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Dardas Z, Fatih JM, Jolly A, Dawood M, Du H, Grochowski CM, Jones EG, Jhangiani SN, Wehrens XHT, Liu P, Bi W, Boerwinkle E, Posey JE, Muzny DM, Gibbs RA, Lupski JR, Coban-Akdemir Z, Morris SA. NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy. Genome Med 2024; 16:53. [PMID: 38570875 PMCID: PMC10988827 DOI: 10.1186/s13073-024-01312-9] [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] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown to cause laterality defects in humans. To further explore this association and improve genetic diagnosis, the study aims to identify and characterize a broader range of NODAL variants in a large number of individuals with laterality defects. METHODS We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses. To this cohort we added 12 affected subjects with known NODAL variants and CHD from institutional research and clinical cohorts to investigate an allelic series. For those with candidate contributory variants, variant allele confirmation and segregation analysis were studied by Sanger sequencing in available family members. Array comparative genomic hybridization and droplet digital PCR were utilized for copy number variants (CNV) validation and characterization. We performed Human Phenotype Ontology (HPO)-based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. RESULTS Missense, nonsense, splice site, indels, and/or structural variants of NODAL were identified as potential causes of heterotaxy and other laterality defects in 33 CHD cases. We describe a recurrent complex indel variant for which the nucleic acid secondary structure predictions implicate secondary structure mutagenesis as a possible mechanism for formation. We identified two CNV deletion alleles spanning NODAL in two unrelated CHD cases. Furthermore, 17 CHD individuals were found (16/17 with known Hispanic ancestry) to have the c.778G > A:p.G260R NODAL missense variant which we propose reclassification from variant of uncertain significance (VUS) to likely pathogenic. Quantitative HPO-based analyses of the observed clinical phenotype for all cases with p.G260R variation, including heterozygous, homozygous, and compound heterozygous cases, reveal clustering of individuals with biallelic variation. This finding provides evidence for a genotypic-phenotypic correlation and an allele-specific gene dosage model. CONCLUSION Our data further support a role for rare deleterious variants in NODAL as a cause for sporadic human laterality defects, expand the repertoire of observed anatomical complexity of potential cardiovascular anomalies, and implicate an allele specific gene dosage model.
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Affiliation(s)
- Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Edward G Jones
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xander H T Wehrens
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Shaine A Morris
- Division of Cardiology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, 77030, USA.
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Lupski J, Dardas Z, Marafi D, Duan R, Fatih J, El-Rashidy O, Grochowski C, Carvalho C, Jhangiani S, Bi W, Du H, Gibbs R, Posey J, Calame D, Zaki M. Genomic Balancing Act: Deciphering DNA rearrangements in the Complex Chromosomal Aberration involving 5p15.2, 2q31.1 and 18q21.32. Res Sq 2024:rs.3.rs-3949622. [PMID: 38464263 PMCID: PMC10925411 DOI: 10.21203/rs.3.rs-3949622/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Despite extensive research into the genetic underpinnings of neurodevelopmental disorders (NDD), many clinical cases remain unresolved. We studied a female proband with a NDD, mildly dysmorphic facial features, and brain stem hypoplasia on neuroimaging. Comprehensive genomic analyses revealed a terminal 5p loss and terminal 18q gain in the proband while a diploid copy number for chromosomes 5 and 18 in both parents. Genomic investigations in the proband identified an unbalanced translocation t(5;18) with additional genetic material from chromosome 2 (2q31.3) inserted at the breakpoint, pointing to a complex chromosomal rearrangement (CCR) involving 5p15.2, 2q31.3, and 18q21.32. Breakpoint junction analyses enabled by long read genome sequencing unveiled the presence of four distinct junctions in the father, who is carrier of a balanced CCR. The proband inherited from the father both the abnormal chromosome 5 resulting in segmental aneusomies of chr5 (loss) and chr18 (gain) and a der(2) homologue. Evidences suggest a chromoplexy mechanism for this CCR derivation, involving double-strand breaks (DSBs) repaired by non-homologous end joining (NHEJ) or alternative end joining (alt-EJ). The complexity of the CCR and the segregation of homologues elucidate the genetic model for this family. This study demonstrates the importance of combining multiple genomic technologies to uncover genetic causes of complex neurodevelopmental syndrome and to better understand genetic disease mechanisms.
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Odom J, Bacino CA, Karaviti LP, Bi W, Hoyos-Martinez A. Intrafamilial phenotypic heterogeneity in siblings with pseudohypoparathyroidism 1B due to maternal STX16 deletion. J Pediatr Endocrinol Metab 2024; 37:84-89. [PMID: 38095637 DOI: 10.1515/jpem-2023-0249] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/15/2023] [Indexed: 01/10/2024]
Abstract
OBJECTIVES Pseudohypoparathyroidism (PHP1B) is most commonly caused by epigenetic defects resulting in loss of methylation at the GNAS locus, although deletions of STX16 leading to GNAS methylation abnormalities have been previously reported. The phenotype of this disorder is variable and can include hormonal resistances and severe infantile obesity with hyperphagia. A possible time relationship between the onset of obesity and endocrinopathies has been previously reported but remains unclear. Understanding of the condition's natural history is limited, partly due to a scarcity of literature, especially in children. CASE PRESENTATION We report three siblings with autosomal dominant PHP1B caused by a deletion in STX16 who presented with early childhood onset PTH-resistance with normocalcemia with a progressive nature, accompanied by TSH-resistance and severe infantile obesity with hyperphagia in some, not all of the affected individuals. CONCLUSIONS PHP1B from a STX16 deletion displays intrafamilial phenotypic variation. It is a novel cause of severe infantile obesity, which is not typically included in commercially available gene panels but must be considered in the genetic work-up. Finally, it does not seem to have a clear time relationship between the onset of obesity and hormonal resistance.
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Affiliation(s)
- John Odom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Lefkothea P Karaviti
- Department of Pediatrics, Division of Pediatric Diabetes and Endocrinology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Alfonso Hoyos-Martinez
- Department of Pediatrics, Division of Pediatric Diabetes and Endocrinology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
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Rios JJ, Li Y, Paria N, Bohlender RJ, Huff C, Rosenfeld JA, Liu P, Bi W, Haga K, Fukuda M, Vashisth S, Kaur K, Chahrour MH, Bober MB, Duker AL, Ladha FA, Hanchard NA, Atala K, Khanshour AM, Smith L, Wise CA, Delgado MR. RAB1A haploinsufficiency phenocopies the 2p14-p15 microdeletion and is associated with impaired neuronal differentiation. Am J Hum Genet 2023; 110:2103-2111. [PMID: 37924809 PMCID: PMC10722380 DOI: 10.1016/j.ajhg.2023.10.009] [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: 08/03/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/06/2023] Open
Abstract
Hereditary spastic parapareses (HSPs) are clinically heterogeneous motor neuron diseases with variable age of onset and severity. Although variants in dozens of genes are implicated in HSPs, much of the genetic basis for pediatric-onset HSP remains unexplained. Here, we re-analyzed clinical exome-sequencing data from siblings with HSP of unknown genetic etiology and identified an inherited nonsense mutation (c.523C>T [p.Arg175Ter]) in the highly conserved RAB1A. The mutation is predicted to produce a truncated protein with an intact RAB GTPase domain but without two C-terminal cysteine residues required for proper subcellular protein localization. Additional RAB1A mutations, including two frameshift mutations and a mosaic missense mutation (c.83T>C [p.Leu28Pro]), were identified in three individuals with similar neurodevelopmental presentations. In rescue experiments, production of the full-length, but not the truncated, RAB1a rescued Golgi structure and cell proliferation in Rab1-depleted cells. In contrast, the missense-variant RAB1a disrupted Golgi structure despite intact Rab1 expression, suggesting a dominant-negative function of the mosaic missense mutation. Knock-down of RAB1A in cultured human embryonic stem cell-derived neurons resulted in impaired neuronal arborization. Finally, RAB1A is located within the 2p14-p15 microdeletion syndrome locus. The similar clinical presentations of individuals with RAB1A loss-of-function mutations and the 2p14-p15 microdeletion syndrome implicate loss of RAB1A in the pathogenesis of neurodevelopmental manifestations of this microdeletion syndrome. Our study identifies a RAB1A-related neurocognitive disorder with speech and motor delay, demonstrates an essential role for RAB1a in neuronal differentiation, and implicates RAB1A in the etiology of the neurodevelopmental sequelae associated with the 2p14-p15 microdeletion syndrome.
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Affiliation(s)
- Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Departments of Pediatrics University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Yang Li
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Nandina Paria
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Ryan J Bohlender
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chad Huff
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Pengfei Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Weimin Bi
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Kentaro Haga
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Mitsunori Fukuda
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shayal Vashisth
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria H Chahrour
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Peter O'Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael B Bober
- Nemours Children's Hospital, Wilmington, DE 19803, USA; Thomas Jefferson University, Philadelphia, PA 19144, USA
| | | | - Farah A Ladha
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil A Hanchard
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristhen Atala
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Anas M Khanshour
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Linsley Smith
- Department of Neurology, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Departments of Pediatrics University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Orthopaedic Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mauricio R Delgado
- Department of Neurology, Scottish Rite for Children, Dallas, TX 75219, USA; Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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5
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Beers BJ, Similuk MN, Ghosh R, Seifert BA, Jamal L, Kamen M, Setzer MR, Jodarski C, Duncan R, Hunt D, Mixer M, Cao W, Bi W, Veltri D, Karlins E, Zhang L, Li Z, Oler AJ, Jevtich K, Yu Y, Hullfish H, Bielekova B, Frischmeyer-Guerrerio P, Dang Do A, Huryn LA, Olivier KN, Su HC, Lyons JJ, Zerbe CS, Rao VK, Keller MD, Freeman AF, Holland SM, Franco LM, Walkiewicz MA, Yan J. Chromosomal microarray analysis supplements exome sequencing to diagnose children with suspected inborn errors of immunity. Front Immunol 2023; 14:1172004. [PMID: 37215141 PMCID: PMC10196392 DOI: 10.3389/fimmu.2023.1172004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
Purpose Though copy number variants (CNVs) have been suggested to play a significant role in inborn errors of immunity (IEI), the precise nature of this role remains largely unexplored. We sought to determine the diagnostic contribution of CNVs using genome-wide chromosomal microarray analysis (CMA) in children with IEI. Methods We performed exome sequencing (ES) and CMA for 332 unrelated pediatric probands referred for evaluation of IEI. The analysis included primary, secondary, and incidental findings. Results Of the 332 probands, 134 (40.4%) received molecular diagnoses. Of these, 116/134 (86.6%) were diagnosed by ES alone. An additional 15/134 (11.2%) were diagnosed by CMA alone, including two likely de novo changes. Three (2.2%) participants had diagnostic molecular findings from both ES and CMA, including two compound heterozygotes and one participant with two distinct diagnoses. Half of the participants with CMA contribution to diagnosis had CNVs in at least one non-immune gene, highlighting the clinical complexity of these cases. Overall, CMA contributed to 18/134 diagnoses (13.4%), increasing the overall diagnostic yield by 15.5% beyond ES alone. Conclusion Pairing ES and CMA can provide a comprehensive evaluation to clarify the complex factors that contribute to both immune and non-immune phenotypes. Such a combined approach to genetic testing helps untangle complex phenotypes, not only by clarifying the differential diagnosis, but in some cases by identifying multiple diagnoses contributing to the overall clinical presentation.
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Affiliation(s)
- Breanna J. Beers
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Morgan N. Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rajarshi Ghosh
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Bryce A. Seifert
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Leila Jamal
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Michael Kamen
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael R. Setzer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Colleen Jodarski
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rylee Duncan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Devin Hunt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Madison Mixer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Wenjia Cao
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Weimin Bi
- Baylor Genetics, Houston, TX, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Daniel Veltri
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Eric Karlins
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingwen Zhang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Zhiwen Li
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew J. Oler
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kathleen Jevtich
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yunting Yu
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Haley Hullfish
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Bibiana Bielekova
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Pamela Frischmeyer-Guerrerio
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - An Dang Do
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Laryssa A. Huryn
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kenneth N. Olivier
- Division of Pulmonary Diseases and Critical Care Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Helen C. Su
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jonathan J. Lyons
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Christa S. Zerbe
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - V. Koneti Rao
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael D. Keller
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alexandra F. Freeman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Steven M. Holland
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Luis M. Franco
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Magdalena A. Walkiewicz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jia Yan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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6
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Chong SC, Cao Y, Fung ELW, Kleppe S, Gripp KW, Hertecant J, El-Hattab AW, Suleiman J, Clark G, von Allmen G, Rodziyevska O, Lewis RA, Rosenfeld JA, Dong J, Wang X, Miller MJ, Bi W, Liu P, Scaglia F. Expansion of the clinical and molecular spectrum of WWOX-related epileptic encephalopathy. Am J Med Genet A 2023; 191:776-785. [PMID: 36537114 DOI: 10.1002/ajmg.a.63074] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 11/21/2022] [Accepted: 11/27/2022] [Indexed: 02/14/2023]
Abstract
WWOX biallelic loss-of-function pathogenic single nucleotide variants (SNVs) and copy number variants (CNVs) including exonic deletions and duplications cause WWOX-related epileptic encephalopathy (WOREE) syndrome. This disorder is characterized by refractory epilepsy, axial hypotonia, peripheral hypertonia, progressive microcephaly, and premature death. Here we report five patients with WWOX biallelic predicted null variants identified by exome sequencing (ES), genome sequencing (GS), and/or chromosomal microarray analysis (CMA). SNVs and intragenic deletions of one or more exons were commonly reported in WOREE syndrome patients which made the genetic diagnosis challenging and required a combination of different diagnostic technologies. These patients presented with severe, developmental and epileptic encephalopathy (DEE), and other cardinal features consistent with WOREE syndrome. This report expands the clinical phenotype associated with this condition, including failure to thrive in most patients and epilepsy that responded to a ketogenic diet in three patients. Dysmorphic features and abnormal prenatal findings were not commonly observed. Additionally, recurrent pancreatitis and sensorineural hearing loss each were observed in single patients. In summary, these phenotypic features broaden the clinical spectrum of WOREE syndrome.
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Affiliation(s)
- Shuk Ching Chong
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China.,Joint BCM-CUHK Center of Medical Genetics, Chinese University of Hong Kong, Hong Kong, China
| | - Ye Cao
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China.,Joint BCM-CUHK Center of Medical Genetics, Chinese University of Hong Kong, Hong Kong, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Eva L W Fung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Soledad Kleppe
- Unidad de Metabolismo, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Karen W Gripp
- Division of Medical Genetics, A. I. du Pont Hospital for Children/Nemours, Wilmington, Delaware, USA
| | - Jozef Hertecant
- Division of Genetic and Metabolic Disorders, Departments of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jehan Suleiman
- Division of Neurology, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates.,Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Gary Clark
- Neurology and Developmental Neuroscience, Baylor College of Medicine, Neurology Service, Texas Children's Hospital, Houston, Texas, USA
| | - Gretchen von Allmen
- Division of Child Neurology, Department of Pediatrics, McGovern Medical School, Houston, Texas, USA
| | - Olga Rodziyevska
- Division of Child Neurology, Department of Pediatrics, McGovern Medical School, Houston, Texas, USA
| | - Richard A Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jie Dong
- Baylor Genetics, Houston, Texas, USA
| | | | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Marcus J Miller
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Fernando Scaglia
- Joint BCM-CUHK Center of Medical Genetics, Chinese University of Hong Kong, Hong Kong, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, China.,Texas Children's Hospital, Houston, Texas, USA
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7
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Sakyu T, Stover SR, Wang Y, Ward P, Gandhi M, Braun MC, Van den Veyver IB, Bi W. Compound heterozygosity of a de novo submicroscopic deletion and an inherited frameshift pathogenic variant in the PKHD1 gene in a fetus with bilaterally enlarged and echogenic kidneys, enlarged abdomen and oligohydramnios. Clin Case Rep 2023; 11:e6692. [PMID: 36846174 PMCID: PMC9950036 DOI: 10.1002/ccr3.6692] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/08/2022] [Indexed: 02/26/2023] Open
Abstract
We present a fetus with bilaterally enlarged and echogenic kidneys. Prenatal testing detected compound heterozygosity for a 0.676 Mb de novo deletion and an inherited pathogenic variant in PKHD1. This is the first case of autosomal recessive polycystic kidney disease (ARPKD) with a prenatally detected disease-causing PKHD1 deletion.
