niyazov D, McCarrier J, Basel D, Hermann M, Werner ER, Chung WK. Biallelic variants in AGMO with diminished enzyme activity are associated with a neurodevelopmental disorder. Hum Genet 2019; 138:1259-1266. [PMID: 31555905 DOI: 10.1007/s00439-019-02065-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/15/2019] [Indexed: 11/30/2022]
Abstract
Alkylglycerol monooxygenase (AGMO) is the only enzyme known to cleave the O-alkyl bonds of ether lipids (alkylglycerols) which are essential components of cell membranes. A homozygous frameshift variant [p.(Glu324LysfsTer12)] in AGMO has recently been reported in two male siblings with syndromic microcephaly. In this study, we identified rare nonsense, in frame deletion, and missense biallelic variants in AGMO in two unrelated individuals with neurodevelopmental disabilities. We assessed the activity of seven disease associated AGMO variants including the four variants identified in our two affected individuals expressed in human embryonic kidney (HEK293T) cells. We demonstrated significantly diminished enzyme activity for all disease-associated variants, supporting the mechanism as decreased AGMO activity. Future mechanistic studies are necessary to understand how decreased AGMO activity leads to the neurologic manifestations.
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Affiliation(s)
- Volkan Okur
- Department of Pediatrics, Columbia University Medical Center, 1150 St. Nicholas Avenue, New York, NY, 10032, USA
| | - Katrin Watschinger
- Institute of Biological Chemistry, Biocenter, Center for Chemistry and Biomedicine (CCB), Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Dmitriy Niyazov
- Department of Pediatrics, Ochsner Clinic, New Orleans, LA, 70394, USA
| | - Julie McCarrier
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Donald Basel
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Martin Hermann
- Department of Anesthesiology and Critical Care Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Ernst R Werner
- Institute of Biological Chemistry, Biocenter, Center for Chemistry and Biomedicine (CCB), Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, 1150 St. Nicholas Avenue, New York, NY, 10032, USA. .,Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA.
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20
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Okur V, LeDuc CA, Guzman E, Valivullah ZM, Anyane-Yeboa K, Chung WK. Homozygous noncanonical splice variant in LSM1 in two siblings with multiple congenital anomalies and global developmental delay. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004101. [PMID: 31010896 PMCID: PMC6549555 DOI: 10.1101/mcs.a004101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
Two siblings, one male and one female, ages 6 and 13 yr old, have similar clinical features of global developmental delay, multiple congenital anomalies affecting the cardiac, genitourinary, and skeletal systems, and abnormal eye movements. Whole-genome sequencing revealed a homozygous splice variant (NM_014462.3:c.231+4A>C) in LSM1 that segregated with the phenotype in the family. LSM1 has a role in pre-mRNA splicing and degradation. Expression studies revealed absence of expression of the canonical isoform in the affected individuals. The Lsm1 knockout mice have a partially overlapping phenotype that affects the brain, heart, and eye. To our knowledge, LSM1 has not been associated with any human disorder; however, the tissue expression pattern, gene constraint, and the similarity of the phenotype in our patients and the knockout mice models suggest it has a role in the development of multiple organ systems in humans.
