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Sun G, Huang W, Wang L, Wu J, Zhao G, Ren H, Liu L, Kong X. Molecular findings in patients for whole exome sequencing and mitochondrial genome assessment. Clin Chim Acta 2024; 561:119774. [PMID: 38852791 DOI: 10.1016/j.cca.2024.119774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
OBJECTIVE Whole exome sequencing (WES) is becoming more widely used as a diagnostic tool in the field of medicine. In this article, we reported the diagnostic yield of WES and mitochondrial genome assessment in 2226 consecutive cases in a single clinical laboratory. MATERIALS AND METHODS We retrospectively analyzed consecutive WES reports from 2226 patients with various genetic disorders. WES-process was focused exclusively on the probands and aimed at a higher diagnostic capacity. We determined the diagnostic rate of WES overall and by phenotypic category, mode of inheritance, mitochondrial genome variant, and copy number variants (CNVs). RESULTS Among the 2226 patients who had diagnostic WES proband-only, the overall diagnostic yield of WES was 34.59% (770/2226). The highest diagnostic yield was observed in autosomal dominant disorders, at 45.58% (351/770), followed by autosomal recessive at 31.95%(246/770), X-linked disorder at 9.61%(74/770), and mitochondrial diseases at a notably lower 0.65%(5/770). The 12.21% (94/770) diagnoses were based on a total of 94 copy number variants reported from WES data. CNVs in children accounted for 67.02% of the total CNVs. While majority of the molecular diagnoses were related to nuclear genes, the inclusion of mitochondrial genome sequencing in the WES test contributed to five diagnoses. all mitochondrial diseases were identified in adults. CONCLUSIONS The proband-only WES provided a definitive molecular diagnosis for 34.59% of a large cohort of patients while analysis of WES simultaneously analyzed the SNVs, exons, mitochondrial genome, and CNVs, thereby improving the diagnostic yield significantly compared to the single-detection WES method; and facilitating the identification of novel candidate genes.
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Affiliation(s)
- Gege Sun
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Huang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Wang
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinlin Wu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ganye Zhao
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanan Ren
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lina Liu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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2
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Reed AE, Peraza J, van den Haak F, Hernandez ER, Gibbs RA, Chinn IK, Lupski JR, Marchi E, Reshef R, Alobeid B, Mace EM, Orange JS. β-Actin G342D as a Cause of NK Cell Deficiency Impairing Lytic Synapse Termination. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:962-973. [PMID: 38315012 DOI: 10.4049/jimmunol.2300671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024]
Abstract
NK cell deficiency (NKD) occurs when an individual's major clinical immunodeficiency derives from abnormal NK cells and is associated with several genetic etiologies. Three categories of β-actin-related diseases with over 60 ACTB (β-actin) variants have previously been identified, none with a distinct NK cell phenotype. An individual with mild developmental delay, macrothrombocytopenia, and susceptibility to infections, molluscum contagiosum virus, and EBV-associated lymphoma had functional NKD for over a decade. A de novo ACTB variant encoding G342D β-actin was identified and was consistent with the individual's developmental and platelet phenotype. This novel variant also was found to have direct impact in NK cells because its expression in the human NK cell line YTS (YTS-NKD) caused increased cell spreading in lytic immune synapses created on activating surfaces. YTS-NKD cells were able to degranulate and perform cytotoxicity, but they demonstrated defective serial killing because of prolonged conjugation to the killed target cell and thus were effectively unable to terminate lytic synapses. G342D β-actin results in a novel, to our knowledge, mechanism of functional NKD via increased synaptic spreading and defective lytic synapse termination with resulting impaired serial killing, leading to overall reductions in NK cell cytotoxicity.
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Affiliation(s)
- Abigail E Reed
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY
| | - Jackeline Peraza
- Department of Biology, Barnard College of Columbia University, New York, NY
| | - Frederique van den Haak
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY
| | - Evelyn R Hernandez
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Ivan K Chinn
- Division of Immunology, Allergy and Retrovirology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Texas Children's Hospital and Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX
| | - Enrica Marchi
- Division of Hematology-Oncology, Department of Medicine, NCI Designated Cancer Center, University of Virginia, Charlottesville, VA
| | - Ran Reshef
- Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, NY
| | - Bachir Alobeid
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Emily M Mace
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Jordan S Orange
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
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3
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Harris RA, Bush AH, Eagar TN, Qian J, Greenwood MP, Opekun AR, Baldassano R, Guthery SL, Noe JD, Otley A, Rosh JR, Kugathasan S, Kellermayer R. Exome Sequencing Implicates DGKZ , ESRRA , and GXYLT1 for Modulating Granuloma Formation in Crohn Disease. J Pediatr Gastroenterol Nutr 2023; 77:354-357. [PMID: 37347142 PMCID: PMC10528115 DOI: 10.1097/mpg.0000000000003873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Non-caseating granulomas may indicate a more aggressive phenotype of Crohn disease (CD). Genetic associations of granulomatous CD (GCD) may help elucidate disease pathogenesis. Whole-exome sequencing was performed on peripheral blood-derived DNA from 17 pediatric patients with GCD and 19 with non-GCD (NGCD), and from an independent validation cohort of 44 GCD and 19 NGCD cases. PLINK (a tool set for whole-genome association and population-based linkage analyses) analysis was used to identify single nucleotide polymorphisms (SNPs) differentiating between groups, and subgroup allele frequencies were also compared to a public genomic database (gnomAD). The Combined Annotation Dependent Depletion scoring tool was used to predict deleteriousness of SNPs. Human leukocyte antigen (HLA) haplotype findings were compared to a control group (n = 8496). PLINK-based analysis between GCD and NGCD groups did not find consistently significant hits. gnomAD control comparisons, however, showed consistent subgroup associations with DGKZ , ESRRA , and GXYLT1 , genes that have been implicated in mammalian granulomatous inflammation. Our findings may guide future research and precision medicine.