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Affiliation(s)
- Takuya Sakyu
- Baylor GeneticsHoustonTexasUSA,Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA,Present address:
H.U. Group Research Institute GKTokyoJapan
| | - Samantha R. Stover
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA,Department of Obstetrics and GynecologyBaylor College of MedicineHoustonTexasUSA,Texas Children's HospitalHoustonTexasUSA,Present address:
Department of Obstetrics and Gynecology, Division of Maternal Fetal MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Yue Wang
- Baylor GeneticsHoustonTexasUSA,Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Patricia Ward
- Baylor GeneticsHoustonTexasUSA,Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Manisha Gandhi
- Department of Obstetrics and GynecologyBaylor College of MedicineHoustonTexasUSA,Texas Children's HospitalHoustonTexasUSA
| | - Michael C. Braun
- Department of Obstetrics and GynecologyBaylor College of MedicineHoustonTexasUSA,Texas Children's HospitalHoustonTexasUSA,Division of Pediatrics NephrologyBaylor College of MedicineHoustonTexasUSA,Department of PediatricsBaylor College of MedicineHoustonTexasUSA
| | - Ignatia B. Van den Veyver
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA,Department of Obstetrics and GynecologyBaylor College of MedicineHoustonTexasUSA,Texas Children's HospitalHoustonTexasUSA
| | - Weimin Bi
- Baylor GeneticsHoustonTexasUSA,Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
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8
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de Prisco N, Ford C, Elrod ND, Lee W, Tang LC, Huang KL, Lin A, Ji P, Jonnakuti VS, Boyle L, Cabaj M, Botta S, Õunap K, Reinson K, Wojcik MH, Rosenfeld JA, Bi W, Tveten K, Prescott T, Gerstner T, Schroeder A, Fong CT, George-Abraham JK, Buchanan CA, Hanson-Khan A, Bernstein JA, Nella AA, Chung WK, Brandt V, Jovanovic M, Targoff KL, Yalamanchili HK, Wagner EJ, Gennarino VA. Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites. Sci Adv 2023; 9:eade4814. [PMID: 36800428 PMCID: PMC9937581 DOI: 10.1126/sciadv.ade4814] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Alternative polyadenylation (APA) creates distinct transcripts from the same gene by cleaving the pre-mRNA at poly(A) sites that can lie within the 3' untranslated region (3'UTR), introns, or exons. Most studies focus on APA within the 3'UTR; however, here, we show that CPSF6 insufficiency alters protein levels and causes a developmental syndrome by deregulating APA throughout the transcript. In neonatal humans and zebrafish larvae, CPSF6 insufficiency shifts poly(A) site usage between the 3'UTR and internal sites in a pathway-specific manner. Genes associated with neuronal function undergo mostly intronic APA, reducing their expression, while genes associated with heart and skeletal function mostly undergo 3'UTR APA and are up-regulated. This suggests that, under healthy conditions, cells toggle between internal and 3'UTR APA to modulate protein expression.
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Affiliation(s)
- Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Caitlin Ford
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ai Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, WC67+HC Dongcheng, Beijing, China
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Venkata S. Jonnakuti
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Lia Boyle
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Maximilian Cabaj
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Salvatore Botta
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H. Wojcik
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Thorsten Gerstner
- Department of Child Neurology and Rehabilitation and Department of Pediatrics, Hospital of Southern Norway, Arendal, Norway
| | - Audrey Schroeder
- Division of Medical Genetics, University of Rochester Medical Center, Rochester, NY, USA
| | - Chin-To Fong
- Department of Pediatrics and of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Jaya K. George-Abraham
- Dell Children’s Medical Group, Austin, TX, USA
- Department of Pediatrics, The University of Texas at Austin Dell Medical School, Austin, TX, USA
| | | | - Andrea Hanson-Khan
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA
- Department of Genetics, Stanford School of Medicine, Palo Alto, CA, USA
| | - Jonathan A. Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA
| | - Aikaterini A. Nella
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Wendy K. Chung
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Vicky Brandt
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kimara L. Targoff
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Hari Krishna Yalamanchili
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J. Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY, USA
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9
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Hijazi H, Reis LM, Pehlivan D, Bernstein JA, Muriello M, Syverson E, Bonner D, Estiar MA, Gan-Or Z, Rouleau GA, Lyulcheva E, Greenhalgh L, Tessarech M, Colin E, Guichet A, Bonneau D, van Jaarsveld R, Lachmeijer A, Ruaud L, Levy J, Tabet AC, Ploski R, Rydzanicz M, Kępczyński Ł, Połatyńska K, Li Y, Fatih JM, Marafi D, Rosenfeld JA, Coban-Akdemir Z, Bi W, Gibbs RA, Hobson GM, Hunter JV, Carvalho CM, Posey JE, Semina EV, Lupski JR. TCEAL1 loss-of-function results in an X-linked dominant neurodevelopmental syndrome and drives the neurological disease trait in Xq22.2 deletions. Am J Hum Genet 2022; 109:2270-2282. [PMID: 36368327 PMCID: PMC9748253 DOI: 10.1016/j.ajhg.2022.10.007] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022] Open
Abstract
An Xq22.2 region upstream of PLP1 has been proposed to underly a neurological disease trait when deleted in 46,XX females. Deletion mapping revealed that heterozygous deletions encompassing the smallest region of overlap (SRO) spanning six Xq22.2 genes (BEX3, RAB40A, TCEAL4, TCEAL3, TCEAL1, and MORF4L2) associate with an early-onset neurological disease trait (EONDT) consisting of hypotonia, intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. None of the genes within the SRO have been associated with monogenic disease in OMIM. Through local and international collaborations facilitated by GeneMatcher and Matchmaker Exchange, we have identified and herein report seven de novo variants involving TCEAL1 in seven unrelated families: three hemizygous truncating alleles; one hemizygous missense allele; one heterozygous TCEAL1 full gene deletion; one heterozygous contiguous deletion of TCEAL1, TCEAL3, and TCEAL4; and one heterozygous frameshift variant allele. Variants were identified through exome or genome sequencing with trio analysis or through chromosomal microarray. Comparison with previously reported Xq22 deletions encompassing TCEAL1 identified a more-defined syndrome consisting of hypotonia, abnormal gait, developmental delay/intellectual disability especially affecting expressive language, autistic-like behavior, and mildly dysmorphic facial features. Additional features include strabismus, refractive errors, variable nystagmus, gastroesophageal reflux, constipation, dysmotility, recurrent infections, seizures, and structural brain anomalies. An additional maternally inherited hemizygous missense allele of uncertain significance was identified in a male with hypertonia and spasticity without syndromic features. These data provide evidence that TCEAL1 loss of function causes a neurological rare disease trait involving significant neurological impairment with features overlapping the EONDT phenotype in females with the Xq22 deletion.
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Affiliation(s)
- Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linda M. Reis
- Department of Pediatrics and Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA,Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Jonathan A. Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Michael Muriello
- Department of Pediatrics and Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI, USA
| | - Erin Syverson
- Department of Pediatrics and Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI, USA
| | - Devon Bonner
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Mehrdad A. Estiar
- Department of Human Genetics, McGill University, Montreal, QC, Canada,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montreal, QC, Canada,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada,Department of Neurology & Neurosurgery, McGill University, Montreal, QC, Canada
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montreal, QC, Canada,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada,Department of Neurology & Neurosurgery, McGill University, Montreal, QC, Canada
| | - Ekaterina Lyulcheva
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | - Lynn Greenhalgh
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | - Marine Tessarech
- Department of Medical Genetics, Angers University Hospital, Angers, France,Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Estelle Colin
- Department of Medical Genetics, Angers University Hospital, Angers, France,Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Agnès Guichet
- Department of Medical Genetics, Angers University Hospital, Angers, France,Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - Dominique Bonneau
- Department of Medical Genetics, Angers University Hospital, Angers, France,Mitovasc Unit, UMR CNRS 6015-INSERM 1083, University of Angers, Angers, France
| | - R.H. van Jaarsveld
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - A.M.A. Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lyse Ruaud
- INSERM UMR1141, Neurodiderot, University of Paris, 75019 Paris, France,APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Jonathan Levy
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Anne-Claude Tabet
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, 75019 Paris, France
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Łukasz Kępczyński
- Department of Genetics, Polish Mother’s Memorial Hospital – Research Institute, Łódź, Poland
| | - Katarzyna Połatyńska
- Department of Developmental Neurology an Epileptology, Polish Mother’s Memorial Hospital – Research Institute, Łódź, Poland
| | - Yidan Li
- 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
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Baylor Genetics, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Baylor Genetics, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Grace M. Hobson
- Department of Research, Nemours Children’s Health, Wilmington, DE, USA
| | - Jill V. Hunter
- E.B. Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, TX, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elena V. Semina
- Department of Pediatrics and Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI, USA,Departments of Ophthalmology and Visual Sciences and Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA,Corresponding author
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Department of Pediatrics, 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,Corresponding author
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10
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Sy MR, Chauhan J, Prescott K, Imam A, Kraus A, Beleza A, Salkeld L, Hosdurga S, Parker M, Vasudevan P, Islam L, Goel H, Bain N, Park SM, Mohammed S, Dieterich K, Coutton C, Satre V, Vieville G, Donaldson A, Beneteau C, Ghoumid J, Bogaert KVD, Boogaerts A, Boudry E, Vanlerberghe C, Petit F, Bernardini L, Torres B, Mattina T, Carli D, Mandrile G, Pinelli M, Brunetti-Pierri N, Neas K, Beddow R, Tørring PM, Faletra F, Spedicati B, Gasparini P, Mussa A, Ferrero GB, Lampe A, Lam W, Bi W, Bacino CA, Kuwahara A, Bush JO, Zhao X, Luna PN, Shaw CA, Rosenfeld JA, Scott DA. Exome sequencing efficacy and phenotypic expansions involving esophageal atresia/tracheoesophageal fistula plus. Am J Med Genet A 2022; 188:3492-3504. [PMID: 36135330 PMCID: PMC9669235 DOI: 10.1002/ajmg.a.62976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/22/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/31/2023]
Abstract
Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a life-threatening birth defect that often occurs with other major birth defects (EA/TEF+). Despite advances in genetic testing, a molecular diagnosis can only be made in a minority of EA/TEF+ cases. Here, we analyzed clinical exome sequencing data and data from the DECIPHER database to determine the efficacy of exome sequencing in cases of EA/TEF+ and to identify phenotypic expansions involving EA/TEF. Among 67 individuals with EA/TEF+ referred for clinical exome sequencing, a definitive or probable diagnosis was made in 11 cases for an efficacy rate of 16% (11/67). This efficacy rate is significantly lower than that reported for other major birth defects, suggesting that polygenic, multifactorial, epigenetic, and/or environmental factors may play a particularly important role in EA/TEF pathogenesis. Our cohort included individuals with pathogenic or likely pathogenic variants that affect TCF4 and its downstream target NRXN1, and FANCA, FANCB, and FANCC, which are associated with Fanconi anemia. These cases, previously published case reports, and comparisons to other EA/TEF genes made using a machine learning algorithm, provide evidence in support of a potential pathogenic role for these genes in the development of EA/TEF.
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Affiliation(s)
- Mary R. Sy
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Jaynee Chauhan
- Yorkshire Regional Genetics Service, Leeds Teaching
Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Katrina Prescott
- Yorkshire Regional Genetics Service, Leeds Teaching
Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Aliza Imam
- Yorkshire Regional Genetics Service, Leeds Teaching
Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Leeds Teaching
Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Ana Beleza
- Clinical Genetics Department, University Hospitals Bristol
and Weston, Bristol NHS Foundation, Bristol, UK
| | - Lee Salkeld
- Whiteladies Medical Group, Whatley Road, Clifton, Bristol,
UK
| | - Saraswati Hosdurga
- Community Children’s Health Partnership, Sirona
Health and Care, Bristol, UK
| | - Michael Parker
- Sheffield Children’s NHS Foundation Trust,
Sheffield, UK
| | | | - Lily Islam
- Birmingham Women’s and Children’s Hospital
NHS Foundation Trust, Birmingham, UK
| | - Himanshu Goel
- Hunter New England Local Health District, Hunter Genetics,
Waratah, NSW, Australia
- University of Newcastle, Callaghan, NSW, Australia
| | - Nicole Bain
- Department of Molecular Medicine, New South Wales Health
Pathology, Newcastle, Australia
| | - Soo-Mi Park
- East Anglian Medical Genetics Service, Cambridge
University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Klaus Dieterich
- Département de Génétique et
Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble Cedex,
France
- INSERM U1216 Grenoble Institut des Neurosciences,
Cellular Myology and Pathology, Grenoble, France
| | - Charles Coutton
- Département de Génétique et
Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble Cedex,
France
- Genetic Epigenetic and Therapies of Infertility team,
Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université
Grenoble Alpes, Grenoble, France
| | - Véronique Satre
- Département de Génétique et
Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble Cedex,
France
- Genetic Epigenetic and Therapies of Infertility team,
Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université
Grenoble Alpes, Grenoble, France
| | - Gaëlle Vieville
- Département de Génétique et
Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble Cedex,
France
| | - Alan Donaldson
- Clinical Genetics Department, St Michaels Hospital,
Bristol, UK
| | - Claire Beneteau
- Nantes Université, CHU de Nantes, UF 9321 de
Fœtopathologie et Génétique, Nantes, France
| | - Jamal Ghoumid
- Université de Lille, ULR7364 RADEME, CHU Lille,
Clinique de Génétique Guy Fontaine, Lille, France
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals
Leuven–KU Leuven, Leuven, Belgium
| | - Anneleen Boogaerts
- Center for Human Genetics, University Hospitals
Leuven–KU Leuven, Leuven, Belgium
| | - Elise Boudry
- CHU Lille, Institut de Génétique
Médicale, Lille, France
| | - Clémence Vanlerberghe
- Université de Lille, ULR7364 RADEME, CHU Lille,
Clinique de Génétique Guy Fontaine, Lille, France
| | - Florence Petit
- Université de Lille, ULR7364 RADEME, CHU Lille,
Clinique de Génétique Guy Fontaine, Lille, France
| | - Laura Bernardini
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo
della Sofferenza, San Giovanni Rotondo, Italy
| | - Barbara Torres
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo
della Sofferenza, San Giovanni Rotondo, Italy
| | - Teresa Mattina
- Department of Biomedical and Biotechnological Sciences,
Medical Genetics, University of Catania, Catania, Italy
- Scientific Foundation and Clinic G. B. Morgagni,
Catania, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University
of Torino, Torino, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit, San Luigi University Hospital,
University of Torino, Orbassano, Italy
| | - Michele Pinelli
- Department of Molecular Medicine and Medical
Biotechnology, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM),
Pozzuoli, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM),
Pozzuoli, Italy
- Department of Translational Medicine, University of
Naples Federico II, Naples, Italy
| | | | - Rachel Beddow
- Wellington Regional Genetics laboratory, Wellington, New
Zealand
| | - Pernille M. Tørring
- Department of Clinical Genetics, Odense University
Hospital, Odense C, Denmark
| | - Flavio Faletra
- Institute for Maternal and Child Health - IRCCS Burlo
Garofolo, Trieste, Italy
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences,
University of Trieste, Trieste, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS Burlo
Garofolo, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences,
University of Trieste, Trieste, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University
of Torino, Torino, Italy
- Pediatric Clinical Genetics Unit, Regina Margherita
Childrens Hospital, Torino, Italy
| | | | - Anne Lampe
- South East Scotland Clinical Genetics Service, Western
General Hospital, Edinburgh, UK
| | - Wayne Lam
- Department of Clinical Genetics, Western General
Hospital, Edinburgh, UK
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Akela Kuwahara
- Department of Cell and Tissue Biology, University of
California San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California
San Francisco, San Francisco, USA
- Eli and Edythe Broad Center of Regeneration Medicine and
Stem Cell Research, University of California San Francisco, San Francisco, USA
| | - Jeffrey O. Bush
- Department of Cell and Tissue Biology, University of
California San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California
San Francisco, San Francisco, USA
- Eli and Edythe Broad Center of Regeneration Medicine and
Stem Cell Research, University of California San Francisco, San Francisco, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Pamela N. Luna
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics,
Baylor College of Medicine, Houston, TX, USA
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11
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Kumar RD, Meng L, Liu P, Miyake CY, Worley KC, Bi W, Lalani SR. Clinical exome sequencing uncovers a high frequency of Mendelian disorders in infants with stroke: A retrospective analysis. Am J Med Genet A 2022; 188:3184-3190. [PMID: 36065636 PMCID: PMC9703357 DOI: 10.1002/ajmg.a.62967] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/23/2022] [Accepted: 08/18/2022] [Indexed: 01/31/2023]
Abstract
Stroke causes significant disability and is a common cause of death worldwide. Previous studies have estimated that 1%-5% of stroke is attributable to monogenic etiologies. We set out to assess the utility of clinical exome sequencing (ES) in the evaluation of stroke. We retrospectively analyzed 124 individuals who received ES at the Baylor Genetics reference lab between 2012 and 2021 who had stroke as a major part of their reported phenotype. Ages ranged from 10 days to 69 years. 8.9% of the cohort received a diagnosis, including 25% of infants less than 1 year old; an additional 10.5% of the cohort received a probable diagnosis. We identified several syndromes that predispose to stroke such as COL4A1-related brain small vessel disease, homocystinuria caused by CBS mutation, POLG-related disorders, TTC19-linked mitochondrial disease, and RNASEH2A associated Aicardi-Goutieres syndrome. We also observed pathogenic variants in NSD1, PKHD1, HRAS, and ATP13A2, which are genes rarely associated with stroke. Although stroke is a complex phenotype with varying pathologies and risk factors, these results show that use of exome sequencing can be highly relevant in stroke, especially for those presenting <1 year of age.