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Affiliation(s)
- Volkan Okur
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Charles A LeDuc
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
| | - Edwin Guzman
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Zaheer M Valivullah
- Center for Mendelian Genomics at the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York 10032, USA.,Department of Medicine, Columbia University, New York, New York 10032, USA
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21
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Nees S, Callahan KP, Besagar S, Lee T, Okur V, Griffin E, Wang J, Shen Y, Chung WK. YIELD OF GENETIC TESTING IN NEONATES WITH CONGENITAL HEART DISEASE AND ASSOCIATION WITH CLINICAL OUTCOMES. J Am Coll Cardiol 2019. [DOI: 10.1016/s0735-1097(19)31211-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Ganapathi M, Padgett LR, Yamada K, Devinsky O, Willaert R, Person R, Au PYB, Tagoe J, McDonald M, Karlowicz D, Wolf B, Lee J, Shen Y, Okur V, Deng L, LeDuc CA, Wang J, Hanner A, Mirmira RG, Park MH, Mastracci TL, Chung WK. Recessive Rare Variants in Deoxyhypusine Synthase, an Enzyme Involved in the Synthesis of Hypusine, Are Associated with a Neurodevelopmental Disorder. Am J Hum Genet 2019; 104:287-298. [PMID: 30661771 PMCID: PMC6369575 DOI: 10.1016/j.ajhg.2018.12.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/20/2018] [Indexed: 01/23/2023] Open
Abstract
Hypusine is formed post-translationally from lysine and is found in a single cellular protein, eukaryotic translation initiation factor-5A (eIF5A), and its homolog eIF5A2. Biosynthesis of hypusine is a two-step reaction involving the enzymes deoxyhypusine synthase (DHPS) and deoxyhypusine hydroxylase (DOHH). eIF5A is highly conserved throughout eukaryotic evolution and plays a role in mRNA translation, cellular proliferation, cellular differentiation, and inflammation. DHPS is also highly conserved and is essential for life, as Dhps-null mice are embryonic lethal. Using exome sequencing, we identified rare biallelic, recurrent, predicted likely pathogenic variants in DHPS segregating with disease in five affected individuals from four unrelated families. These individuals have similar neurodevelopmental features that include global developmental delay and seizures. Two of four affected females have short stature. All five affected individuals share a recurrent missense variant (c.518A>G [p.Asn173Ser]) in trans with a likely gene disrupting variant (c.1014+1G>A, c.912_917delTTACAT [p.Tyr305_Ile306del], or c.1A>G [p.Met1?]). cDNA studies demonstrated that the c.1014+1G>A variant causes aberrant splicing. Recombinant DHPS enzyme harboring either the p.Asn173Ser or p.Tyr305_Ile306del variant showed reduced (20%) or absent in vitro activity, respectively. We co-transfected constructs overexpressing HA-tagged DHPS (wild-type or mutant) and GFP-tagged eIF5A into HEK293T cells to determine the effect of these variants on hypusine biosynthesis and observed that the p.Tyr305_Ile306del and p.Asn173Ser variants resulted in reduced hypusination of eIF5A compared to wild-type DHPS enzyme. Our data suggest that rare biallelic variants in DHPS result in reduced enzyme activity that limits the hypusination of eIF5A and are associated with a neurodevelopmental disorder.
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Affiliation(s)
- Mythily Ganapathi
- Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Leah R Padgett
- Regenerative Medicine & Metabolic Biology, Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Kentaro Yamada
- Department of Pediatrics and the Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Orrin Devinsky
- Neurology Department, NYU Langone Medical Center, New York, NY 10016, USA
| | | | | | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Julia Tagoe
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Danielle Karlowicz
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Barry Wolf
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joanna Lee
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Volkan Okur
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Liyong Deng
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Charles A LeDuc
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Jiayao Wang
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ashleigh Hanner
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892-4340, USA
| | - Raghavendra G Mirmira
- Department of Pediatrics and the Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Myung Hee Park
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892-4340, USA
| | - Teresa L Mastracci
- Regenerative Medicine & Metabolic Biology, Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA.
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23
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Okur V, Ganapathi M, Wilson A, Chung WK. Biallelic variants in VARS in a family with two siblings with intellectual disability and microcephaly: case report and review of the literature. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003301. [PMID: 30275004 PMCID: PMC6169829 DOI: 10.1101/mcs.a003301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/24/2018] [Indexed: 12/29/2022] Open
Abstract
Two male siblings ages 15 and 10 yr old had similar features of intellectual disability, developmental delay, severe speech impairment, microcephaly, prematurity, and transient elevation of liver enzymes in infancy. Exome sequencing revealed one novel (c.65C>A; p.Ala22Asp) and one ultra-rare (c.3214T>C; p.Phe1072Leu) predicted damaging missense variant in trans in the gene encoding cytoplasmic valyl-tRNA synthetase (VARS). Biallelic variants in VARS have previously been associated with a neurodevelopmental disorder characterized by microcephaly, seizures, and cortical atrophy (NDMSCA; MIM #617802). Although our patients have no history of seizures or cortical atrophy, we suggest that the biallelic variants in VARS p.Ala22Asp and p.Phe1072Leu in this family are likely pathogenic and associated with NDMSCA, expanding the clinical phenotype of the condition.
