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Wilke MVMB, Wick M, Schwab TL, Starosta RT, Clark KJ, Connolly HM, Klee EW. Nuclear Abnormalities in LMNA p.(Glu2Lys) Variant Segregating with LMNA-Associated Cardiocutaneous Progeria Syndrome. Genes (Basel) 2024; 15:112. [PMID: 38255001 PMCID: PMC10815864 DOI: 10.3390/genes15010112] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The LMNA gene encodes lamin A and lamin C, which play important roles in nuclear organization. Pathogenic variants in LMNA cause laminopathies, a group of disorders with diverse phenotypes. There are two main groups of disease-causing variants: missense variants affecting dimerization and intermolecular interactions, and heterozygous substitutions activating cryptic splice sites. These variants lead to different disorders, such as dilated cardiomyopathy and Hutchinson-Gilford progeria (HGP). Among these, the phenotypic terms for LMNA-associated cardiocutaneous progeria syndrome (LCPS), which does not alter lamin A processing and has an older age of onset, have been described. Here, we present the workup of an LMNA variant of uncertain significance, NM_170707.2 c. 4G>A, p.(Glu2Lys), in a 36-year-old female with severe calcific aortic stenosis, a calcified mitral valve, premature aging, and a family history of similar symptoms. Due to the uncertainty of in silico predictions for this variant, an assessment of nuclear morphology was performed using the immunocytochemistry of stable cell lines to indicate whether the p.(Glu2Lys) had a similar pathogenic mechanism as a previously described pathogenic variant associated with LCPS, p.Asp300Gly. Indirect immunofluorescence analysis of nuclei from stable cell lines showed abnormal morphology, including lobulation and occasional ringed nuclei. Relative to the controls, p.Glu2Lys and p.Asp300Gly nuclei had significantly (p < 0.001) smaller average nuclear areas than controls (mean = 0.10 units, SD = 0.06 for p.Glu2Lys; and mean = 0.09 units, SD = 0.05 for p.Asp300Gly versus mean = 0.12, SD = 0.05 for WT). After functional studies and segregation studies, this variant was upgraded to likely pathogenic. In summary, our findings suggest that p.Glu2Lys impacts nuclear morphology in a manner comparable to what was observed in p.Asp300Gly cells, indicating that the variant is the likely cause of the LCPS segregating within this family.
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Affiliation(s)
| | - Myra Wick
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Tanya L. Schwab
- Department of Molecular Hematology, Mayo Clinic, Rochester, MN 55905, USA
| | - Rodrigo Tzovenos Starosta
- Division of Medical Genetics and Genomics, Washington University in Saint Louis, Saint Louis, MO 63130, USA;
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil
| | - Karl J. Clark
- Department of Biochemical and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Eric W. Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
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Wilke MVMB, Schimmenti L, Lopour MQR, Tollefson MM, Klee EW. A somatic splice-site variant in PIK3R1 in a patient with vascular overgrowth and low immunoglobulin levels: A case report. Mol Genet Genomic Med 2023; 11:e2271. [PMID: 37641480 PMCID: PMC10724508 DOI: 10.1002/mgg3.2271] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND The PI3K/AKT pathway, extensively studied in cancer, is vital for regulating cell metabolism, differentiation, and proliferation. Pathogenic variants in the PIK3R1 gene, which encodes three regulatory units of class IA PI3Ks, have been found in affected tissue of individuals with vascular lesions. These variants predominantly occur in the iSH2 domain, disrupting inhibitory contacts with the catalytic unit and leading to PI3K activation. Germline variants in this gene are also linked to an immunological condition called Activated PI3K delta syndrome type 2 (APDS2). METHODS This is a case report and literature review. Clinical data were retrieved from medical records. RESULTS A male patient presented with extensive vascular malformation covering over 90% of his body, along with complete 2-3 toe syndactyly, suggesting a vascular malformation syndrome called PROS. Low levels of IgA and IgG were detected. The patient achieved his developmental milestones and had above-average weight, height, and head circumference. Exome sequencing of skin and blood DNA revealed a de novo variant in PIK3R1 (c.1746-2A>G, p.?) in 9% of the patient's blood cells and 25% of cultured fibroblasts. Initially, classified as a variant of uncertain significance, this variant was later confirmed to be the cause. CONCLUSIONS This is the first intronic SNV in a canonical splice site within iSH2 described, highlighting the importance of iSH2 in the regulation of the PI3K/AKT pathway and its involvement in the development of vascular overgrowth and antibody deficiency.