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Affiliation(s)
- Runjun D. Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA,Baylor Genetics Laboratories, Houston, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA,Baylor Genetics Laboratories, Houston, Texas, USA
| | - Christina Y. Miyake
- Department of Pediatrics, Division of Cardiology, Baylor College of Medicine, Houston, Texas, USA,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
| | - Kim C. Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA,Baylor Genetics Laboratories, Houston, Texas, USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA,Corresponding Author: Seema R. Lalani, One Baylor Plaza, R806, BCM225, Houston, TX 77030,
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12
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Du H, Jolly A, Grochowski CM, Yuan B, Dawood M, Jhangiani SN, Li H, Muzny D, Fatih JM, Coban-Akdemir Z, Carlin ME, Scheuerle AE, Witzl K, Posey JE, Pendleton M, Harrington E, Juul S, Hastings PJ, Bi W, Gibbs RA, Sedlazeck FJ, Lupski JR, Carvalho CMB, Liu P. The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation. Genome Med 2022; 14:122. [PMID: 36303224 PMCID: PMC9609164 DOI: 10.1186/s13073-022-01123-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The multiple de novo copy number variant (MdnCNV) phenotype is described by having four or more constitutional de novo CNVs (dnCNVs) arising independently throughout the human genome within one generation. It is a rare peri-zygotic mutational event, previously reported to be seen once in every 12,000 individuals referred for genome-wide chromosomal microarray analysis due to congenital abnormalities. These rare families provide a unique opportunity to understand the genetic factors of peri-zygotic genome instability and the impact of dnCNV on human diseases. METHODS Chromosomal microarray analysis (CMA), array-based comparative genomic hybridization, short- and long-read genome sequencing (GS) were performed on the newly identified MdnCNV family to identify de novo mutations including dnCNVs, de novo single-nucleotide variants (dnSNVs), and indels. Short-read GS was performed on four previously published MdnCNV families for dnSNV analysis. Trio-based rare variant analysis was performed on the newly identified individual and four previously published MdnCNV families to identify potential genetic etiologies contributing to the peri-zygotic genomic instability. Lin semantic similarity scores informed quantitative human phenotype ontology analysis on three MdnCNV families to identify gene(s) driving or contributing to the clinical phenotype. RESULTS In the newly identified MdnCNV case, we revealed eight de novo tandem duplications, each ~ 1 Mb, with microhomology at 6/8 breakpoint junctions. Enrichment of de novo single-nucleotide variants (SNV; 6/79) and de novo indels (1/12) was found within 4 Mb of the dnCNV genomic regions. An elevated post-zygotic SNV mutation rate was observed in MdnCNV families. Maternal rare variant analyses identified three genes in distinct families that may contribute to the MdnCNV phenomenon. Phenotype analysis suggests that gene(s) within dnCNV regions contribute to the observed proband phenotype in 3/3 cases. CNVs in two cases, a contiguous gene duplication encompassing PMP22 and RAI1 and another duplication affecting NSD1 and SMARCC2, contribute to the clinically observed phenotypic manifestations. CONCLUSIONS Characteristic features of dnCNVs reported here are consistent with a microhomology-mediated break-induced replication (MMBIR)-driven mechanism during the peri-zygotic period. Maternal genetic variants in DNA repair genes potentially contribute to peri-zygotic genomic instability. Variable phenotypic features were observed across a cohort of three MdnCNV probands, and computational quantitative phenotyping revealed that two out of three had evidence for the contribution of more than one genetic locus to the proband's phenotype supporting the hypothesis of de novo multilocus pathogenic variation (MPV) in those families.
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Affiliation(s)
- Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher M Grochowski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
- Seattle Children's Hospital, Seattle, WA, 98105, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Mary Esther Carlin
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Angela E Scheuerle
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Division of Genetics Diagnostics, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Karin Witzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, 10013, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX, 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fritz J Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 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.
- Texas Children's Hospital, Houston, TX, 77030, USA.
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Pacific Northwest Research Institute, 720 Broadway, Seattle, WA, 98122, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Baylor Genetics Laboratory, Houston, TX, 77021, USA.
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13
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Yuan B, Schulze KV, Assia Batzir N, Sinson J, Dai H, Zhu W, Bocanegra F, Fong CT, Holder J, Nguyen J, Schaaf CP, Yang Y, Bi W, Eng C, Shaw C, Lupski JR, Liu P. Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits. Genome Med 2022; 14:113. [PMID: 36180924 PMCID: PMC9526336 DOI: 10.1186/s13073-022-01113-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Received: 11/02/2021] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In medical genetics, discovery and characterization of disease trait contributory genes and alleles depends on genetic reasoning, study design, and patient ascertainment; we suggest a segmental haploid genetics approach to enhance gene discovery and molecular diagnostics. METHODS We constructed a genome-wide map for nonallelic homologous recombination (NAHR)-mediated recurrent genomic deletions and used this map to estimate population frequencies of NAHR deletions based on large-scale population cohorts and region-specific studies. We calculated recessive disease carrier burden using high-quality pathogenic or likely pathogenic variants from ClinVar and gnomAD. We developed a NIRD (NAHR deletion Impact to Recessive Disease) score for recessive disorders by quantifying the contribution of NAHR deletion to the overall allele load that enumerated all pairwise combinations of disease-causing alleles; we used a Punnett square approach based on an assumption of random mating. Literature mining was conducted to identify all reported patients with defects in a gene with a high NIRD score; meta-analysis was performed on these patients to estimate the representation of NAHR deletions in recessive traits from contemporary human genomics studies. Retrospective analyses of extant clinical exome sequencing (cES) were performed for novel rare recessive disease trait gene and allele discovery from individuals with NAHR deletions. RESULTS We present novel genomic insights regarding the genome-wide impact of NAHR recurrent segmental variants on recessive disease burden; we demonstrate the utility of NAHR recurrent deletions to enhance discovery in the challenging context of autosomal recessive (AR) traits and biallelic variation. Computational results demonstrate new mutations mediated by NAHR, involving recurrent deletions at 30 genomic regions, likely drive recessive disease burden for over 74% of loci within these segmental deletions or at least 2% of loci genome-wide. Meta-analyses on 170 literature-reported patients implicate that NAHR deletions are depleted from the ascertained pool of AR trait alleles. Exome reanalysis of personal genomes from subjects harboring recurrent deletions uncovered new disease-contributing variants in genes including COX10, ERCC6, PRRT2, and OTUD7A. CONCLUSIONS Our results demonstrate that genomic sequencing of personal genomes with NAHR deletions could dramatically improve allele and gene discovery and enhance clinical molecular diagnosis. Moreover, results suggest NAHR events could potentially enable human haploid genetic screens as an approach to experimental inquiry into disease biology.
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Affiliation(s)
- Bo Yuan
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Katharina V. Schulze
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Nurit Assia Batzir
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Jefferson Sinson
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Hongzheng Dai
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Wenmiao Zhu
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | | | - Chin-To Fong
- grid.412750.50000 0004 1936 9166Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Jimmy Holder
- grid.39382.330000 0001 2160 926XDepartment of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Joanne Nguyen
- grid.267308.80000 0000 9206 2401Department of Pediatrics, University of Texas Health Science Center, Houston, TX USA
| | - Christian P. Schaaf
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.7700.00000 0001 2190 4373Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Yaping Yang
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Weimin Bi
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Christine Eng
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Chad Shaw
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.21940.3e0000 0004 1936 8278Department of Statistics, Rice University, Houston, TX USA
| | - James R. Lupski
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Pediatrics, Baylor College of Medicine, Houston, TX USA ,grid.416975.80000 0001 2200 2638Texas Children’s Hospital, Houston, TX USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Baylor Genetics, Houston, TX, USA.
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14
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Bi W, Yuan B, Liu P, Murry JB, Qin X, Xia F, Quach T, Cooper LM, Wiszniewska J, Hixson P, Peacock S, Tonk VS, Huff RW, Ortega V, Lupski JR, Scherer SE, Littlejohn RO, Velagaleti GVN, Roeder ER, Cheung SW. Recurring germline mosaicism in a family due to reversion of an inherited derivative chromosome 8 from an 8;21 translocation with interstitial telomeric sequences. J Med Genet 2022; 60:547-556. [PMID: 36150828 DOI: 10.1136/jmg-2022-108586] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/14/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mosaicism for chromosomal structural abnormalities, other than marker or ring chromosomes, is rarely inherited. METHODS We performed cytogenetics studies and breakpoint analyses on a family with transmission of mosaicism for a derivative chromosome 8 (der(8)), resulting from an unbalanced translocation between the long arms of chromosomes 8 and 21 over three generations. RESULTS The proband and his maternal half-sister had mosaicism for a der(8) cell line leading to trisomy of the distal 21q, and both had Down syndrome phenotypic features. Mosaicism for a cell line with the der(8) and a normal cell line was also detected in a maternal half-cousin. The der(8) was inherited from the maternal grandmother who had four abnormal cell lines containing the der(8), in addition to a normal cell line. One maternal half-aunt had the der(8) and an isodicentric chromosome 21 (idic(21)). Sequencing studies revealed microhomologies at the junctures of the der(8) and idic(21) in the half-aunt, suggesting a replicative mechanism in the rearrangement formation. Furthermore, interstitial telomeric sequences (ITS) were identified in the juncture between chromosomes 8 and 21 in the der(8). CONCLUSION Mosaicism in the proband, his half-sister and half-cousin resulting from loss of chromosome 21 material from the der(8) appears to be a postzygotic event due to the genomic instability of ITS and associated with selective growth advantage of normal cells. The reversion of the inherited der(8) to a normal chromosome 8 in this family resembles revertant mosaicism of point mutations. We propose that ITS could mediate recurring revertant mosaicism for some constitutional chromosomal structural abnormalities.
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Affiliation(s)
- Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Jaclyn B Murry
- Baylor Genetics, Houston, Texas, USA.,Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | | | | | - Joanna Wiszniewska
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | | | - Sandra Peacock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Vijay S Tonk
- Departments of Pediatrics, Obstetrics and Gynecology, Pathology, Texas Tech University Health Science Centers, Lubbock, Texas, USA
| | - Robert W Huff
- Department of Obstetrics and Gynecology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Veronica Ortega
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Steven E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Rebecca Okashah Littlejohn
- Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas, USA
| | - Gopalrao V N Velagaleti
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Elizabeth R Roeder
- Department of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, Texas, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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15
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Similuk MN, Yan J, Ghosh R, Oler AJ, Franco LM, Setzer M, Kamen M, Jodarski C, DiMaggio T, Davis J, Gore R, Jamal L, Borges A, Gentile N, Niemela J, Lowe C, Jevtich K, Yu Y, Hullfish H, Hsu AP, Hong C, Littel P, Seifert BA, Milner J, Johnston JJ, Cheng X, Li Z, Veltri D, Huang K, Kaladi K, Barnett J, Zhang L, Vlasenko N, Fan Y, Karlins E, Ganakammal SR, Gilmore R, Tran E, Yun A, Mackey J, Yazhuk S, Lack J, Kuram V, Cao W, Huse S, Frank K, Fahle G, Rosenzweig S, Su Y, Hwang S, Bi W, Bennett J, Myles IA, De Ravin SS, Fussm I, Strober W, Bielekova B, Almeida de Jesus A, Goldbach-Mansky R, Williamson P, Kumar K, Dempsy C, Frischmeyer-Guerrerio P, Eisch R, Bolan H, Metcalfe DD, Komarow H, Carter M, Druey KM, Sereti I, Dropulic L, Klion AD, Khoury P, O' Connell EM, Holland-Thomas NC, Brown T, McDermott DH, Murphy PM, Bundy V, Keller MD, Peng C, Kim H, Norman S, Delmonte OM, Kang E, Su HC, Malech H, Freeman A, Zerbe C, Uzel G, Bergerson JRE, Rao VK, Olivier KN, Lyons JJ, Lisco A, Cohen JI, Lionakis MS, Biesecker LG, Xirasagar S, Notarangelo L, Holland SM, Walkiewicz MA. Clinical Exome Sequencing of 1000 Families with Complex Immune Phenotypes: Towards comprehensive genomic evaluations. J Allergy Clin Immunol 2022; 150:947-954. [PMID: 35753512 PMCID: PMC9547837 DOI: 10.1016/j.jaci.2022.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 12/17/2021] [Revised: 05/07/2022] [Accepted: 06/02/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND Prospective genetic evaluation of patients at our referral research hospital presents clinical research challenges. OBJECTIVE This study sought not only a single-gene explanation for participants' immune-related presentations, but viewed each participant holistically, with the potential to have multiple genetic contributions to their immune-phenotype and other heritable comorbidities relevant to their presentation and health. METHODS We developed a program integrating exome sequencing, chromosomal microarray, phenotyping, results return with genetic counseling, and reanalysis in 1505 individuals from 1000 families with suspected or known inborn errors of immunity. RESULTS Probands were 50.8% female, 71.5% >18 years, and had diverse immune presentations. Overall, 327/1000 probands (32.7%) received 361 molecular diagnoses. These included 17 probands with diagnostic copy number variants, 32 probands with secondary findings, and 31 probands with multiple molecular diagnoses. Reanalysis added 22 molecular diagnoses, predominantly due to new disease-gene associations (9/22, 40.9%). One-quarter of the molecular diagnoses (92/361) did not involve immune-associated genes. Molecular diagnosis was correlated with younger age, male sex, and a higher number of organ systems involved. This program also facilitated the discovery of new gene-disease associations such as SASH3-related immunodeficiency. A review of treatment options and ClinGen actionability curations suggest that at least 251/361 (69.5%) of these molecular diagnoses could translate into >1 management option. CONCLUSION This program contributes to our understanding of the diagnostic and clinical utility whole exome analysis on a large scale. CLINICAL Implication: Comprehensive analysis of exome data has diagnostic and clinical utility for patients with suspected inborn errors of immunity.
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Affiliation(s)
| | - Jia Yan
- Centralized Sequencing Program
- DIR
- NIAID
| | | | - Andrew J Oler
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Luis M Franco
- Functional Immunogenomics Unit
- Systemic Autoimmunity Branch
- National Institute of Arthritis and Musculoskeletal and Skin Diseases
| | | | | | | | - Thomas DiMaggio
- Fungal Pathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
| | - Joie Davis
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Leila Jamal
- Johns Hopkins/NIH Genetic Counseling Training Program; Genetics Branch, Center for Cancer Research, National Cancer Institute; NIH Clinical Center Department of Bioethics
| | | | | | | | - Chenery Lowe
- Health, Behavior, and Society
- Johns Hopkins Bloomberg School of Public Health
| | - Kathleen Jevtich
- School of Medicine
- Uniformed Services University of Health Sciences
| | | | | | - Amy P Hsu
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Patricia Littel
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | | | | | | | - Xi Cheng
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Zhiwen Li
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Daniel Veltri
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Ke Huang
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Krishnaveni Kaladi
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Jason Barnett
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Lingwen Zhang
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Nikita Vlasenko
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Yongjie Fan
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Eric Karlins
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | | | - Robert Gilmore
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Emily Tran
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Alvin Yun
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Joseph Mackey
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Svetlana Yazhuk
- Operations and Engineering Branch
- Office of Cyber Infrastructure and Computational Biology
- NIAID
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Vasu Kuram
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Wen Cao
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | - Susan Huse
- NIAID Collaborative Bioinformatics Resource
- Leidos Biomedical Research, Inc
| | | | | | | | - Yan Su
- Immunology Service
- Laboratory Medicine
- NIH
| | - SuJin Hwang
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration
| | - Weimin Bi
- Department of Molecular and Human Genetics
- Baylor Genetics
| | - John Bennett
- Clinical Mycology
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Ian A Myles
- Epithelial Therapeutics Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Suk See De Ravin
- Laboratory of Host Defenses
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Ivan Fussm
- Mucosal Immunity Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Warren Strober
- Mucosal Immunity Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Bibiana Bielekova
- Neuroimmunological Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Adriana Almeida de Jesus
- Translational Autoinflammatory Disease Studies Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Disease Studies Unit
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Peter Williamson
- Translational Mycology Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Caeden Dempsy
- Food Allergy Research Unit
- Laboratory of Allergic Diseases
- NIAID
| | | | - Robin Eisch
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Hyejeong Bolan
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Dean D Metcalfe
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Hirsh Komarow
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Melody Carter
- Mast Cell Biology Section
- Laboratory of Allergic Diseases
- NIAID
| | - Kirk M Druey
- Lung and Vascular Inflammation Section
- Laboratory of Allergic Diseases
- NIAID
| | - Irini Sereti
- HIV Pathogenesis Section
- Laboratory of Immunoregulation
- NIAID
| | - Lesia Dropulic
- Medical Virology Section
- Laboratory of Immunoregulation
- NIAID
| | - Amy D Klion
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | - Paneez Khoury
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | | | | | - Thomas Brown
- Human Eosinophil Section
- Laboratory of Parasitic Diseases
- NIAID
| | | | - Philip M Murphy
- Molecular Signaling Section
- Laboratory of Molecular Immunology
- NIAID
| | - Vanessa Bundy
- Division of Allergy and Immunology
- Children's National Health System
| | - Michael D Keller
- Division of Allergy and Immunology
- Children's National Health System
| | - Christine Peng
- Division of Allergy and Immunology
- Children's National Health System
| | - Helen Kim
- Division of Allergy and Immunology
- Children's National Health System
| | - Stephanie Norman
- Division of Allergy and Immunology
- Children's National Health System
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Elizabeth Kang
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | - Helen C Su
- Human Immunological Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Harry Malech
- Genetic Immunotherapy Section
- Laboratory of Clinical Immunology and Microbiology
| | - Alexandra Freeman
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Christa Zerbe
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Gulbu Uzel
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Jenna R E Bergerson
- Primary Immune Deficiency Clinic
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - V Koneti Rao
- Primary Immune Deficiency Clinic
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | | | - Jonathan J Lyons
- Translational Allergic Immunopathology Unit
- Laboratory of Allergic Diseases
- NIAID
| | - Andrea Lisco
- HIV Pathogenesis Section
- Laboratory of Immunoregulation
- NIAID
| | - Jeffrey I Cohen
- Medical Virology Section
- Laboratory of Infectious Diseases
- NIAID
| | - Michail S Lionakis
- Fungal Pathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
| | | | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences
- Office of Cyber Infrastructure and Computational Biology
| | - Luigi Notarangelo
- Immune Deficiency Genetics Diseases Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
| | - Steven M Holland
- Immunopathogenesis Section
- Laboratory of Clinical Immunology and Microbiology
- NIAID
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16
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Seifert B, Similuk M, Setzer M, Yan J, Kamen M, Jodarski C, Jamal L, Jevtich K, Yu Y, Duncan R, Hunt D, Mixer M, Beers B, Kuram V, Lack J, Karlins E, Oler A, Ghosh R, Bergerson J, Freeman A, Fuss I, Lionakis M, Strober W, Uzel G, Zerbe C, Holland S, Bi W, Franco L, Walkiewicz-Yvon M. eP400: Utility of genome sequencing in CNV identification in an immune disorders cohort. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.435] [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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17
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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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18
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Lay E, Azamian MS, Denfield SW, Dreyer W, Spinner JA, Kearney D, Zhang L, Worley KC, Bi W, Lalani SR. LMOD2-related dilated cardiomyopathy presenting in late infancy. Am J Med Genet A 2022; 188:1858-1862. [PMID: 35188328 DOI: 10.1002/ajmg.a.62699] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/19/2022] [Accepted: 02/05/2022] [Indexed: 11/10/2022]
Abstract
Leiomodin-2 (LMOD2) is an important regulator of the thin filament length, known to promote elongation of actin through polymerization at pointed ends. Mice with Lmod2 deficiency die around 3 weeks of age due to severe dilated cardiomyopathy (DCM), resulting from decreased heart contractility due to shorter thin filaments. To date, there have been three infants from two families reported with biallelic variants in LMOD2, presenting with perinatal onset DCM. Here, we describe a third family with a child harboring a previously described homozygous frameshift variant, c.1243_1244delCT (p.L415Vfs*108) with DCM, presenting later in infancy at 9 months of age. Family history was relevant for a sibling who died suddenly at 1 year of age after being diagnosed with cardiomegaly. LMOD2-related cardiomyopathy is a rare form of inherited cardiomyopathy resulting from thin filament length dysregulation and should be considered in genetic evaluation of newborns and infants with suspected autosomal recessive inheritance or sporadic early onset cardiomyopathy.