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Affiliation(s)
- Volkan Okur
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Mythily Ganapathi
- Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University, New York, New York 10032, USA
| | - Ashley Wilson
- Department of Pediatrics, Columbia University, New York, New York 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York 10032, USA.,Department of Medicine, Columbia University, New York, New York 10032, USA
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24
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Okur V, Nees S, Chung WK, Krishnan U. Pulmonary hypertension in patients with 9q34.3 microdeletion-associated Kleefstra syndrome. Am J Med Genet A 2018; 176:1773-1777. [PMID: 30063093 DOI: 10.1002/ajmg.a.38852] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/23/2018] [Accepted: 05/01/2018] [Indexed: 11/09/2022]
Abstract
Kleefstra Syndrome is a rare genetic disorder caused by mutations in EHMT1, Euchromatin Histone Methyl Transferase 1, or deletions encompassing EHMT1 on 9q34.3. Congenital heart defects are among the major findings in patients with 9q34.3 microdeletion/Kleefstra Syndrome along with recognizable facial appearance, developmental delay/intellectual disability including severely delayed or absent speech, hypotonia, seizures, behavioral and sleep abnormalities. Pulmonary hypertension (PH) is a rare condition associated with increased pulmonary artery and right heart pressures that can lead to right heart failure and death if untreated. PH can be idiopathic, heritable, or associated with co-morbid conditions including congenital heart disease (CHD), lung diseases and other metabolic disorders. Genetic factors play important roles in heritable and idiopathic PH development and are particularly relevant but more diverse in etiology in children. PH is also reported in some chromosomal disorders such as Down syndrome in which congenital heart defects are common; however, PH has rarely been reported in patients with 9q34.3 microdeletion/Kleefstra Syndrome. Here, we present three patients with 9q34.3 microdeletions with CHD and PH along with review of five similar cases reported in the literature and discuss the potential association of PH with Kleefstra syndrome.
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Affiliation(s)
- Volkan Okur
- Department of Pediatrics, Columbia University, New York, New York
| | - Shannon Nees
- Department of Pediatrics, Columbia University, New York, New York
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York.,Department of Medicine, Columbia University, New York, New York
| | - Usha Krishnan
- Department of Pediatrics, Columbia University, New York, New York
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25
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Abstract
Mutations in hereditary cancer syndromes account for a modest fraction of all cancers; however, identifying patients with these germline mutations offers tremendous health benefits to both patients and their family members. There are about 60 genes that confer a high lifetime risk of specific cancers, and this information can be used to tailor prevention, surveillance, and treatment. With advances in next-generation sequencing technologies and the elimination of gene patents for evaluating genetic information, we are now able to analyze multiple genes simultaneously, leading to the widespread clinical use of gene panels for germline cancer testing. Over the last 4 years since these panels were introduced, we have learned about the diagnostic yield of testing, the expanded phenotypes of the patients with mutations, and the clinical utility of genetic testing in patients with cancer and/or without cancer but with a family history of cancer. We have also experienced challenges including the large number of variants of unknown significance (VUSs), identification of somatic mutations and need to differentiate these from germline mutations, technical issues with particular genes and mutations, insurance coverage and reimbursement issues, lack of access to data, and lack of clinical management guidelines for newer and, especially, moderate and low-penetrance genes. The lessons learned from cancer genetic testing panels are applicable to other clinical areas as well and highlight the problems to be solved as we advance genomic medicine.