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Affiliation(s)
- R. Alan Harris
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- contributed equally
| | - Allyson H Bush
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX
- contributed equally
| | - Todd N Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Justin Qian
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX
| | - Michael P Greenwood
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Antone R Opekun
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology and Nutrition, University of Pennsylvania, Children’s Hospital of Philadelphia, PA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah and Intermountain Primary Children’s Hospital, Salt Lake City, UT
| | - Joshua D Noe
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI
| | - Anthony Otley
- IWK Health/Dalhousie University, Halifax, Nova Scotia, Canada
| | - Joel R. Rosh
- Goryeb Children’s Hospital/Atlantic Children’s Health, Morristown, NJ
| | - Subra Kugathasan
- Departments of Pediatrics and Human Genetics at Emory University School of Medicine, Atlanta, GA
| | - Richard Kellermayer
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX
- Children’s Nutrition and Research Center, Houston, TX
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4
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Geraghty RM, Orr S, Olinger E, Neatu R, Barroso-Gil M, Mabillard H, Consortium GER, Wilson I, Sayer JA. Use of whole genome sequencing to determine the genetic basis of visceral myopathies including Prune Belly syndrome. JOURNAL OF RARE DISEASES (BERLIN, GERMANY) 2023; 2:9. [PMID: 37288276 PMCID: PMC10241726 DOI: 10.1007/s44162-023-00012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/21/2023] [Indexed: 06/09/2023]
Abstract
Objectives/aims The visceral myopathies (VM) are a group of disorders characterised by poorly contractile or acontractile smooth muscle. They manifest in both the GI and GU tracts, ranging from megacystis to Prune Belly syndrome. We aimed to apply a bespoke virtual genetic panel and describe novel variants associated with this condition using whole genome sequencing data within the Genomics England 100,000 Genomes Project. Methods We screened the Genomics England 100,000 Genomes Project rare diseases database for patients with VM-related phenotypes. These patients were screened for sequence variants and copy number variants (CNV) in ACTG2, ACTA2, MYH11, MYLK, LMOD1, CHRM3, MYL9, FLNA and KNCMA1 by analysing whole genome sequencing data. The identified variants were analysed using variant effect predictor online tool, and any possible segregation in other family members and novel missense mutations was modelled using in silico tools. The VM cohort was also used to perform a genome-wide variant burden test in order to identify confirm gene associations in this cohort. Results We identified 76 patients with phenotypes consistent with a diagnosis of VM. The range of presentations included megacystis/microcolon hypoperistalsis syndrome, Prune Belly syndrome and chronic intestinal pseudo-obstruction. Of the patients in whom we identified heterozygous ACTG2 variants, 7 had likely pathogenic variants including 1 novel likely pathogenic allele. There were 4 patients in whom we identified a heterozygous MYH11 variant of uncertain significance which leads to a frameshift and a predicted protein elongation. We identified one family in whom we found a heterozygous variant of uncertain significance in KCNMA1 which in silico models predicted to be disease causing and may explain the VM phenotype seen. We did not find any CNV changes in known genes leading to VM-related disease phenotypes. In this phenotype selected cohort, ACTG2 is the largest monogenic cause of VM-related disease accounting for 9% of the cohort, supported by a variant burden test approach, which identified ACTG2 variants as the largest contributor to VM-related phenotypes. Conclusions VM are a group of disorders that are not easily classified and may be given different diagnostic labels depending on their phenotype. Molecular genetic analysis of these patients is valuable as it allows precise diagnosis and aids understanding of the underlying disease manifestations. We identified ACTG2 as the most frequent genetic cause of VM. We recommend a nomenclature change to 'autosomal dominant ACTG2 visceral myopathy' for patients with pathogenic variants in ACTG2 and associated VM phenotypes. Supplementary Information The online version contains supplementary material available at 10.1007/s44162-023-00012-z.