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Affiliation(s)
- Erica Lay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Mahshid S Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Susan W Denfield
- Department of Pediatrics, Section of Cardiology, Texas Children's Hospital, Houston, Texas, USA
| | - William Dreyer
- Department of Pediatrics, Section of Cardiology, Texas Children's Hospital, Houston, Texas, USA
| | - Joseph A Spinner
- Department of Pediatrics, Section of Cardiology, Texas Children's Hospital, Houston, Texas, USA
| | - Debra Kearney
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Lilei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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19
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Chen CA, Lattier J, Zhu W, Rosenfeld J, Wang L, Scott TM, Du H, Patel V, Dang A, Magoulas P, Streff H, Sebastian J, Svihovec S, Curry K, Delgado MR, Hanchard N, Lalani S, Marom R, Madan-Khetarpal S, Saenz M, Dai H, Meng L, Xia F, Bi W, Liu P, Posey JE, Scott DA, Lupski JR, Eng CM, Xiao R, Yuan B. Retrospective analysis of a clinical exome sequencing cohort reveals the mutational spectrum and identifies candidate disease-associated loci for BAFopathies. Genet Med 2022; 24:364-373. [PMID: 34906496 PMCID: PMC8957292 DOI: 10.1016/j.gim.2021.09.017] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 02/03/2023] Open
Abstract
PURPOSE BRG1/BRM-associated factor (BAF) complex is a chromatin remodeling complex that plays a critical role in gene regulation. Defects in the genes encoding BAF subunits lead to BAFopathies, a group of neurodevelopmental disorders with extensive locus and phenotypic heterogeneity. METHODS We retrospectively analyzed data from 16,243 patients referred for clinical exome sequencing (ES) with a focus on the BAF complex. We applied a genotype-first approach, combining predicted genic constraints to propose candidate BAFopathy genes. RESULTS We identified 127 patients carrying pathogenic variants, likely pathogenic variants, or de novo variants of unknown clinical significance in 11 known BAFopathy genes. Those include 34 patients molecularly diagnosed using ES reanalysis with new gene-disease evidence (n = 21) or variant reclassifications in known BAFopathy genes (n = 13). We also identified de novo or predicted loss-of-function variants in 4 candidate BAFopathy genes, including ACTL6A, BICRA (implicated in Coffin-Siris syndrome during this study), PBRM1, and SMARCC1. CONCLUSION We report the mutational spectrum of BAFopathies in an ES cohort. A genotype-driven and pathway-based reanalysis of ES data identified new evidence for candidate genes involved in BAFopathies. Further mechanistic and phenotypic characterization of additional patients are warranted to confirm their roles in human disease and to delineate their associated phenotypic spectrums.
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Affiliation(s)
- Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | | | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lei Wang
- Baylor Genetics Laboratory, Houston, TX
| | - Tiana M. Scott
- Texas Children’s Hospital, Houston, TX, Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Anh Dang
- Baylor Genetics Laboratory, Houston, TX
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | | | - Shayna Svihovec
- University of Colorado Anschutz Medical Campus; Children’s Hospital Colorado, Aurora, CO
| | - Kathryn Curry
- Genetics and Metabolic Department, St. Luke’s Health System
| | - Mauricio R. Delgado
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA, Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Neil Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX
| | | | - Margarita Saenz
- University of Colorado Anschutz Medical Campus; Children’s Hospital Colorado, Aurora, CO
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX, Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Texas Children’s Hospital, Houston, TX, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Baylor Genetics Laboratory, Houston, TX, Current address: Department of Laboratories, Seattle Children’s Hospital, Seattle, WA
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20
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Wang L, Liu P, Bi W, Sim T, Wang X, Walkiewicz M, Leduc MS, Meng L, Xia F, Eng CM, Yang Y, Yuan B, Dai H. Contribution of uniparental disomy in a clinical trio exome cohort of 2675 patients. Mol Genet Genomic Med 2021; 9:e1792. [PMID: 34587367 PMCID: PMC8606208 DOI: 10.1002/mgg3.1792] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/23/2021] [Accepted: 08/16/2021] [Indexed: 11/12/2022] Open
Abstract
Background Uniparental disomy (UPD) is the inheritance of two homologous chromosomes from the same parent. UPD may result in clinical phenotypes when occurring on chromosomes with specific imprinting pattern, when leading to homozygosity of a deleterious recessive allele inherited from one carrier parent, or when associated with a mosaic aneuploidy. Due to the importance of UPD in genetic disease etiology, UPD analysis has started to be implemented in the context of exome sequencing (ES) or genome sequencing. Methods We developed an in‐house algorithm TRIPS (Trio Parentage/UPD Studies) to identify UPD events in trio ES cases. This method identifies regions with uniparental inheritance by utilizing the trio genotyping data obtained from the concurrent SNP array to delineate the parental origin of the SNPs in the proband. Results We identified 16 UPD events from 2675 ES trios. Among those, four events led to imprinting disorders, seven unmasked a pathogenic/likely pathogenic variant in a recessive disease gene, and two were consistent with a mosaic genome wide paternal UPD pattern. Twelve of these UPD events directly contributed to the molecular diagnosis of the patients. Conclusion Our study demonstrated the contribution of UPD to the molecular diagnosis in one clinical ES cohort, thus UPD analysis should be incorporated into routine clinical ES interpretation.
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Affiliation(s)
- Lei Wang
- Baylor Genetics Laboratory, Houston, Texas, USA
| | - Pengfei Liu
- Baylor Genetics Laboratory, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weimin Bi
- Baylor Genetics Laboratory, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Xia Wang
- AiLife Diagnostics, Houston, Texas, USA
| | | | | | - Linyan Meng
- Baylor Genetics Laboratory, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Fan Xia
- Baylor Genetics Laboratory, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Christine M Eng
- Baylor Genetics Laboratory, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Bo Yuan
- Baylor Genetics Laboratory, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Hongzheng Dai
- Baylor Genetics Laboratory, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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21
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Panneerselvam S, Wang J, Zhu W, Dai H, Pappas JG, Rabin R, Low KJ, Rosenfeld JA, Emrick L, Xiao R, Xia F, Yang Y, Eng CM, Anderson A, Chau V, Soler-Alfonso C, Streff H, Lalani SR, Mercimek-Andrews S, Bi W. PPP3CA truncating variants clustered in the regulatory domain cause early-onset refractory epilepsy. Clin Genet 2021; 100:227-233. [PMID: 33963760 DOI: 10.1111/cge.13979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/01/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 12/27/2022]
Abstract
PPP3CA encodes the catalytic subunit of calcineurin, a calcium-calmodulin-regulated serine-threonine phosphatase. Loss-of-function (LoF) variants in the catalytic domain have been associated with epilepsy, while gain-of-function (GoF) variants in the auto-inhibitory domain cause multiple congenital abnormalities. We herein report five new patients with de novo PPP3CA variants. Interestingly, the two frameshift variants in this study and the six truncating variants reported previously are all located within a 26-amino acid region in the regulatory domain (RD). Patients with a truncating variant had more severe earlier onset seizures compared to patients with a LoF missense variant, while autism spectrum disorder was a more frequent feature in the latter. Expression studies of a truncating variant showed apparent RNA expression from the mutant allele, but no detectable mutant protein. Our data suggest that PPP3CA truncating variants clustered in the RD, causing more severe early-onset refractory epilepsy and representing a type of variants distinct from LoF or GoF missense variants.
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Affiliation(s)
- Sugi Panneerselvam
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Julia Wang
- Medical Scientist Training Program and Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Wenmiao Zhu
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - John G Pappas
- Department of Pediatrics, Clinical Genetic Services, NYU School of Medicine, New York, New York, USA
| | - Rachel Rabin
- Department of Pediatrics, Clinical Genetic Services, NYU School of Medicine, New York, New York, USA
| | - Karen J Low
- University Hospital Bristol NHS Foundation Trust, Bristol, UK
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lisa Emrick
- Texas Children's Hospital, Houston, Texas, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Anne Anderson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Vann Chau
- Division of Neurology, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudia Soler-Alfonso
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Genetics, University of Alberta, Stollery Children's Hospital, Edmonton, Alberta, Canada
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
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22
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Manor J, Dinu D, Azamian MS, Bi W, Darilek S, Lalani SR. A rare description of pure partial trisomy of 16q12.2q24.3 and review of the literature. Am J Med Genet A 2021; 185:2903-2912. [PMID: 34061437 DOI: 10.1002/ajmg.a.62368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/09/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/11/2022]
Abstract
Trisomy 16 is the most common autosomal trisomy in humans, which is almost uniformly embryonic lethal. Partial trisomy 16 including a segment of the long arm of chromosome 16 is occasionally compatible with life and has been associated with severe congenital defects, growth retardation, and early lethality. Segmental trisomy of 16q is usually described concomitantly with partial monosomy of another chromosome, often resulting from a parental balanced translocation. Pure partial chromosome 16q trisomy is exceedingly rare. About nine children with 16q12→qter and 16q13→qter duplication have been reported in the literature, almost all described with monosomy of a second chromosome, and highlighting very few long-term survivors. A single individual with pure partial distal 16q12.1q23.3 duplication has been reported in an infant, underscoring complexities of genetic counseling and management, especially in view of life-limiting congenital anomalies in rare survivors. Here, we present a 12-month-old child with pure 16q12.2q24.3 trisomy, having continued morbidity related to pulmonary hypertension and chronic lung disease. The features of intrauterine growth retardation, facial dysmorphism, hypotonia, congenital heart defect, distal contractures, urogenital abnormalities, and hearing loss support the association with 16q partial trisomy, as in previous studies. This report expands our current understanding related to the survival of infants with large segmental aneusomy of the long arm of chromosome 16.
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Affiliation(s)
- Joshua Manor
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniela Dinu
- Department of Pediatrics, Neonatology section, Texas Children's Hospital, Houston, Texas, USA
| | - Mahshid S Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics Laboratories, Houston, Texas, USA
| | - Sandra Darilek
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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23
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Ernst ME, Baugh EH, Thomas A, Bier L, Lippa N, Stong N, Mulhern MS, Kushary S, Akman CI, Heinzen EL, Yeh R, Bi W, Hanchard NA, Burrage LC, Leduc MS, Chong JSC, Bend R, Lyons MJ, Lee JA, Suwannarat P, Brilstra E, Simon M, Koopmans M, van Binsbergen E, Groepper D, Fleischer J, Nava C, Keren B, Mignot C, Mathieu S, Mancini GMS, Madan-Khetarpal S, Infante EM, Bluvstein J, Seeley A, Bachman K, Klee EW, Schultz-Rogers LE, Hasadsri L, Barnett S, Ellingson MS, Ferber MJ, Narayanan V, Ramsey K, Rauch A, Joset P, Steindl K, Sheehan T, Poduri A, Vasquez A, Ruivenkamp C, White SM, Pais L, Monaghan KG, Goldstein DB, Sands TT, Aggarwal V. CSNK2B: A broad spectrum of neurodevelopmental disability and epilepsy severity. Epilepsia 2021; 62:e103-e109. [PMID: 34041744 DOI: 10.1111/epi.16931] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/17/2020] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 11/29/2022]
Abstract
CSNK2B has recently been implicated as a disease gene for neurodevelopmental disability (NDD) and epilepsy. Information about developmental outcomes has been limited by the young age and short follow-up for many of the previously reported cases, and further delineation of the spectrum of associated phenotypes is needed. We present 25 new patients with variants in CSNK2B and refine the associated NDD and epilepsy phenotypes. CSNK2B variants were identified by research or clinical exome sequencing, and investigators from different centers were connected via GeneMatcher. Most individuals had developmental delay and generalized epilepsy with onset in the first 2 years. However, we found a broad spectrum of phenotypic severity, ranging from early normal development with pharmacoresponsive seizures to profound intellectual disability with intractable epilepsy and recurrent refractory status epilepticus. These findings suggest that CSNK2B should be considered in the diagnostic evaluation of patients with a broad range of NDD with treatable or intractable seizures.
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Affiliation(s)
- Michelle E Ernst
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Amanda Thomas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Maureen S Mulhern
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sulagna Kushary
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Cigdem I Akman
- Department of Neurology, The Neurological Institute of New York, Columbia University Irving Medical Center, New York, NY, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Raymond Yeh
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Magalie S Leduc
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Josephine S C Chong
- Joint CUHK-Baylor Center of Medical Genetics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC, USA
| | | | | | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, MD, USA
| | - Eva Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marleen Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marije Koopmans
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Daniel Groepper
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Julie Fleischer
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Caroline Nava
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, APHP Sorbonne University, Paris, France.,Reference Center for Intellectual Disabilities of Rare Causes, Paris, France
| | - Sophie Mathieu
- Department of Neuropediatrics, APHP Sorbonne University, Trousseau Hospital, Paris, France
| | - Grazia M S Mancini
- Department of Clinical Genetics, ErasmusMC University Medical Center, Rotterdam, The Netherlands
| | | | - Elena M Infante
- Department of Medical Genetics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Linda Hasadsri
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sarah Barnett
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Marissa S Ellingson
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Clinical Genome Sequencing Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zürich, Schlieren, Zürich, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zürich, Schlieren, Zürich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zürich, Schlieren, Zürich, Switzerland
| | - Theodore Sheehan
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Annapurna Poduri
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Alejandra Vasquez
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA.,Division of Child and Adolescent Neurology, Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Susan M White
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tristan T Sands
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Department of Neurology, The Neurological Institute of New York, Columbia University Irving Medical Center, New York, NY, USA
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
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24
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Liu Q, Grochowski CM, Bi W, Lupski JR, Stankiewicz P. Quantitative Assessment of Parental Somatic Mosaicism for Copy-Number Variant (CNV) Deletions. ACTA ACUST UNITED AC 2021; 106:e99. [PMID: 32176465 DOI: 10.1002/cphg.99] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As genome sequencing methodologies have become more sensitive in detecting low-frequency rare-variant events, the link between post-zygotic mutagenesis and somatic mosaicism in the etiology of several human genetic conditions other than cancers has become more clear. Given that current clinical-genomics diagnostic methods have limited detection sensitivity for mosaic events, a copy-number variant (CNV) deletion inherited from a parent with low-level (<10%) mosaicism can be erroneously interpreted in the proband to represent a de novo germline event. Here, we describe three sensitive, precise, and cost-efficient methods that can quantitatively assess the potential degree of parental somatic mosaicism levels for CNV deletions: droplet digital PCR (ddPCR), PCR amplicon-based next-generation sequencing (NGS), and quantitative PCR. ddPCR using the EvaGreen fluorescent dye protocol can specifically quantify the deleted or non-deleted alleles by analyzing the number of droplets positive for a fluorescent signal for each event. PCR amplicon-based NGS assesses the allele frequencies of a heterozygous single-nucleotide polymorphism within a deletion region. The difference in number of reads between the two genotypes indicates the level of somatic mosaicism for the CNV deletion. Quantitative PCR can be applied where the relative quantity of the deletion junction-specific product represents the level of mosaicism. Clinical implementation of these quantitative variant-detection methods enables potentially more accurate assessment of disease recurrence risk in family-based genetic counseling, allowing couples to engage in more informed family planning. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Droplet digital PCR (ddPCR) Alternate Protocol 1: PCR amplicon-based next-generation sequencing Alternate Protocol 2: Quantitative real-time PCR (qPCR).