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Affiliation(s)
- Volkan Okur
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA
| | - Wendy K Chung
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, New York 10032, USA; .,Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
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26
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Yaylali GF, Bichet DG, Okur V, Levin K, Semerci CN. Analysis of a Novel AVPR2 Mutation in a Turkish Family with Nephrogenic Diabetes Insipidus. INT J HUM GENET 2017. [DOI: 10.1080/09723757.2013.11886213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Güzin Fidan Yaylali
- Department of Endocrinology and Metabolism, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Daniel G. Bichet
- Department of Medicine and Physiology, University of Montreal, Montreal, Quebec, Canada
| | - Volkan Okur
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Klaus Levin
- Department of Endocrinology, Odense University Hospital, Svendborg, Denmark
| | - C. Nur Semerci
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
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27
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Kasparis C, Reid D, Wilson NJ, Okur V, Cole C, Hansen CD, Bosse K, Betz RC, Khan M, Smith FJD. Isolated recessive nail dysplasia caused by FZD6 mutations: report of three families and review of the literature. Clin Exp Dermatol 2016; 41:884-889. [PMID: 27786367 PMCID: PMC5132090 DOI: 10.1111/ced.12934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2016] [Indexed: 12/16/2022]
Abstract
Congenital abnormalities of the nail are rare conditions that are most frequently associated with congenital ectodermal syndromes involving several of the epidermal appendages including the skin, teeth, hair and nails. Isolated recessive nail dysplasia (IRND) is much rarer but has recently been recognized as a condition resulting in 20‐nail dystrophy in the absence of other cutaneous or extracutaneous findings. A few case reports have identified mutations in the Frizzled 6 (FZD6) gene in families presenting with abnormal nails consistent with IRND. These reports have highlighted the role of Wnt–FZD signalling in the process of nail formation. We report three families presenting with features of IRND, in whom we identified mutations in FZD6, including one previously unreported mutation.
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Affiliation(s)
- C Kasparis
- Dermatology Department, Walsall Healthcare NHS Trust, Walsall, UK
| | - D Reid
- Dermatology Department, Walsall Healthcare NHS Trust, Walsall, UK
| | - N J Wilson
- Centre for Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - V Okur
- Department of Medical Genetics, Haydarpasa Numune Hospital, Istanbul, Turkey.,Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - C Cole
- Centre for Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.,Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - C D Hansen
- Department of Dermatology, University of Utah, Salt Lake City, UT, USA
| | - K Bosse
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Institute of Medical Genetics and Applied Genomics and Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - R C Betz
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - M Khan
- Dermatology Department, Walsall Healthcare NHS Trust, Walsall, UK
| | - F J D Smith
- Centre for Dermatology and Genetic Medicine, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.,Pachyonychia Congenita Project, Salt Lake City, UT, USA
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28
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Umu SU, Onur MI, Okur V, Tuncan M, Tuncan A. Reliability Evaluation of Dynamic Characteristics of Clean Sand Soils Based on Soft Computing Methods. Arab J Sci Eng 2015. [DOI: 10.1007/s13369-015-1883-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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Okur V, Cetin O, Cetin E, Tepeli E, Bulgu Y, Yildirim C. HIF1Aas a major vascular endothelial growth factor regulator: do its polymorphisms have an association with age-related macular degeneration? Clin Exp Ophthalmol 2014; 43:47-53. [DOI: 10.1111/ceo.12376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/13/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Volkan Okur
- Department of Medical Genetics; Medical School of Pamukkale University; Denizli Turkey
| | - Ozan Cetin
- Department of Medical Genetics; Medical School of Pamukkale University; Denizli Turkey
| | - Ebru Cetin
- Department of Ophthalmology; Medical School of Pamukkale University; Denizli Turkey
| | - Emre Tepeli
- Department of Medical Genetics; Medical School of Pamukkale University; Denizli Turkey
| | - Yunus Bulgu
- Department of Ophthalmology; Medical School of Pamukkale University; Denizli Turkey
| | - Cem Yildirim
- Department of Ophthalmology; Medical School of Pamukkale University; Denizli Turkey
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Semerci CN, Kalay E, Yıldırım C, Dinçer T, Olmez A, Toraman B, Koçyiğit A, Bulgu Y, Okur V, Satıroğlu-Tufan L, Akarsu NA. Novel splice-site and missense mutations in the ALDH1A3 gene underlying autosomal recessive anophthalmia/microphthalmia. Br J Ophthalmol 2014; 98:832-40. [PMID: 24568872 DOI: 10.1136/bjophthalmol-2013-304058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIM This study aimed to identify the underlying genetic defect responsible for anophthalmia/microphthalmia. METHODS In total, two Turkish families with a total of nine affected individuals were included in the study. Affymetrix 250 K single nucleotide polymorphism genotyping and homozygosity mapping were used to identify the localisation of the genetic defect in question. Coding region of the ALDH1A3 gene was screened via direct sequencing. cDNA samples were generated from primary fibroblast cell cultures for expression analysis. Reverse transcriptase PCR (RT-PCR) analysis was performed using direct sequencing of the obtained fragments. RESULTS The causative genetic defect was mapped to chromosome 15q26.3. A homozygous G>A substitution (c.666G>A) at the last nucleotide of exon 6 in the ALDH1A3 gene was identified in the first family. Further cDNA sequencing of ALDH1A3 showed that the c.666G>A mutation caused skipping of exon 6, which predicted in-frame loss of 43 amino acids (p.Trp180_Glu222del). A novel missense c.1398C>A mutation in exon 12 of ALDH1A3 that causes the substitution of a conserved asparagine by lysine at amino acid position 466 (p.Asn466Lys) was observed in the second family. No extraocular findings-except for nevus flammeus in one affected individual and a variant of Dandy-Walker malformation in another affected individual-were observed. Autistic-like behaviour and mental retardation were observed in three cases. CONCLUSIONS In conclusion, novel ALDH1A3 mutations identified in the present study confirm the pivotal role of ALDH1A3 in human eye development. Autistic features, previously reported as an associated finding, were considered to be the result of social deprivation and inadequate parenting during early infancy in the presented families.