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Affiliation(s)
| | - Lisa Schimmenti
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
- Department of OphthalmologyMayo ClinicRochesterMinnesotaUSA
- Department of Otorhinolaryngology, Head and Neck SurgeryMayo ClinicRochesterMinnesotaUSA
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMinnesotaUSA
| | | | | | - Eric W. Klee
- Center for Individualized MedicineMayo ClinicRochesterMinnesotaUSA
- Department of Clinical GenomicsMayo ClinicRochesterMinnesotaUSA
- Department of Quantitative Health SciencesMayo ClinicRochesterMinnesotaUSA
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Wilke MVMB, Morava-Kozicz E, Koster MJ, Schmitz CT, Foster SK, Patnaik M, Warrington KJ, Klee EW, Pinto E Vairo F. Exome sequencing can misread high variant allele fraction of somatic variants in UBA1 as hemizygous in VEXAS syndrome: a case report. BMC Rheumatol 2022; 6:54. [PMID: 36038944 PMCID: PMC9426024 DOI: 10.1186/s41927-022-00281-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 01/29/2022] [Accepted: 06/09/2022] [Indexed: 11/11/2022] Open
Abstract
Background VEXAS syndrome (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic syndrome) is a recently described syndrome caused by a somatic missense variant at the methionine-41 (p.(Met41)) position in the ubiquitin-like modifier activating enzyme 1 (UBA1) in Xp11.3. Germline pathogenic variants in UBA1 are associated with a distinct phenotype: a syndrome with severe neurologic features associated with loss of anterior horn cells and infantile death denominated X-Linked Spinal Muscular Atrophy 2 (SMAX2) (OMIM 301,830).
Case presentation We report a male individual with the phenotype of VEXAS syndrome that was initially identified through exome sequencing (ES) as having a hemizygous germline variant in UBA1 due to high variant allele frequency (VAF). Research Sanger sequencing was able to confirm the absence of the p.(Met41Val) variant in a skin biopsy and in gastric mucosa tissue sample confirming the variant happened as a postzygotic event.
Conclusions The present case exemplifies the diagnostic challenge that was imposed by the high VAF detected by ES that failed to correctly demonstrate that the variant was in a mosaic state. Sequencing of different tissues should be considered when there is conflict between the UBA1 variant status and the clinical findings. Supplementary Information The online version contains supplementary material available at 10.1186/s41927-022-00281-z.
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Affiliation(s)
| | - Eva Morava-Kozicz
- Department of Clinical Genomics, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Matthew J Koster
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Christopher T Schmitz
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shannon Kaye Foster
- Division of Dermatology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Mrinal Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kenneth J Warrington
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Clinical Genomics, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.,Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Clinical Genomics, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
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Kubaski F, Herbst ZM, Burin MG, Michelin‐Tirelli K, Trapp FB, Gus R, Netto ABO, Brusius‐Facchin AC, Leistner‐Segal S, Sanseverino MT, Souza CMFD, Wilke MVMB, Oliveira T, Magalhães JAA, Giugliani R. Measurement of sulfatides in the amniotic fluid supernatant: A useful tool in the prenatal diagnosis of metachromatic leukodystrophy. JIMD Rep 2022; 63:162-167. [PMID: 35281662 PMCID: PMC8898714 DOI: 10.1002/jmd2.12270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 12/02/2022] Open
Abstract
Metachromatic leukodystrophy (MLD) is an autosomal recessive lysosomal disorder caused by deficiency of arylsulfatase A (ARSA), leading to an accumulation of sulfatides. Sulfatides have been quantified in urine, dried blood spots (DBS), and tissues of patients with MLD. Newborn screening (NBS) for MLD has already been proposed based on a two‐tier approach with the quantification of sulfatides in DBS followed by the quantification of ARSA by liquid chromatography–tandem mass spectrometry (LC–MS/MS). Prenatal screening for MLD is also crucial, and sulfatide quantification in amniotic fluid (AF) can aid diagnosis. The prenatal study was initiated due to a family history of MLD at 19 weeks of gestation. ARSA was quantified in cultured amniocytes. C16:0 sulfatide was quantified by LC‐MS/MS in the supernatant of AF. Molecular analysis of the ARSA gene was performed in cultured amniocytes. ARSA was deficient in fetal cells, and C16:0 sulfatides were significantly elevated in comparison to age‐matched controls (3‐fold higher). Genetic studies identified the c.465+1G>A variant in homozygosis in the ARSA gene. Our study shows that sulfatides can be quantified in the supernatant of AF of MLD fetuses, and it could potentially aid in a faster and more accurate diagnosis of MLD patients.