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Affiliation(s)
- Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics, Houston, Texas
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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25
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Edwards SD, Schulze KV, Rosenfeld JA, Westerfield LE, Gerard A, Yuan B, Grigorenko EL, Posey JE, Bi W, Liu P. Clinical characterization of individuals with the distal 1q21.1 microdeletion. Am J Med Genet A 2021; 185:1388-1398. [PMID: 33576134 DOI: 10.1002/ajmg.a.62104] [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: 10/22/2020] [Accepted: 01/09/2021] [Indexed: 11/12/2022]
Abstract
Distal 1q21.1 microdeletions have shown highly variable clinical expressivity and incomplete penetrance, with affected individuals manifesting a broad spectrum of nonspecific features. The goals of this study were to better describe the phenotypic spectrum of patients with distal 1q21.1 microdeletions and to compare the clinical features among affected individuals. We performed a retrospective chart review of 47 individuals with distal 1q21.1 microdeletions tested at a large clinical genetic testing laboratory, with most patients being clinically evaluated in the same children's hospital. Health information such as growth charts, results of imaging studies, developmental history, and progress notes were collected. Statistical analysis was performed using Fisher's exact test to compare clinical features among study subjects. Common features in our cohort include microcephaly (51.2%), seizures (29.8%), developmental delay (74.5%), failure to thrive (FTT) (68.1%), dysmorphic features (63.8%), and a variety of congenital anomalies such as cardiac abnormalities (23.4%) and genitourinary abnormalities (19.1%). Compared to prior literature, we found that seizures, brain anomalies, and FTT were more prevalent among our study cohort. Females were more likely than males to have microcephaly (p = 0.0199) and cardiac abnormalities (p = 0.0018). Based on existing genome-wide clinical testing results, at least a quarter of the cohort had additional genetic findings that may impact the phenotype of the individual. Our study represents the largest cohort of distal 1q21.1 microdeletion carriers available in the literature thus far, and it further illustrates the wide spectrum of clinical manifestations among symptomatic individuals. These results may allow for improved genetic counseling and management of affected individuals. Future studies may help to elucidate the underlying molecular mechanisms impacting the phenotypic variability observed with this microdeletion.
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Affiliation(s)
- Stacey D Edwards
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lauren E Westerfield
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Elena L Grigorenko
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,St. Petersburg State University, St Petersburg, Russia
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Baylor Genetics, Houston, Texas, USA
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26
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Robak LA, Du R, Yuan B, Gu S, Alfradique-Dunham I, Kondapalli V, Hinojosa E, Stillwell A, Young E, Zhang C, Song X, Du H, Gambin T, Jhangiani SN, Coban Akdemir Z, Muzny DM, Tejomurtula A, Ross OA, Shaw C, Jankovic J, Bi W, Posey JE, Lupski JR, Shulman JM. Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease. Neurol Genet 2020; 6:e498. [PMID: 32802956 PMCID: PMC7413630 DOI: 10.1212/nxg.0000000000000498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
Abstract
Objective To determine how single nucleotide variants (SNVs) and copy number variants (CNVs) contribute to molecular diagnosis in familial Parkinson disease (PD), we integrated exome sequencing (ES) and genome-wide array-based comparative genomic hybridization (aCGH) and further probed CNV structure to reveal mutational mechanisms. Methods We performed ES on 110 subjects with PD and a positive family history; 99 subjects were also evaluated using genome-wide aCGH. We interrogated ES and aCGH data for pathogenic SNVs and CNVs at Mendelian PD gene loci. We confirmed SNVs via Sanger sequencing and further characterized CNVs with custom-designed high-density aCGH, droplet digital PCR, and breakpoint sequencing. Results Using ES, we discovered individuals with known pathogenic SNVs in GBA (p.Glu365Lys, p.Thr408Met, p.Asn409Ser, and p.Leu483Pro) and LRRK2 (p.Arg1441Gly and p.Gly2019Ser). Two subjects were each double heterozygotes for variants in GBA and LRRK2. Based on aCGH, we additionally discovered cases with an SNCA duplication and heterozygous intragenic GBA deletion. Five additional subjects harbored both SNVs (p.Asn52Metfs*29, p.Thr240Met, p.Pro437Leu, and p.Trp453*) and likely disrupting CNVs at the PRKN locus, consistent with compound heterozygosity. In nearly all cases, breakpoint sequencing revealed microhomology, a mutational signature consistent with CNV formation due to DNA replication errors. Conclusions Integrated ES and aCGH yielded a genetic diagnosis in 19.3% of our familial PD cohort. Our analyses highlight potential mechanisms for SNCA and PRKN CNV formation, uncover multilocus pathogenic variation, and identify novel SNVs and CNVs for further investigation as potential PD risk alleles.
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Affiliation(s)
- Laurie A Robak
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Renqian Du
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Bo Yuan
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Shen Gu
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Isabel Alfradique-Dunham
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Vismaya Kondapalli
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Evelyn Hinojosa
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Amanda Stillwell
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Emily Young
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Chaofan Zhang
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Xiaofei Song
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Haowei Du
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Tomasz Gambin
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Donna M Muzny
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Anusha Tejomurtula
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Owen A Ross
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Chad Shaw
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Joseph Jankovic
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Weimin Bi
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Jennifer E Posey
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - James R Lupski
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
| | - Joshua M Shulman
- Department of Molecular and Human Genetics (L.A.R., R.D., B.Y., S.G., V.K., E.H., A.S., E.Y., C.Z., X.S., H.D., T.G., Z.C.A., A.T., C.S., W.B., J.E.P., J.R.L., J.M.S.), Department of Neurology (I.A.-D., J.J., J.M.S.), and Human Genome Sequencing Center (S.N.J., D.M.M., J.R.L.), Baylor College of Medicine, Houston, TX; Baylor Genetics (W.B.), Houston, TX; Department of Neurology (O.A.R.), Department of Neuroscience (O.A.R.), and Department of Clinical Genomics (O.A.R.), Mayo Clinic, Jacksonville, FL; Parkinson's Disease Center and Movement Disorders Clinic (J.J.) and Department of Pediatrics (J.R.L., J.M.S.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (J.R.L.), Texas Children's Hospital, Houston; Department of Neuroscience (J.M.S.), Baylor College of Medicine, Houston, TX; and Jan and Dan Duncan Neurological Research Institute (J.M.S.), Texas Children's Hospital, Houston
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27
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Yuan B, Wang L, Liu P, Shaw C, Dai H, Cooper L, Zhu W, Anderson SA, Meng L, Wang X, Wang Y, Xia F, Xiao R, Braxton A, Peacock S, Schmitt E, Ward PA, Vetrini F, He W, Chiang T, Muzny D, Gibbs RA, Beaudet AL, Breman AM, Smith J, Cheung SW, Bacino CA, Eng CM, Yang Y, Lupski JR, Bi W. CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Genet Med 2020; 22:1633-1641. [PMID: 32576985 DOI: 10.1038/s41436-020-0864-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 02/10/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Improved resolution of molecular diagnostic technologies enabled detection of smaller sized exonic level copy-number variants (CNVs). The contribution of CNVs to autosomal recessive (AR) conditions may be better recognized using a large clinical cohort. METHODS We retrospectively investigated the CNVs' contribution to AR conditions in cases subjected to chromosomal microarray analysis (CMA, N = ~70,000) and/or clinical exome sequencing (ES, N = ~12,000) at Baylor Genetics; most had pediatric onset neurodevelopmental disorders. RESULTS CNVs contributed to biallelic variations in 87 cases, including 81 singletons and three affected sibling pairs. Seventy cases had CNVs affecting both alleles, and 17 had a CNV and a single-nucleotide variant (SNV)/indel in trans. In total, 94.3% of AR-CNVs affected one gene; among these 41.4% were single-exon and 35.0% were multiexon partial-gene events. Sixty-nine percent of homozygous AR-CNVs were embedded in homozygous genomic intervals. Five cases had large deletions unmasking an SNV/indel on the intact allele for a recessive condition, resulting in multiple molecular diagnoses. CONCLUSIONS AR-CNVs are often smaller in size, transmitted through generations, and underrecognized due to limitations in clinical CNV detection methods. Our findings from a large clinical cohort emphasized integrated CNV and SNV/indel analyses for precise clinical and molecular diagnosis especially in the context of genomic disorders.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics Laboratory, Houston, TX, USA.
| | - Lei Wang
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | | | - Wenmiao Zhu
- Baylor Genetics Laboratory, Houston, TX, USA
| | | | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Alicia Braxton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Sandra Peacock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Eric Schmitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Francesco Vetrini
- Baylor Genetics Laboratory, Houston, TX, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Weimin He
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Janice Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, 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
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics Laboratory, Houston, TX, USA.
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28
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Liu Q, Karolak JA, Grochowski CM, Wilson TA, Rosenfeld JA, Bacino CA, Lalani SR, Patel A, Breman A, Smith JL, Cheung SW, Lupski JR, Bi W, Stankiewicz P. Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings. Genomics 2020; 112:2937-2941. [PMID: 32387503 DOI: 10.1016/j.ygeno.2020.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 03/31/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 10/25/2022]
Abstract
To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.
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Affiliation(s)
- Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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29
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Markovitz R, Ghosh R, Kuo ME, Hong W, Lim J, Bernes S, Manberg S, Crosby K, Tanpaiboon P, Bharucha-Goebel D, Bonnemann C, Mohila CA, Mizerik E, Woodbury S, Bi W, Lotze T, Antonellis A, Xiao R, Potocki L. GARS-related disease in infantile spinal muscular atrophy: Implications for diagnosis and treatment. Am J Med Genet A 2020; 182:1167-1176. [PMID: 32181591 PMCID: PMC8297662 DOI: 10.1002/ajmg.a.61544] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 12/12/2019] [Revised: 02/06/2020] [Accepted: 02/21/2020] [Indexed: 01/05/2023]
Abstract
The majority of patients with spinal muscular atrophy (SMA) identified to date harbor a biallelic exonic deletion of SMN1. However, there have been reports of SMA-like disorders that are independent of SMN1, including those due to pathogenic variants in the glycyl-tRNA synthetase gene (GARS1). We report three unrelated patients with de novo variants in GARS1 that are associated with infantile-onset SMA (iSMA). Patients were ascertained during inpatient hospital evaluations for complications of neuropathy. Evaluations were completed as indicated for clinical care and management and informed consent for publication was obtained. One newly identified, disease-associated GARS1 variant, identified in two out of three patients, was analyzed by functional studies in yeast complementation assays. Genomic analyses by exome and/or gene panel and SMN1 copy number analysis of three patients identified two previously undescribed de novo missense variants in GARS1 and excluded SMN1 as the causative gene. Functional studies in yeast revealed that one of the de novo GARS1 variants results in a loss-of-function effect, consistent with other pathogenic GARS1 alleles. In sum, the patients' clinical presentation, assessments of previously identified GARS1 variants and functional assays in yeast suggest that the GARS1 variants described here cause iSMA. GARS1 variants have been previously associated with Charcot-Marie-Tooth disease (CMT2D) and distal SMA type V (dSMAV). Our findings expand the allelic heterogeneity of GARS-associated disease and support that severe early-onset SMA can be caused by variants in this gene. Distinguishing the SMA phenotype caused by SMN1 variants from that due to pathogenic variants in other genes such as GARS1 significantly alters approaches to treatment.
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Affiliation(s)
- Rebecca Markovitz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Rajarshi Ghosh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Molly E. Kuo
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan
| | - William Hong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
| | - Jaehyung Lim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
| | - Saunder Bernes
- Division of Child Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, Arizona
| | - Stephanie Manberg
- Division of Child Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, Arizona
| | - Kathleen Crosby
- Division of Genetics and Metabolism, Children’s National Hospital, Rare Disease Institute, Washington, District of Columbia
| | - Pranoot Tanpaiboon
- Division of Genetics and Metabolism, Children’s National Hospital, Rare Disease Institute, Washington, District of Columbia
| | - Diana Bharucha-Goebel
- Division of Neurology, Children’s National Hospital, Washington, District of Columbia
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, Maryland
| | - Carsten Bonnemann
- Division of Neurology, Children’s National Hospital, Washington, District of Columbia
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, Maryland
| | - Carrie A. Mohila
- Department of Pathology, Texas Children’s Hospital, Houston, Texas
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Elizabeth Mizerik
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
| | - Suzanne Woodbury
- Texas Children’s Hospital, Houston, Texas
- Baylor College of Medicine, Department of Physical Medicine and Rehabilitation, Houston, Texas
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Timothy Lotze
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
| | - Anthony Antonellis
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Neurology, University of Michigan, Ann Arbor, Michigan
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
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30
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Wang W, Wilson C, Collum S, Bi W, Ko J, Rajagopal K, Karmouty-Quintana H. Beta Adrenoceptor Ligands for the Treatment of Group 3 Pulmonary Hypertension and Cor Pulmonale: A Novel Therapeutic Target? J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.731] [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: 10/24/2022] Open
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31
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Granadillo JL, P A Stegmann A, Guo H, Xia K, Angle B, Bontempo K, Ranells JD, Newkirk P, Costin C, Viront J, Stumpel CT, Sinnema M, Panis B, Pfundt R, Krapels IPC, Klaassens M, Nicolai J, Li J, Jiang Y, Marco E, Canton A, Latronico AC, Montenegro L, Leheup B, Bonnet C, M Amudhavalli S, Lawson CE, McWalter K, Telegrafi A, Pearson R, Kvarnung M, Wang X, Bi W, Rosenfeld JA, Shinawi M. Pathogenic variants in TNRC6B cause a genetic disorder characterised by developmental delay/intellectual disability and a spectrum of neurobehavioural phenotypes including autism and ADHD. J Med Genet 2020; 57:717-724. [PMID: 32152250 DOI: 10.1136/jmedgenet-2019-106470] [Citation(s) in RCA: 5] [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: 09/12/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Rare variants in hundreds of genes have been implicated in developmental delay (DD), intellectual disability (ID) and neurobehavioural phenotypes. TNRC6B encodes a protein important for RNA silencing. Heterozygous truncating variants have been reported in three patients from large cohorts with autism, but no full phenotypic characterisation was described. METHODS Clinical and molecular characterisation was performed on 17 patients with TNRC6B variants. Clinical data were obtained by retrospective chart review, parent interviews, direct patient interaction with providers and formal neuropsychological evaluation. RESULTS Clinical findings included DD/ID (17/17) (speech delay in 94% (16/17), fine motor delay in 82% (14/17) and gross motor delay in 71% (12/17) of subjects), autism or autistic traits (13/17), attention deficit and hyperactivity disorder (ADHD) (11/17), other behavioural problems (7/17) and musculoskeletal findings (12/17). Other congenital malformations or clinical findings were occasionally documented. The majority of patients exhibited some dysmorphic features but no recognisable gestalt was identified. 17 heterozygous TNRC6B variants were identified in 12 male and five female unrelated subjects by exome sequencing (14), a targeted panel (2) and a chromosomal microarray (1). The variants were nonsense (7), frameshift (5), splice site (2), intragenic deletions (2) and missense (1). CONCLUSIONS Variants in TNRC6B cause a novel genetic disorder characterised by recurrent neurocognitive and behavioural phenotypes featuring DD/ID, autism, ADHD and other behavioural abnormalities. Our data highly suggest that haploinsufficiency is the most likely pathogenic mechanism. TNRC6B should be added to the growing list of genes of the RNA-induced silencing complex associated with ID/DD, autism and ADHD.