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Affiliation(s)
- C Nur Semerci
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Ersan Kalay
- Department of Medical Biology, School of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Cem Yıldırım
- Department of Ophthalmology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Tuba Dinçer
- Department of Medical Biology, School of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Akgün Olmez
- Department of Pediatric Neurology, Denizli State Hospital of Ministry of Health, Denizli, Turkey
| | - Bayram Toraman
- Department of Medical Biology, School of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Ali Koçyiğit
- Department of Radiology, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Yunus Bulgu
- Department of Ophthalmology, State Hospital, Şuhut-Afyonkarahisar, Afyon, Turkey
| | - Volkan Okur
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Lale Satıroğlu-Tufan
- Department of Medical Genetics, School of Medicine, Pamukkale University, Denizli, Turkey
| | - Nurten A Akarsu
- Department of Medical Genetics, Gene Mapping Laboratory, School of Medicine, Hacettepe University, Ankara, Turkey
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Oguz A, Citak C, Karadeniz C, Okur V, Okur A. 1414 POSTER The relationship between nutritional status and IGF-I and IGFBP-3 in patients with childhood solid tumours. EJC Suppl 2007. [DOI: 10.1016/s1359-6349(07)70753-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Akman M, Cebeci D, Okur V, Angin H, Abali O, Akman AC. The effects of iron deficiency on infants' developmental test performance. Acta Paediatr 2004; 93:1391-6. [PMID: 15499963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
AIM To assess the effects of iron deficiency on developmental test scores in infants. METHODS This prospective, single-blind, controlled clinical intervention study was made on 108 children aged 6-30 mo who applied to our paediatric outpatient clinic. The cases were classified as control (n = 31, haemoglobin > or = 11 g/dl, serum ferritin > 12 microg/l, MCV > or = 70 fl), non-anaemic iron deficiency (NAID, n = 40, haemoglobin > or = 11 g/dl, serum ferritin < or = 12 microg/l, MCV > or = 70 fl) and iron deficiency anaemia (IDA, n = 37, haemoglobin < 11 g/dl, ferritin < or = 12 microg/l, MCV < 70 fl) due to their anaemia status. In each group, MCV, haemoglobin and ferritin levels were measured, and Denver Developmental Screening Test (DDST) and Bayley Scales of Infant Development (BSID-I) were administered before and after a 3-mo follow-up. IDA and about half of the NAID subjects were treated with oral iron for 3 mo. RESULTS Subjects with iron deficiency showed significantly lower developmental test scores both with BSID-I and DDST-II compared to their iron-sufficient peers (p < 0.05). After 3 mo of iron treatment, lower mental developmental test scores were no longer observed among the IDA and NAID groups whose anaemia and iron deficiency were also corrected. No significant differences were found between control NAID and control IDA groups on DGTT-II results after treatment. The difference in motor and mental developmental scores did not appear to depend on environmental and family factors considered in the analyses. CONCLUSION These findings support the conclusions that iron deficiency may cause lower mental and motor test scores in infants and these adverse effects can be improved by iron therapy.
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Affiliation(s)
- M Akman
- Department of Family Medicine, Marmara University, School of Medicine, Istanbul, Turkey.
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