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Affiliation(s)
- Francyne Kubaski
- PPGBM UFRGS Porto Alegre Brazil
- Medical Genetics Service HCPA Porto Alegre Brazil
- INAGEMP Porto Alegre Brazil
| | - Zackary M. Herbst
- Department of Chemistry University of Washington Seattle Washington USA
| | | | | | | | - Rejane Gus
- Medical Genetics Service HCPA Porto Alegre Brazil
| | - Alice B. O. Netto
- PPGBM UFRGS Porto Alegre Brazil
- Medical Genetics Service HCPA Porto Alegre Brazil
| | | | | | | | | | | | | | | | - Roberto Giugliani
- PPGBM UFRGS Porto Alegre Brazil
- Medical Genetics Service HCPA Porto Alegre Brazil
- INAGEMP Porto Alegre Brazil
- PPGCM UFRGS Porto Alegre Brazil
- Department of Genetics UFRGS Porto Alegre Brazil
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Wilke MVMB, Oliveira BM, Pereira A, Doriqui MJR, Kok F, Souza CFM. Two different presentations of de novo variants of CSNK2B: two case reports. J Med Case Rep 2022; 16:4. [PMID: 34983633 PMCID: PMC8728954 DOI: 10.1186/s13256-021-03184-8] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Poirier–Bienvenu neurodevelopmental syndrome is a neurologic disorder caused by mutations in the CSNK2B gene. It is mostly characterized by early-onset seizures, hypotonia, and mild dysmorphic features. Craniodigital syndrome is a recently described disorder also related to CSNK2B, with a single report in the literature. Objective To report two unrelated cases of children harboring CSNK2B variants (NM_001320.6) who presented with distinct diseases. Case report Case 1 is a 7-month-old, Caucasian, female patient with chief complaints of severe hypotonia and drug-refractory myoclonic epilepsy, with a likely pathogenic de novo variant c.494A>G (p.His165Arg). Case 2 is a 5-year-old male, Latino patient with craniodigital intellectual disability syndrome subjacent to a de novo, likely pathogenic variant c.94G>T (p.Asp32Tyr). His dysmorphic features included facial dysmorphisms, supernumerary nipples, and left-hand postaxial polydactyly. Conclusion This report suggest that the CSNK2B gene may be involved in the physiopathology of neurodevelopmental disorders and variable dysmorphic features.
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Affiliation(s)
- Matheus V M B Wilke
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos, 2350 - 3º andar, Porto Alegre, RS, 90035-007, Brazil.,Post Graduate Program in Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Bibiana M Oliveira
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos, 2350 - 3º andar, Porto Alegre, RS, 90035-007, Brazil.,Post Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Mendelics Genomic Analysis, São Paulo, SP, Brazil
| | - Alessandra Pereira
- Pediatrics Service, Neuropediatrics, Hospital Moinhos de Vento, Porto Alegre, RS, Brazil
| | | | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo, SP, Brazil
| | - Carolina F M Souza
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos, 2350 - 3º andar, Porto Alegre, RS, 90035-007, Brazil.