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Affiliation(s)
- Jorge Luis Granadillo
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine in Saint Louis, Saint Louis, Missouri, USA
| | - Alexander P A Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Hui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Brad Angle
- Advocate Lutheran General Hospital, Park Ridge, Illinois, USA
| | - Kelly Bontempo
- Advocate Lutheran General Hospital, Park Ridge, Illinois, USA
| | - Judith D Ranells
- Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | - Patricia Newkirk
- Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | | | | | - Constanze T Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Bianca Panis
- Zuyderland Medical Centre Heerlen, Heerlen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre, Nijmgen, The Netherlands
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University, Maastricht, The Netherlands
| | - Merel Klaassens
- Department of Pediatrics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Joost Nicolai
- Department of Neurology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Jinliang Li
- Peking University First Hospital, Beijing, Beijing, China
| | - Yuwu Jiang
- Peking University First Hospital, Beijing, Beijing, China
| | - Elysa Marco
- UCSF Pediatric Brain Center, UCSF, San Francisco, California, USA
| | - Ana Canton
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana Claudia Latronico
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luciana Montenegro
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Leheup
- Service de Génétique clinique, Höpital Brabois, Centre Hospitalier Universitaire de Nancy, Nancy, Lorraine, France
| | - Celine Bonnet
- Centre Hospitalier Universitaire de Nancy, Nancy, Lorraine, France
| | | | | | | | | | | | - Malin Kvarnung
- Department of Clinical Genetics & Department of Molecular Medicine and Surgery, Karolinska University Hospital & Karolinska Institute, Stockholm, Sweden
| | - Xia Wang
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Weimin Bi
- Baylor College of Medicine Department of Molecular and Human Genetics, Houston, Texas, USA
| | - Jill Anne Rosenfeld
- Baylor Genetics Laboratories, Houston, Texas, USA.,Baylor College of Medicine Department of Molecular and Human Genetics, Houston, Texas, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine in Saint Louis, Saint Louis, Missouri, USA
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32
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Scott TM, Guo H, Eichler EE, Rosenfeld JA, Pang K, Liu Z, Lalani S, Bi W, Yang Y, Bacino CA, Streff H, Lewis AM, Koenig MK, Thiffault I, Bellomo A, Everman DB, Jones JR, Stevenson RE, Bernier R, Gilissen C, Pfundt R, Hiatt SM, Cooper GM, Holder JL, Scott DA. BAZ2B haploinsufficiency as a cause of developmental delay, intellectual disability, and autism spectrum disorder. Hum Mutat 2020; 41:921-925. [PMID: 31999386 DOI: 10.1002/humu.23992] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/21/2019] [Revised: 01/08/2020] [Accepted: 01/19/2020] [Indexed: 12/13/2022]
Abstract
The bromodomain adjacent to zinc finger 2B gene (BAZ2B) encodes a protein involved in chromatin remodeling. Loss of BAZ2B function has been postulated to cause neurodevelopmental disorders. To determine whether BAZ2B deficiency is likely to contribute to the pathogenesis of these disorders, we performed bioinformatics analyses that demonstrated a high level of functional convergence during fetal cortical development between BAZ2B and genes known to cause autism spectrum disorder (ASD) and neurodevelopmental disorder. We also found an excess of de novo BAZ2B loss-of-function variants in exome sequencing data from previously published cohorts of individuals with neurodevelopmental disorders. We subsequently identified seven additional individuals with heterozygous deletions, stop-gain, or de novo missense variants affecting BAZ2B. All of these individuals have developmental delay (DD), intellectual disability (ID), and/or ASD. Taken together, our findings suggest that haploinsufficiency of BAZ2B causes a neurodevelopmental disorder, whose cardinal features include DD, ID, and ASD.
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Affiliation(s)
| | - Hui Guo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Center for Medical Genetics, Central Southern University, Changsha, Hunan, China
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Kaifang Pang
- Department of Pediatrics and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Zhandong Liu
- Department of Pediatrics and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mary K Koenig
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas
| | - Isabelle Thiffault
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri.,Department of Pathology, Children's Mercy Hospitals and Clinics, Kansas City, Missouri
| | | | | | | | | | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington.,Seattle Children's Autism Center, University of Washington, Seattle, Washington.,Center on Human Development and Disability, University of Washington, Seattle, Washington
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Jimmy L Holder
- Department of Pediatrics and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
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33
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Wang J, Rousseau J, Kim E, Ehresmann S, Cheng YT, Duraine L, Zuo Z, Park YJ, Li-Kroeger D, Bi W, Wong LJ, Rosenfeld J, Gleeson J, Faqeih E, Alkuraya FS, Wierenga KJ, Chen J, Afenjar A, Nava C, Doummar D, Keren B, Juusola J, Grompe M, Bellen HJ, Campeau PM. Loss of Oxidation Resistance 1, OXR1, Is Associated with an Autosomal-Recessive Neurological Disease with Cerebellar Atrophy and Lysosomal Dysfunction. Am J Hum Genet 2019; 105:1237-1253. [PMID: 31785787 PMCID: PMC6904826 DOI: 10.1016/j.ajhg.2019.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 06/23/2019] [Accepted: 11/01/2019] [Indexed: 12/28/2022] Open
Abstract
We report an early-onset autosomal-recessive neurological disease with cerebellar atrophy and lysosomal dysfunction. We identified bi-allelic loss-of-function (LoF) variants in Oxidative Resistance 1 (OXR1) in five individuals from three families; these individuals presented with a history of severe global developmental delay, current intellectual disability, language delay, cerebellar atrophy, and seizures. While OXR1 is known to play a role in oxidative stress resistance, its molecular functions are not well established. OXR1 contains three conserved domains: LysM, GRAM, and TLDc. The gene encodes at least six transcripts, including some that only consist of the C-terminal TLDc domain. We utilized Drosophila to assess the phenotypes associated with loss of mustard (mtd), the fly homolog of OXR1. Strong LoF mutants exhibit late pupal lethality or pupal eclosion defects. Interestingly, although mtd encodes 26 transcripts, severe LoF and null mutations can be rescued by a single short human OXR1 cDNA that only contains the TLDc domain. Similar rescue is observed with the TLDc domain of NCOA7, another human homolog of mtd. Loss of mtd in neurons leads to massive cell loss, early death, and an accumulation of aberrant lysosomal structures, similar to what we observe in fibroblasts of affected individuals. Our data indicate that mtd and OXR1 are required for proper lysosomal function; this is consistent with observations that NCOA7 is required for lysosomal acidification.
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Affiliation(s)
- Julia Wang
- Program in Developmental Biology, Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justine Rousseau
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada
| | - Emily Kim
- Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
| | - Sophie Ehresmann
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada
| | - Yi-Ting Cheng
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lita Duraine
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ye-Jin Park
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Li-Kroeger
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph Gleeson
- Rady Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eissa Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, 11525, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11525, Saudi Arabia
| | - Klaas J Wierenga
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, OK 26901, USA; Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Jiani Chen
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, OK 26901, USA; Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandra Afenjar
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France; Département de Génétique et Embryologie Médicale, CRMR des Malformations et Maladies Congénitales du Cervelet, GRC ConCer-LD, Sorbonne Universités, Hôpital Trousseau, Paris, 75012 France
| | - Caroline Nava
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France
| | - Diane Doummar
- Assistance Publique des Hôpitaux de Paris, Service de Neuropédiatrie, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012 France
| | - Boris Keren
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012, France
| | | | - Markus Grompe
- Department of Pediatrics, Oregon Health and Science University, Portland, Oregon 97201, USA; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97201, USA
| | - Hugo J Bellen
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada.
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Vossaert L, Wang Q, Salman R, McCombs AK, Patel V, Qu C, Mancini MA, Edwards DP, Malovannaya A, Liu P, Shaw CA, Levy B, Wapner RJ, Bi W, Breman AM, Van den Veyver IB, Beaudet AL. Validation Studies for Single Circulating Trophoblast Genetic Testing as a Form of Noninvasive Prenatal Diagnosis. Am J Hum Genet 2019; 105:1262-1273. [PMID: 31785788 PMCID: PMC6904821 DOI: 10.1016/j.ajhg.2019.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/03/2019] [Indexed: 02/07/2023] Open
Abstract
It has long been appreciated that genetic analysis of fetal or trophoblast cells in maternal blood could revolutionize prenatal diagnosis. We implemented a protocol for single circulating trophoblast (SCT) testing using positive selection by magnetic-activated cell sorting and single-cell low-coverage whole-genome sequencing to detect fetal aneuploidies and copy-number variants (CNVs) at ∼1 Mb resolution. In 95 validation cases, we identified on average 0.20 putative trophoblasts/mL, of which 55% were of high quality and scorable for both aneuploidy and CNVs. We emphasize the importance of analyzing individual cells because some cells are apoptotic, in S-phase, or otherwise of poor quality. When two or more high-quality trophoblast cells were available for singleton pregnancies, there was complete concordance between all trophoblasts unless there was evidence of confined placental mosaicism. SCT results were highly concordant with available clinical data from chorionic villus sampling (CVS) or amniocentesis procedures. Although determining the exact sensitivity and specificity will require more data, this study further supports the potential for SCT testing to become a diagnostic prenatal test.
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Affiliation(s)
- Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roseen Salman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne K McCombs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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35
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Boone PM, Paterson S, Mohajeri K, Zhu W, Genetti CA, Tai DJC, Nori N, Agrawal PB, Bacino CA, Bi W, Talkowski ME, Hogan BM, Rodan LH. Biallelic mutation of FBXL7 suggests a novel form of Hennekam syndrome. Am J Med Genet A 2019; 182:189-194. [PMID: 31633297 PMCID: PMC10081920 DOI: 10.1002/ajmg.a.61392] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/16/2019] [Accepted: 09/27/2019] [Indexed: 01/25/2023]
Abstract
Hennekam lymphangiectasia-lymphedema syndrome is an autosomal recessive disorder characterized by congenital lymphedema, intestinal lymphangiectasia, facial dysmorphism, and variable intellectual disability. Known disease genes include CCBE1, FAT4, and ADAMTS3. In a patient with clinically diagnosed Hennekam syndrome but without mutations or copy-number changes in the three known disease genes, we identified a homozygous single-exon deletion affecting FBXL7. Specifically, exon 3, which encodes the F-box domain and several leucine-rich repeats of FBXL7, is eliminated. Our analyses of databases representing >100,000 control individuals failed to identify biallelic loss-of-function variants in FBXL7. Published studies in Drosophila indicate Fbxl7 interacts with Fat, of which human FAT4 is an ortholog, and mutation of either gene yields similar morphological consequences. These data suggest that FBXL7 may be the fourth gene for Hennekam syndrome, acting via a shared pathway with FAT4.
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Affiliation(s)
- Philip M Boone
- Harvard Genetics Training Program, Boston, Massachusetts.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.,Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Scott Paterson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.,Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | | | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts
| | - Derek J C Tai
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.,Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Neeharika Nori
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts
| | | | | | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.,Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Benjamin M Hogan
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
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Cao Y, Tokita MJ, Chen ES, Ghosh R, Chen T, Feng Y, Gorman E, Gibellini F, Ward PA, Braxton A, Wang X, Meng L, Xiao R, Bi W, Xia F, Eng CM, Yang Y, Gambin T, Shaw C, Liu P, Stankiewicz P. A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Genome Med 2019; 11:48. [PMID: 31349857 PMCID: PMC6660700 DOI: 10.1186/s13073-019-0658-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [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: 01/22/2019] [Accepted: 07/11/2019] [Indexed: 12/23/2022] Open
Abstract
Background Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have only recently emerged as routine clinical diagnostic tests. To date, few systematic analyses of mosaic variants detected by diagnostic exome sequencing for diverse clinical indications have been performed. Methods To investigate the frequency, type, allelic fraction, and phenotypic consequences of clinically relevant somatic mosaic single nucleotide variants (SNVs) and characteristics of the corresponding genes, we retrospectively queried reported mosaic variants from a cohort of ~ 12,000 samples submitted for clinical exome sequencing (ES) at Baylor Genetics. Results We found 120 mosaic variants involving 107 genes, including 80 mosaic SNVs in proband samples and 40 in parental/grandparental samples. Average mosaic alternate allele fraction (AAF) detected in autosomes and in X-linked disease genes in females was 18.2% compared with 34.8% in X-linked disease genes in males. Of these mosaic variants, 74 variants (61.7%) were classified as pathogenic or likely pathogenic and 46 (38.3%) as variants of uncertain significance. Mosaic variants occurred in disease genes associated with autosomal dominant (AD) or AD/autosomal recessive (AR) (67/120, 55.8%), X-linked (33/120, 27.5%), AD/somatic (10/120, 8.3%), and AR (8/120, 6.7%) inheritance. Of note, 1.7% (2/120) of variants were found in genes in which only somatic events have been described. Nine genes had recurrent mosaic events in unrelated individuals which accounted for 18.3% (22/120) of all detected mosaic variants in this study. The proband group was enriched for mosaicism affecting Ras signaling pathway genes. Conclusions In sum, an estimated 1.5% of all molecular diagnoses made in this cohort could be attributed to a mosaic variant detected in the proband, while parental mosaicism was identified in 0.3% of families analyzed. As ES design favors breadth over depth of coverage, this estimate of the prevalence of mosaic variants likely represents an underestimate of the total number of clinically relevant mosaic variants in our cohort. Electronic supplementary material The online version of this article (10.1186/s13073-019-0658-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mari J Tokita
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Rajarshi Ghosh
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | | | | | | | | | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | | | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, USA.
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, USA.
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Suleiman J, Riedhammer KM, Jicinsky T, Mundt M, Werner L, Gusic M, Burgemeister AL, Alsaif HS, Abdulrahim M, Moghrabi NN, Nicolas-Jilwan M, AlSayed M, Bi W, Sampath S, Alkuraya FS, El-Hattab AW. Homozygous loss-of-function variants of TASP1, a gene encoding an activator of the histone methyltransferases KMT2A and KMT2D, cause a syndrome of developmental delay, happy demeanor, distinctive facial features, and congenital anomalies. Hum Mutat 2019; 40:1985-1992. [PMID: 31209944 DOI: 10.1002/humu.23844] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/27/2019] [Revised: 05/31/2019] [Accepted: 06/09/2019] [Indexed: 12/20/2022]
Abstract
We report four unrelated children with homozygous loss-of-function variants in TASP1 and an overlapping phenotype comprising developmental delay with hypotonia and microcephaly, feeding difficulties with failure-to-thrive, recurrent respiratory infections, cardiovascular malformations, cryptorchidism, happy demeanor, and distinctive facial features. Two children had a homozygous founder deletion encompassing exons 5-11 of TASP1, the third had a homozygous missense variant, c.701 C>T (p.Thr234Met), affecting the active site of the encoded enzyme, and the fourth had a homozygous nonsense variant, c.199 C>T (p.Arg67*). TASP1 encodes taspase 1 (TASP1), which is responsible for cleaving, thus activating, the lysine methyltransferases KMT2A and KMT2D, which are essential for histone methylation and transcription regulation. The consistency of the phenotype, the critical biological function of TASP1, the deleterious nature of the TASP1 variants, and the overlapping features with Wiedemann-Steiner and Kabuki syndromes respectively caused by pathogenic variants in KMT2A and KMT2D all support that TASP1 is a disease-related gene.
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Affiliation(s)
- Jehan Suleiman
- Division of Neurology, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates.,Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany.,Department of Nephrology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | | | | | | | - Mirjana Gusic
- Institute of Human Genetics, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | | | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha Abdulrahim
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nabil N Moghrabi
- Molecular Diagnostic Laboratory, Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Manal Nicolas-Jilwan
- Division of Neuroradiology, Department of Radiology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Moeenaldeen AlSayed
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics, Houston, Texas
| | | | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Genetics Clinics, KidsHeart Medical Center, Abu Dhabi, United Arab Emirates
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38
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Liu P, Meng L, Normand EA, Xia F, Song X, Ghazi A, Rosenfeld J, Magoulas PL, Braxton A, Ward P, Dai H, Yuan B, Bi W, Xiao R, Wang X, Chiang T, Vetrini F, He W, Cheng H, Dong J, Gijavanekar C, Benke PJ, Bernstein JA, Eble T, Eroglu Y, Erwin D, Escobar L, Gibson JB, Gripp K, Kleppe S, Koenig MK, Lewis AM, Natowicz M, Mancias P, Minor L, Scaglia F, Schaaf CP, Streff H, Vernon H, Uhles CL, Zackai EH, Wu N, Sutton VR, Beaudet AL, Muzny D, Gibbs RA, Posey JE, Lalani S, Shaw C, Eng CM, Lupski JR, Yang Y. Reanalysis of Clinical Exome Sequencing Data. N Engl J Med 2019; 380:2478-2480. [PMID: 31216405 PMCID: PMC6934160 DOI: 10.1056/nejmc1812033] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
| | | | | | - Fan Xia
- Baylor College of Medicine, Houston, TX
| | | | | | | | | | | | | | | | - Bo Yuan
- Baylor College of Medicine, Houston, TX
| | - Weimin Bi
- Baylor College of Medicine, Houston, TX
| | - Rui Xiao
- Baylor College of Medicine, Houston, TX
| | - Xia Wang
- Baylor College of Medicine, Houston, TX
| | | | | | | | | | | | | | | | | | | | | | | | - Luis Escobar
- St. Vincent's Peyton Manning Children's Hospital, Indianapolis, IN
| | | | - Karen Gripp
- A.I. DuPont Hospital for Children, Wilmington, DE
| | - Soledad Kleppe
- Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | | | | | | | | | | | | | | | | | | | | | | | - Nan Wu
- Peking Union Medical College Hospital, Beijing, China
| | | | | | | | | | | | | | - Chad Shaw
- Baylor College of Medicine, Houston, TX
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39
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Dharmadhikari AV, Ghosh R, Yuan B, Liu P, Dai H, Al Masri S, Scull J, Posey JE, Jiang AH, He W, Vetrini F, Braxton AA, Ward P, Chiang T, Qu C, Gu S, Shaw CA, Smith JL, Lalani S, Stankiewicz P, Cheung SW, Bacino CA, Patel A, Breman AM, Wang X, Meng L, Xiao R, Xia F, Muzny D, Gibbs RA, Beaudet AL, Eng CM, Lupski JR, Yang Y, Bi W. Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. Genome Med 2019; 11:30. [PMID: 31101064 PMCID: PMC6525387 DOI: 10.1186/s13073-019-0639-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 09/18/2018] [Accepted: 04/09/2019] [Indexed: 02/02/2023] Open
Abstract
Background Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES. Methods In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array. Results The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities. Conclusions Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations. Electronic supplementary material The online version of this article (10.1186/s13073-019-0639-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Rajarshi Ghosh
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Bo Yuan
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Pengfei Liu
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Hongzheng Dai
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | | | - Jennifer Scull
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | | | - Weimin He
- Baylor Genetics Laboratories, Houston, TX, USA
| | | | - Alicia A Braxton
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Patricia Ward
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Chunjing Qu
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Chad A Shaw
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Janice L Smith
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Seema Lalani
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Pawel Stankiewicz
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sau-Wai Cheung
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Ankita Patel
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Amy M Breman
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Xia Wang
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Linyan Meng
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Rui Xiao
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Fan Xia
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Christine M Eng
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Yaping Yang
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Weimin Bi
- Baylor Genetics Laboratories, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.
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40
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Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KM, Roeder E, Littlejohn RO, Holder S, Zhu W, Alaimo JT, Graham B, Harris JM, Gibson JB, Pastore M, McBride KL, Komara M, Al-Gazali L, Al Shamsi A, Fanning EA, Wierenga KJ, Scott DA, Ben-Neriah Z, Meiner V, Cassuto H, Elpeleg O, Lloyd Holder J, Burrage LC, Seaver LH, Van Maldergem L, Mahida S, Soul JS, Marlatt M, Matyakhina L, Vogt J, Gold JA, Park SM, Varghese V, Lampe AK, Kumar A, Lees M, Holder-Espinasse M, McConnell V, Bernhard B, Blair E, Harrison V, Muzny DM, Gibbs RA, Elsea SH, Posey JE, Bi W, Lalani S, Xia F, Yang Y, Eng CM, Lupski JR, Liu P. Correction to: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. Genome Med 2019; 11:16. [PMID: 30909959 PMCID: PMC6434874 DOI: 10.1186/s13073-019-0630-1] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 11/23/2022] Open
Affiliation(s)
- Francesco Vetrini
- Baylor Genetics, Houston, TX, 77021, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mohnish Suri
- Nottingham Genetics Service, Nottingham City Hospital, Nottingham, UK
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberly Margaret Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Rebecca O Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Sue Holder
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | | | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brett Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jill M Harris
- Dell Children's Medical Group, Austin, TX, 78723, USA
| | | | - Matthew Pastore
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Kim L McBride
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Makanko Komara
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | | | - Elizabeth A Fanning
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Present address: Mayo Clinic Florida, Department of Clinical Genomics, Jacksonville, FL, 32224, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ziva Ben-Neriah
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, 91120, Jerusalem, Israel
| | - J Lloyd Holder
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurie H Seaver
- Department of Pediatrics, University of Hawaii, Honolulu, HI, 96826, USA
| | | | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Janet S Soul
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Margaret Marlatt
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | | | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - June-Anne Gold
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Soo-Mi Park
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Vinod Varghese
- All-Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - Anne K Lampe
- South East of Scotland Clinical Genetic Service, Western General Hospital, Edinburgh, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Melissa Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | | | - Vivienne McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Birgitta Bernhard
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | - Ed Blair
- Oxford Regional Genetics Service, Oxford University Hospitals, Oxford, UK
| | - Victoria Harrison
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sarah H Elsea
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Weimin Bi
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema Lalani
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine M Eng
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Pengfei Liu
- Baylor Genetics, Houston, TX, 77021, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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41
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Chiang T, Liu X, Wu TJ, Hu J, Sedlazeck FJ, White S, Schaid D, Andrade MD, Jarvik GP, Crosslin D, Stanaway I, Carrell DS, Connolly JJ, Hakonarson H, Groopman EE, Gharavi AG, Fedotov A, Bi W, Leduc MS, Murdock DR, Jiang Y, Meng L, Eng CM, Wen S, Yang Y, Muzny DM, Boerwinkle E, Salerno W, Venner E, Gibbs RA. Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel. Genet Med 2019; 21:2135-2144. [PMID: 30890783 PMCID: PMC6752313 DOI: 10.1038/s41436-019-0475-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 09/24/2018] [Accepted: 02/25/2019] [Indexed: 12/24/2022] Open
Abstract
PURPOSE To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs. METHODS DNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples, when the target log2 ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap). RESULTS Thirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation, and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multiexon and 29 single-exon CNVs with high C-scores were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA). CONCLUSION Atlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We propose guidelines and criteria to identify high confidence single-exon CNVs.
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Affiliation(s)
- Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Xiuping Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tsung-Jung Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Daniel Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Gail P Jarvik
- University of Washington Medical Center, Seattle, WA, USA
| | - David Crosslin
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Ian Stanaway
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | | | - Emily E Groopman
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY, USA
| | - Alexander Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | | | - David R Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yunyun Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratories, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,UTHealth School of Public Health, Houston, TX, USA
| | - William Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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42
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Burrage LC, Reynolds JJ, Baratang NV, Phillips JB, Wegner J, McFarquhar A, Higgs MR, Christiansen AE, Lanza DG, Seavitt JR, Jain M, Li X, Parry DA, Raman V, Chitayat D, Chinn IK, Bertuch AA, Karaviti L, Schlesinger AE, Earl D, Bamshad M, Savarirayan R, Doddapaneni H, Muzny D, Jhangiani SN, Eng CM, Gibbs RA, Bi W, Emrick L, Rosenfeld JA, Postlethwait J, Westerfield M, Dickinson ME, Beaudet AL, Ranza E, Huber C, Cormier-Daire V, Shen W, Mao R, Heaney JD, Orange JS, Bertola D, Yamamoto GL, Baratela WAR, Butler MG, Ali A, Adeli M, Cohn DH, Krakow D, Jackson AP, Lees M, Offiah AC, Carlston CM, Carey JC, Stewart GS, Bacino CA, Campeau PM, Lee B. Bi-allelic Variants in TONSL Cause SPONASTRIME Dysplasia and a Spectrum of Skeletal Dysplasia Phenotypes. Am J Hum Genet 2019; 104:422-438. [PMID: 30773277 PMCID: PMC6408318 DOI: 10.1016/j.ajhg.2019.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 08/10/2018] [Accepted: 01/17/2019] [Indexed: 12/14/2022] Open
Abstract
SPONASTRIME dysplasia is an autosomal-recessive spondyloepimetaphyseal dysplasia characterized by spine (spondylar) abnormalities, midface hypoplasia with a depressed nasal bridge, metaphyseal striations, and disproportionate short stature. Scoliosis, coxa vara, childhood cataracts, short dental roots, and hypogammaglobulinemia have also been reported in this disorder. Although an autosomal-recessive inheritance pattern has been hypothesized, pathogenic variants in a specific gene have not been discovered in individuals with SPONASTRIME dysplasia. Here, we identified bi-allelic variants in TONSL, which encodes the Tonsoku-like DNA repair protein, in nine subjects (from eight families) with SPONASTRIME dysplasia, and four subjects (from three families) with short stature of varied severity and spondylometaphyseal dysplasia with or without immunologic and hematologic abnormalities, but no definitive metaphyseal striations at diagnosis. The finding of early embryonic lethality in a Tonsl-/- murine model and the discovery of reduced length, spinal abnormalities, reduced numbers of neutrophils, and early lethality in a tonsl-/- zebrafish model both support the hypomorphic nature of the identified TONSL variants. Moreover, functional studies revealed increased amounts of spontaneous replication fork stalling and chromosomal aberrations, as well as fewer camptothecin (CPT)-induced RAD51 foci in subject-derived cell lines. Importantly, these cellular defects were rescued upon re-expression of wild-type (WT) TONSL; this rescue is consistent with the hypothesis that hypomorphic TONSL variants are pathogenic. Overall, our studies in humans, mice, zebrafish, and subject-derived cell lines confirm that pathogenic variants in TONSL impair DNA replication and homologous recombination-dependent repair processes, and they lead to a spectrum of skeletal dysplasia phenotypes with numerous extra-skeletal manifestations.
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Affiliation(s)
- Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - John J Reynolds
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Nissan Vida Baratang
- Centre Hospitalier Universitaire Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T1J4, Canada
| | | | - Jeremy Wegner
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Ashley McFarquhar
- Centre Hospitalier Universitaire Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T1J4, Canada
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Audrey E Christiansen
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Denise G Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahim Jain
- Department of Bone and Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Xiaohui Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Parry
- Medical Research Council Institute of Genetics & Molecular Medicine, the University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Vandana Raman
- Division of Pediatric Endocrinology and Diabetes, University of Utah, Salt Lake City, UT 84112, USA
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON M5G 1Z5, Canada; Department of Pediatrics, Division of Clinical and Metabolic Genetics, the Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Division of Pediatric Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Alison A Bertuch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lefkothea Karaviti
- Division of Diabetes and Endocrinology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Alan E Schlesinger
- Department of Pediatric Radiology, Texas Children's Hospital, Houston, TX 77030, USA; Department of Radiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dawn Earl
- Seattle Children's Hospital, Seattle, WA 98195, USA
| | - Michael Bamshad
- Seattle Children's Hospital, Seattle, WA 98195, USA; Departments of Pediatrics and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, University of Melbourne, Parkville, VIC 3052, Australia
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77030, USA
| | - Lisa Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Division of Neurology and Developmental Neuroscience and Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Mary E Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emmanuelle Ranza
- Service of Genetic Medicine, University of Geneva Medical School, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Celine Huber
- Department of Genetics, INSERM UMR1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, AP-HP, Hôpital Necker Enfants Malades, Paris 75015, France
| | - Valérie Cormier-Daire
- Department of Genetics, INSERM UMR1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, AP-HP, Hôpital Necker Enfants Malades, Paris 75015, France
| | - Wei Shen
- Associated Regional and University Pathologists Laboratories, Salt Lake City, UT 84108, USA; Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Rong Mao
- Associated Regional and University Pathologists Laboratories, Salt Lake City, UT 84108, USA; Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jordan S Orange
- Division of Pediatric Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX 77030, USA; Current affiliation: Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York Presbyterian, New York, NY 10032, USA
| | - Débora Bertola
- Clinical Genetics Unit, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403-000, Brazil; Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Instituto de Biociências da Universidade de São Paulo, SP 05508-0900, Brazil
| | - Guilherme L Yamamoto
- Clinical Genetics Unit, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403-000, Brazil; Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, Instituto de Biociências da Universidade de São Paulo, SP 05508-0900, Brazil
| | - Wagner A R Baratela
- Clinical Genetics Unit, Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403-000, Brazil
| | - Merlin G Butler
- Departments of Psychiatry and Behavioral Sciences and Pediatrics, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Asim Ali
- Department of Ophthalmology and Vision Sciences, the Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Mehdi Adeli
- Department of Allergy and Immunology, Sidra Medicine, Hamad Medical Corporation, Weill Cornell Medicine, Qatar, Doha, Qatar
| | - Daniel H Cohn
- Department of Molecular, Cell, and Developmental Biology and Department of Orthopaedic Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Deborah Krakow
- Department of Orthopaedic Surgery, Department of Human Genetics and Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew P Jackson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Melissa Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Amaka C Offiah
- Department of Oncology and Metabolism, Academic Unit of Child Health, University of Sheffield, Sheffield S10 2TH, UK
| | - Colleen M Carlston
- Associated Regional and University Pathologists Laboratories, Salt Lake City, UT 84108, USA; Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - John C Carey
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T1J4, Canada
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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43
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Yuan B, Neira J, Pehlivan D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, Baple EL, Dean J, Fong CT, Hickey SE, Hudgins L, Leon E, Madan-Khetarpal S, Rawlins L, Rustad CF, Stray-Pedersen A, Tveten K, Wenger O, Diaz J, Jenkins L, Martin L, McGuire M, Pietryga M, Ramsdell L, Slattery L, Abid F, Bertuch AA, Grange D, Immken L, Schaaf CP, Van Esch H, Bi W, Cheung SW, Breman AM, Smith JL, Shaw C, Crosby AH, Eng C, Yang Y, Lupski JR, Xiao R, Liu P. Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet Med 2019; 21:663-675. [PMID: 30158690 PMCID: PMC6395558 DOI: 10.1038/s41436-018-0085-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 06/01/2018] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective. METHODS We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization. RESULTS Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS. CONCLUSION CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Juanita Neira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Teresa Santiago-Sim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | | | - Margaret P Adam
- Seattle Children's Hospital, Seattle, Washington, 98105, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, 98105, USA
| | - Emma L Baple
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, EX1 2ED, UK
| | - John Dean
- Clinical Genetics Service, NHS Grampian, Aberdeen, AB25 2ZA, Scotland
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642, USA
| | - Scott E Hickey
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio, 43205, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University, Stanford, California, 94305, USA
| | - Eyby Leon
- Rare Disease Institute, Children's National Health System, Washington, DC, 20010, USA
| | | | - Lettie Rawlins
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, EX1 2ED, UK
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710, Skien, Norway
| | - Olivia Wenger
- New Leaf Center, Clinic for Special Children, Mt. Eaton, Ohio, 44659, USA
| | - Jullianne Diaz
- Rare Disease Institute, Children's National Health System, Washington, DC, 20010, USA
| | - Laura Jenkins
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, 15224, USA
| | - Laura Martin
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642, USA
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Marguerite Pietryga
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Linda Ramsdell
- Seattle Children's Hospital, Seattle, Washington, 98105, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, 98105, USA
| | - Leah Slattery
- Division of Medical Genetics, Stanford University, Stanford, California, 94305, USA
| | - Farida Abid
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alison A Bertuch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Dorothy Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - LaDonna Immken
- Dell Children's Medical Center of Central Texas, Austin, Texas, 78723, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases, University Hospital Cologne, Cologne, Germany
| | - Hilde Van Esch
- Center for Human Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Andrew H Crosby
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA.
- Baylor Genetics, Houston, Texas, 77021, USA.
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Vetrini F, McKee S, Rosenfeld JA, Suri M, Lewis AM, Nugent KM, Roeder E, Littlejohn RO, Holder S, Zhu W, Alaimo JT, Graham B, Harris JM, Gibson JB, Pastore M, McBride KL, Komara M, Al-Gazali L, Al Shamsi A, Fanning EA, Wierenga KJ, Scott DA, Ben-Neriah Z, Meiner V, Cassuto H, Elpeleg O, Holder JL, Burrage LC, Seaver LH, Van Maldergem L, Mahida S, Soul JS, Marlatt M, Matyakhina L, Vogt J, Gold JA, Park SM, Varghese V, Lampe AK, Kumar A, Lees M, Holder-Espinasse M, McConnell V, Bernhard B, Blair E, Harrison V, Muzny DM, Gibbs RA, Elsea SH, Posey JE, Bi W, Lalani S, Xia F, Yang Y, Eng CM, Lupski JR, Liu P. De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome. Genome Med 2019; 11:12. [PMID: 30819258 PMCID: PMC6393995 DOI: 10.1186/s13073-019-0623-0] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 02/15/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormalities, and neurological manifestations with variants in a large number of genes (hundreds) associated. To date, a few de novo mutations potentially disrupting TCF20 function in patients with ID, ASD, and hypotonia have been reported. TCF20 encodes a transcriptional co-regulator structurally related to RAI1, the dosage-sensitive gene responsible for Smith-Magenis syndrome (deletion/haploinsufficiency) and Potocki-Lupski syndrome (duplication/triplosensitivity). METHODS Genome-wide analyses by exome sequencing (ES) and chromosomal microarray analysis (CMA) identified individuals with heterozygous, likely damaging, loss-of-function alleles in TCF20. We implemented further molecular and clinical analyses to determine the inheritance of the pathogenic variant alleles and studied the spectrum of phenotypes. RESULTS We report 25 unique inactivating single nucleotide variants/indels (1 missense, 1 canonical splice-site variant, 18 frameshift, and 5 nonsense) and 4 deletions of TCF20. The pathogenic variants were detected in 32 patients and 4 affected parents from 31 unrelated families. Among cases with available parental samples, the variants were de novo in 20 instances and inherited from 4 symptomatic parents in 5, including in one set of monozygotic twins. Two pathogenic loss-of-function variants were recurrent in unrelated families. Patients presented with a phenotype characterized by developmental delay, intellectual disability, hypotonia, variable dysmorphic features, movement disorders, and sleep disturbances. CONCLUSIONS TCF20 pathogenic variants are associated with a novel syndrome manifesting clinical characteristics similar to those observed in Smith-Magenis syndrome. Together with previously described cases, the clinical entity of TCF20-associated neurodevelopmental disorders (TAND) emerges from a genotype-driven perspective.