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Wilke MVMB, Dornelles AD, Schuh AS, Vairo FP, Basgalupp SP, Siebert M, Nalin T, Piltcher OB, Schwartz IVD. Evaluation of the frequency of non-motor symptoms of Parkinson's disease in adult patients with Gaucher disease type 1. Orphanet J Rare Dis 2019; 14:103. [PMID: 31077260 PMCID: PMC6509774 DOI: 10.1186/s13023-019-1079-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 02/10/2019] [Accepted: 04/23/2019] [Indexed: 01/13/2023] Open
Abstract
Background Gaucher disease (GD) is caused by deficiency of beta-glucocerebrosidase (GCase) due to biallelic variations in the GBA1 gene. Parkinson’s disease (PD) is the second most common neurodegenerative condition. The classic motor symptoms of PD may be preceded by many non-motor symptoms (NMS), which include hyposmia, rapid eye movement (REM) sleep behavior disorder, constipation, cognitive impairment, and depression. Population studies have identified mutations in GBA1 as the main risk factor for idiopathic PD. The present study sought to evaluate the prevalence of NMS in a cohort of patients with GD type 1 from Southern Brazil. Methodology This is an observational, cross-sectional study, with a convenience sampling strategy. Cognition was evaluated by the Montreal Cognitive assessment (MoCa), daytime sleepiness by the Epworth Scale, depression by the Beck Inventory, constipation by the Unified Multiple System Atrophy Rating Scale, and REM sleep behavior disorder by the Single-Question Screen; hyposmia by the Sniffin’ Sticks. Motor symptoms were assessed with part III of the Unified Parkinson’s Disease Rating Scale. All patients were also genotyped for the GBA1 3′-UTR SNP (rs708606). Results Twenty-three patients (female = 13; on enzyme replacement therapy = 21, substrate reduction therapy = 2) with a mean age of 41.45 ± 15.3 years (range, 22–67) were included. Eight patients were found to be heterozygous for the 3′-UTR SNP (rs708606). Fourteen patients (8 over age 40 years) presented at least one NMS; daytime sleepiness was the most frequent (n = 10). Two patients (aged 63 and 64, respectively) also presented motor symptoms, probably drug-related. Conclusions NMS were prevalent in this cohort. We highlight the importance of a multidisciplinary follow-up focusing on earlier diagnosis of PD, especially for patients with GD type 1 over the age of 40.
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Affiliation(s)
- Matheus V M B Wilke
- Postgraduate Program in Medical Sciences, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil. .,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.
| | - Alícia D Dornelles
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Artur S Schuh
- Postgraduate Program in Medical Sciences, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Department of Pharmacology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Filippo P Vairo
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Suelen P Basgalupp
- Postgraduate Program in Medical Sciences, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,BRAIN Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Marina Siebert
- Graduate Program in Sciences of Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Laboratory Research Unit, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil.,BRAIN Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Tatiele Nalin
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Otavio B Piltcher
- Department of Ophthalmology and Otorhinolaryngology, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Ida V D Schwartz
- Postgraduate Program in Medical Sciences, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,BRAIN Laboratory, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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Wilke MVMB, de Kleine RH, Wietasch JKG, van Amerongen CCA, Blokzijl H, van Spronsen FJ, Schwartz IVD, Derks TGJ. Orthotopic Liver Transplantation in Glycogen Storage Disease Type 1a. Journal of Inborn Errors of Metabolism and Screening 2016. [DOI: 10.1177/2326409816649599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Matheus V. M. B. Wilke
- Section of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- School of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ruben H. de Kleine
- Department of Hepato-Pancreato-Biliary Surgery & Liver Transplantation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - J. K. G. Wietasch
- Department of Anesthesiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cynthia C. A. van Amerongen
- Section of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Francjan J. van Spronsen
- Section of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ida V. D. Schwartz
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Terry G. J. Derks
- Section of Metabolic Diseases, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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