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Affiliation(s)
- Francesco Vetrini
- Baylor Genetics, Houston, TX, 77021, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mohnish Suri
- Nottingham Genetics Service, Nottingham City Hospital, Nottingham, UK
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberly Margaret Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Rebecca O Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Sue Holder
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | | | - Joseph T Alaimo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Brett Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jill M Harris
- Dell Children's Medical Group, Austin, TX, 78723, USA
| | | | - Matthew Pastore
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Kim L McBride
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital; and Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH, 43205, USA
| | - Makanko Komara
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine & Health Sciences, United Arab University, Al Ain, UAE
| | | | - Elizabeth A Fanning
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Present address: Mayo Clinic Florida, Department of Clinical Genomics, Jacksonville, FL, 32224, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ziva Ben-Neriah
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, 91120, Jerusalem, Israel
| | - J Lloyd Holder
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurie H Seaver
- Department of Pediatrics, University of Hawaii, Honolulu, HI, 96826, USA
| | | | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Janet S Soul
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | - Margaret Marlatt
- Department of Neurology, Boston Children's Hospital, Boston, MA, 0211, USA
| | | | - Julie Vogt
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners; and Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - June-Anne Gold
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Soo-Mi Park
- East Anglia Regional Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Vinod Varghese
- All-Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - Anne K Lampe
- South East of Scotland Clinical Genetic Service, Western General Hospital, Edinburgh, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Melissa Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | | | - Vivienne McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Birgitta Bernhard
- North West Thames Regional Genetics Service, 759 Northwick Park Hospital, London, UK
| | - Ed Blair
- Oxford Regional Genetics Service, Oxford University Hospitals, Oxford, UK
| | - Victoria Harrison
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | | | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sarah H Elsea
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Weimin Bi
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema Lalani
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Fan Xia
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaping Yang
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine M Eng
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Baylor Genetics, Houston, TX, 77021, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Pengfei Liu
- Baylor Genetics, Houston, TX, 77021, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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Wu F, Xing YZ, Bi W, Liu JX. [The value of lean nystagmus and sitting to supine positioning nystagmus in the diagnosis of horizontal semicircular canal benign paroxysmal positional vertigo]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2019; 33:106-109. [PMID: 30808132 DOI: 10.13201/j.issn.1001-1781.2019.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Indexed: 11/12/2022]
Abstract
Objective: To explore the value of 1ean nystagmus and sitting to supine positioning nystagmus in the diagnosis of horizontal semicircular canal benign paroxysmal positional vertigo. Method: One hundred cases of patients with definitive diagnosis of horizontal semicircular canal benign paroxysmal positional vertigo were tested by 1ean nystagmus and sitting to supine positioning nystagmus and supine roll test. The affected side was recorded according to the nystagmus direction. After diagnosis, they were treated with canalith repositioning procedure. The canalith repositioning procedure was made according to the supine roll test result when 1ean nystagmus and sitting to supine positioning nystagmuscannot be induced. Furthermore,the canalith repositioning procedure was made according to the1ean nystagmus and sitting to supine positioning nystagmuswhenthe supine roll test cannot diagnose. The patients with canalolithiasis were randomly divided into two groups when both 1ean nystagmus and sitting to supine positioning nystagmusand the supine roll test can be induced. One group was treated with canalith repositioning procedure based on results of supine roll test and the other group was treated based on the results of1ean nystagmus and sitting to supine positioning nystagmus. The detection rate and diagnostic coincidence rate of 1ean nystagmus and sitting to supine positioning nystagmus were calculated and the shortterm outcome were evaluated one day after treatment. Result: The detection rate of 1ean nystagmus and sitting to supine positioning nystagmus was 83% and the coincidence rate with the roll test was 90.1%,respectively. There was no significant statistical difference between the treatment effect according to lean nystagmus and sitting to supine positioning nystagmus and supine roll test. Conclusion: Lean nystagmus and sitting to supine positioning nystagmus cannot be used alone in the diagnosis ofhorizontal semicircular canal benign paroxysmal positional vertigo. They need to be combined with supine roll test. However, when the supine roll test is difficult to demonstrate the affected side, it can be used as an auxiliary diagnostic method. When the results of 1ean nystagmus and sitting to supine positioning nystagmusand the supine roll test are inconsistent, repeat the test and conduct a comprehensive assessment to avoid missed diagnosis and misdiagnosis..
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Affiliation(s)
- F Wu
- Department of Otorhinolaryngology, Tianjin Union Medical Center, Tianjin, 300121, China
| | - Y Z Xing
- Department of Otorhinolaryngology, Tianjin Union Medical Center, Tianjin, 300121, China
| | - W Bi
- Department of Otorhinolaryngology, Tianjin Union Medical Center, Tianjin, 300121, China
| | - J X Liu
- Department of Otorhinolaryngology, Tianjin Union Medical Center, Tianjin, 300121, China
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Fountain MD, Oleson DS, Rech ME, Segebrecht L, Hunter JV, McCarthy JM, Lupo PJ, Holtgrewe M, Moran R, Rosenfeld JA, Isidor B, Le Caignec C, Saenz MS, Pedersen RC, Morgan TM, Pfotenhauer JP, Xia F, Bi W, Kang SHL, Patel A, Krantz ID, Raible SE, Smith W, Cristian I, Torti E, Juusola J, Millan F, Wentzensen IM, Person RE, Küry S, Bézieau S, Uguen K, Férec C, Munnich A, van Haelst M, Lichtenbelt KD, van Gassen K, Hagelstrom T, Chawla A, Perry DL, Taft RJ, Jones M, Masser-Frye D, Dyment D, Venkateswaran S, Li C, Escobar LF, Horn D, Spillmann RC, Peña L, Wierzba J, Strom TM, Parenti I, Kaiser FJ, Ehmke N, Schaaf CP. Pathogenic variants in USP7 cause a neurodevelopmental disorder with speech delays, altered behavior, and neurologic anomalies. Genet Med 2019; 21:1797-1807. [PMID: 30679821 PMCID: PMC6752677 DOI: 10.1038/s41436-019-0433-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 08/17/2018] [Accepted: 01/02/2019] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Haploinsufficiency of USP7, located at chromosome 16p13.2, has recently been reported in seven individuals with neurodevelopmental phenotypes, including developmental delay/intellectual disability (DD/ID), autism spectrum disorder (ASD), seizures, and hypogonadism. Further, USP7 was identified to critically incorporate into the MAGEL2-USP7-TRIM27 (MUST), such that pathogenic variants in USP7 lead to altered endosomal F-actin polymerization and dysregulated protein recycling. METHODS We report 16 newly identified individuals with heterozygous USP7 variants, identified by genome or exome sequencing or by chromosome microarray analysis. Clinical features were evaluated by review of medical records. Additional clinical information was obtained on the seven previously reported individuals to fully elucidate the phenotypic expression associated with USP7 haploinsufficiency. RESULTS The clinical manifestations of these 23 individuals suggest a syndrome characterized by DD/ID, hypotonia, eye anomalies,feeding difficulties, GERD, behavioral anomalies, and ASD, and more specific phenotypes of speech delays including a nonverbal phenotype and abnormal brain magnetic resonance image findings including white matter changes based on neuroradiologic examination. CONCLUSION The consistency of clinical features among all individuals presented regardless of de novo USP7 variant type supports haploinsufficiency as a mechanism for pathogenesis and refines the clinical impact faced by affected individuals and caregivers.
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Affiliation(s)
- Michael D Fountain
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David S Oleson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Megan E Rech
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lara Segebrecht
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Jill V Hunter
- Department of Radiology, Texas Children's Hospital, Houston, TX, USA
| | - John M McCarthy
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Philip J Lupo
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany
| | - Rocio Moran
- Department of Genetics, Cleveland Clinic Children's, Cleveland, OH, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Bertrand Isidor
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | | | - Margarita S Saenz
- Clinical Genetics and Metabolism, Children's Hospital Colorado, Aurora, CO, USA
| | - Robert C Pedersen
- Department of Pediatrics, Tripler Army Medical Center, Honolulu, HI, USA
| | - Thomas M Morgan
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jean P Pfotenhauer
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sung-Hae L Kang
- Department of Pathology & Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Ian D Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarah E Raible
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wendy Smith
- Department of Pediatrics, The Barbara Bush Children's Hospital, Maine Medical Center, Portland, ME, USA
| | - Ingrid Cristian
- Division of Genetics, Department of Pediatrics, Arnold Palmer Hospital, Orlando, FL, USA
| | | | | | | | | | | | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Stéphane Bézieau
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Kévin Uguen
- Service de Génétique Médicale, CHRU de Brest, INSERM, Brest, France
| | - Claude Férec
- Service de Génétique Médicale, CHRU de Brest, INSERM, Brest, France
| | - Arnold Munnich
- UMR1163, Université Paris Descartes, Sorbonne Paris Cité, Institut IMAGINE, Paris, France
| | - Mieke van Haelst
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.,Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - 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
| | | | - Aditi Chawla
- Illumina Clinical Services Laboratory, Illumina, San Diego, CA, USA
| | - Denise L Perry
- Illumina Clinical Services Laboratory, Illumina, San Diego, CA, USA
| | - Ryan J Taft
- Illumina Clinical Services Laboratory, Illumina, San Diego, CA, USA
| | - Marilyn Jones
- Division of Genetics, Department of Pediatrics, UC San Diego School of Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Diane Masser-Frye
- Division of Genetics, Department of Pediatrics, UC San Diego School of Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - David Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sunita Venkateswaran
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Chumei Li
- McMaster University Medical Center, Hamilton, ON, Canada
| | - Luis F Escobar
- Medical Genetics and Neurodevelopment Center, St Vincent Children's Hospital, Indianapolis, IN, USA
| | - Denise Horn
- Charité-Universtitätsmedizin Berlin, Institute for Medical Genetics and Human Genetics, Berlin, Germany
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Loren Peña
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jolanta Wierzba
- Department of General Nursery, Medical University of Gdańsk, Gdańsk, Poland
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ilaria Parenti
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | - Frank J Kaiser
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | - Nadja Ehmke
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Christian P Schaaf
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Institute of Human Genetics, University Hospital Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Center for Rare Diseases, University Hospital Cologne, Cologne, Germany.
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47
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Vossaert L, Wang Q, Salman R, McCombs A, Henke D, Qu C, Bi W, Levy B, Yang Y, Shaw C, Wapner R, Breman A, Van den Veyver I, Beaudet A. 900: A pilot validation study for cell-based noninvasive prenatal testing (NIPT) in 42 cases. Am J Obstet Gynecol 2019. [DOI: 10.1016/j.ajog.2018.11.924] [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: 10/27/2022]
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48
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Hashmi SK, Bergstrom K, Bertuch AA, Despotovic JM, Muscal E, Xia F, Bi W, Marcogliese A, Diaz R. PSTPIP1-associated myeloid-related proteinemia inflammatory syndrome: A rare cause of childhood neutropenia associated with systemic inflammation and hyperzincemia. Pediatr Blood Cancer 2019; 66:e27439. [PMID: 30198636 DOI: 10.1002/pbc.27439] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 07/27/2018] [Accepted: 08/06/2018] [Indexed: 11/09/2022]
Abstract
Neutropenia in pediatric patients can be due to a variety of disorders. We describe two patients who underwent extensive evaluation over many years for arthralgias and moderate neutropenia of unclear etiology. Genetic testing identified a pathogenic variant in PSTPIP1 (proline-serine-threonine phosphatase-interacting protein 1) in both patients. Markedly elevated inflammatory markers and zinc levels confirmed the rare diagnosis of PSTPIP1-associated myeloid-related proteinemia inflammatory (PAMI) syndrome, tailoring treatment. Neutropenia is common in patients with PAMI syndrome. Unique mutations seen in PAMI syndrome may account for the specific phenotypic features of this disorder.
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Affiliation(s)
- Saman K Hashmi
- Department of Pediatrics, Section of Hematology Oncology, Baylor College of Medicine, Houston, Texas
| | - Katie Bergstrom
- Department of Pediatrics, Section of Hematology Oncology, Baylor College of Medicine, Houston, Texas
| | - Alison A Bertuch
- Department of Pediatrics, Section of Hematology Oncology, Baylor College of Medicine, Houston, Texas
| | - Jenny M Despotovic
- Department of Pediatrics, Section of Hematology Oncology, Baylor College of Medicine, Houston, Texas
| | - Eyal Muscal
- Department of Pediatrics, Section of Immunology/Allergy/Rheumatology, Baylor College of Medicine, Houston, Texas
| | - Fan Xia
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Weimin Bi
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Rosa Diaz
- Department of Pediatrics, Section of Hematology Oncology, Baylor College of Medicine, Houston, Texas
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49
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Metz KA, Teng X, Coppens I, Lamb HM, Wagner BE, Rosenfeld JA, Chen X, Zhang Y, Kim HJ, Meadow ME, Wang TS, Haberlandt ED, Anderson GW, Leshinsky-Silver E, Bi W, Markello TC, Pratt M, Makhseed N, Garnica A, Danylchuk NR, Burrow TA, Jayakar P, McKnight D, Agadi S, Gbedawo H, Stanley C, Alber M, Prehl I, Peariso K, Ong MT, Mordekar SR, Parker MJ, Crooks D, Agrawal PB, Berry GT, Loddenkemper T, Yang Y, Maegawa GHB, Aouacheria A, Markle JG, Wohlschlegel JA, Hartman AL, Hardwick JM. KCTD7 deficiency defines a distinct neurodegenerative disorder with a conserved autophagy-lysosome defect. Ann Neurol 2018; 84:766-780. [PMID: 30295347 DOI: 10.1002/ana.25351] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/27/2018] [Accepted: 09/23/2018] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Several small case series identified KCTD7 mutations in patients with a rare autosomal recessive disorder designated progressive myoclonic epilepsy (EPM3) and neuronal ceroid lipofuscinosis (CLN14). Despite the name KCTD (potassium channel tetramerization domain), KCTD protein family members lack predicted channel domains. We sought to translate insight gained from yeast studies to uncover disease mechanisms associated with deficiencies in KCTD7 of unknown function. METHODS Novel KCTD7 variants in new and published patients were assessed for disease causality using genetic analyses, cell-based functional assays of patient fibroblasts and knockout yeast, and electron microscopy of patient samples. RESULTS Patients with KCTD7 mutations can exhibit movement disorders or developmental regression before seizure onset, and are distinguished from similar disorders by an earlier age of onset. Although most published KCTD7 patient variants were excluded from a genome sequence database of normal human variations, most newly identified patient variants are present in this database, potentially challenging disease causality. However, genetic analysis and impaired biochemical interactions with cullin 3 support a causal role for patient KCTD7 variants, suggesting deleterious alleles of KCTD7 and other rare disease variants may be underestimated. Both patient-derived fibroblasts and yeast lacking Whi2 with sequence similarity to KCTD7 have impaired autophagy consistent with brain pathology. INTERPRETATION Biallelic KCTD7 mutations define a neurodegenerative disorder with lipofuscin and lipid droplet accumulation but without defining features of neuronal ceroid lipofuscinosis or lysosomal storage disorders. KCTD7 deficiency appears to cause an underlying autophagy-lysosome defect conserved in yeast, thereby assigning a biological role for KCTD7. Ann Neurol 2018;84:774-788.
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Affiliation(s)
- Kyle A Metz
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Xinchen Teng
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu Province, People's Republic of China
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Heather M Lamb
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Bart E Wagner
- Histopathology Department, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Xianghui Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu Province, People's Republic of China
| | - Yu Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu Province, People's Republic of China
| | - Hee Jong Kim
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Michael E Meadow
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Tim Sen Wang
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Edda D Haberlandt
- Clinical Department of Pediatrics I, Innsbruck Medical University, Innsbruck, Austria.,Department of Child and Youth Health, Hospital of Dornbirn, Dornbirn, Austria
| | - Glenn W Anderson
- Histopathology Department, Great Ormond Street Hospital for Children, London, United Kingdom
| | | | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Marsha Pratt
- Department of Pediatrics, University of Oklahoma College of Medicine, Oklahoma City, OK
| | - Nawal Makhseed
- Department of Pediatrics, Jahra Hospital, Ministry of Health, Al Jahra, Kuwait
| | - Adolfo Garnica
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR
| | - Noelle R Danylchuk
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR
| | - Thomas A Burrow
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, AR
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital, Miami, FL
| | | | - Satish Agadi
- Department of Neurology, Texas Children's Hospital, Houston, TX
| | | | | | - Michael Alber
- Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | | | - Katrina Peariso
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Min Tsui Ong
- Department of Paediatric Neurology, Sheffield Children's National Health Service Foundation Trust, Sheffield, United Kingdom
| | - Santosh R Mordekar
- Department of Paediatric Neurology, Sheffield Children's National Health Service Foundation Trust, Sheffield, United Kingdom
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's National Health Service Foundation Trust, Sheffield, United Kingdom
| | - Daniel Crooks
- Department of Neuropathology, Walton Centre National Health Service Foundation Trust, Liverpool, United Kingdom
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Gerard T Berry
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | | | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Gustavo H B Maegawa
- Department of Pediatrics/Genetics and Metabolism, University of Florida, Gainesville, FL
| | - Abdel Aouacheria
- Montpellier Institute of Evolution Sciences, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Janet G Markle
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Adam L Hartman
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
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50
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Streff H, Bi W, Colón AG, Adesina AM, Miyake CY, Lalani SR. Amish nemaline myopathy and dilated cardiomyopathy caused by a homozygous contiguous gene deletion of TNNT1 and TNNI3 in a Mennonite child. Eur J Med Genet 2018; 62:103567. [PMID: 30395933 DOI: 10.1016/j.ejmg.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 03/15/2018] [Revised: 10/05/2018] [Accepted: 11/01/2018] [Indexed: 12/28/2022]
Abstract
Amish nemaline myopathy (ANM) is a severe congenital form of NM, known to be fatal in early childhood due to pulmonary insufficiency. Homozygous mutation in TNNT1 was originally ascertained in an Older Amish community in 2000. To date, only five reports with six pathogenic variants in TNNT1 have been described in both Amish and non-Amish families. Here, we describe a 16-month old female from a small Mennonite community from Mexico, presenting with congenital hypotonia and dilated cardiomyopathy, with a novel homozygous deletion of 19q13.42 of about 11 kb in size, encompassing TNNT1 and TNNI3. Cardiomyopathy has not been observed in association with ANM in previous reports. Conversely, homozygous mutation in TNNI3 have been described with dilated cardiomyopathy. Our report underscores the consideration of contiguous gene deletion in children with ANM who present with congenital hypotonia and cardiomyopathy. The report also expands the known spectrum of non-Amish related ANM mutations to include homozygous multi-exonic TNNT1 deletion.
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Affiliation(s)
- Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Baylor Genetics Laboratories, Houston, TX, 77030, USA
| | - Athos G Colón
- Department of Pediatrics, Texas Tech University School of Medicine, Lubbock, TX, 79430, USA
| | - Adekunle M Adesina
- Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christina Y Miyake
- Division of Cardiology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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