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Affiliation(s)
- Robert M. Geraghty
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Sarah Orr
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Eric Olinger
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Ruxandra Neatu
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Miguel Barroso-Gil
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Holly Mabillard
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - Genomics England Research Consortium
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle Upon Tyne, NE4 5PL UK
| | - Ian Wilson
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
| | - John A. Sayer
- Renal Services, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle Upon Tyne, NE7 7DN UK
- Faculty of Medical Sciences, Translational and Clinical Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ UK
- National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle Upon Tyne, NE4 5PL UK
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5
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Salinas SA, Mace EM, Conte MI, Park CS, Li Y, Rosario-Sepulveda JI, Mahapatra S, Moore EK, Hernandez ER, Chinn IK, Reed AE, Lee BJ, Frumovitz A, Gibbs RA, Posey JE, Forbes Satter LR, Thatayatikom A, Allenspach EJ, Wensel TG, Lupski JR, Lacorazza HD, Orange JS. An ELF4 hypomorphic variant results in NK cell deficiency. JCI Insight 2022; 7:155481. [PMID: 36477361 PMCID: PMC9746917 DOI: 10.1172/jci.insight.155481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/13/2022] [Indexed: 12/12/2022] Open
Abstract
NK cell deficiencies (NKD) are a type of primary immune deficiency in which the major immunologic abnormality affects NK cell number, maturity, or function. Since NK cells contribute to immune defense against virally infected cells, patients with NKD experience higher susceptibility to chronic, recurrent, and fatal viral infections. An individual with recurrent viral infections and mild hypogammaglobulinemia was identified to have an X-linked damaging variant in the transcription factor gene ELF4. The variant does not decrease expression but disrupts ELF4 protein interactions and DNA binding, reducing transcriptional activation of target genes and selectively impairing ELF4 function. Corroborating previous murine models of ELF4 deficiency (Elf4-/-) and using a knockdown human NK cell line, we determined that ELF4 is necessary for normal NK cell development, terminal maturation, and function. Through characterization of the NK cells of the proband, expression of the proband's variant in Elf4-/- mouse hematopoietic precursor cells, and a human in vitro NK cell maturation model, we established this ELF4 variant as a potentially novel cause of NKD.
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Affiliation(s)
- Sandra Andrea Salinas
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Emily M. Mace
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Matilde I. Conte
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Yu Li
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Sanjana Mahapatra
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas, USA
| | - Emily K. Moore
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Evelyn R. Hernandez
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Ivan K. Chinn
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas, USA
| | - Abigail E. Reed
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Barclay J. Lee
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Alexander Frumovitz
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, and,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Lisa R. Forbes Satter
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas, USA
| | - Akaluck Thatayatikom
- Division of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, University of Florida, Shands Children’s Hospital, Gainesville, Florida, USA
| | - Eric J. Allenspach
- Division of Immunology, Seattle Children’s Hospital, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | | | - James R. Lupski
- Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, and,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Jordan S. Orange
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
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6
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Lupski JR. Biology in balance: human diploid genome integrity, gene dosage, and genomic medicine. Trends Genet 2022; 38:554-571. [PMID: 35450748 DOI: 10.1016/j.tig.2022.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023]
Abstract
The path to completion of the functional annotation of the haploid human genome reference build, exploration of the clan genomics hypothesis, understanding human gene and genome functional biology, and gene genome and organismal evolution, is in reach.
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Affiliation(s)
- James R Lupski
- Genetics & Genomics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
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7
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Khan TR, Dolce A, Goodspeed K. A case of Bainbridge-Ropers syndrome with breath holding spells and intractable epilepsy: challenges in diagnosis and management. BMC Neurol 2022; 22:60. [PMID: 35172777 PMCID: PMC8848676 DOI: 10.1186/s12883-022-02573-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/25/2022] [Indexed: 12/20/2022] Open
Abstract
Background Bainbridge-Ropers syndrome is caused by monoallelic ASXL3 variants on chromosome 18. Clinical features include dysmorphic facies, developmental delay, intellectual disability, autistic traits, hypotonia, failure to thrive, seizures and hyperventilation. Breath-holding spells with choreathetoid movements have been previously described. Case presentation We describe an 11-year old boy who has daily intractable seizures reported since birth, developmental delay, autistic features and feeding difficulties. He was eventually found to have de novo, heterozygous pathogenic variant (c.1612G > T, p.E538*) in the ASXL3 gene. He has frequent episodes of breath-holding accompanied by dystonic posturing with right leg extension and head turning without ictal EEG correlate. The breath-holding spells have been refractory to several medication trials including iron supplementation, acetazolamide, and desipramine. Conclusions This case represents a more severe phenotype of Bainbridge-Ropers Syndrome than previously described with refractory breath-holding spells with dystonia, intractable epilepsy, and progressive cerebral/cerebellar atrophy. Breath-holding spells cause significant morbidity, are poorly understood, and have very limited treatment options.
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Affiliation(s)
- Tuba Rashid Khan
- Department of Pediatrics, Division of Child Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Pediatrics, Division of Pediatric Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Alison Dolce
- Department of Pediatrics, Division of Child Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kimberly Goodspeed
- Department of Pediatrics, Division of Child Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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8
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Forbes LR, Eckstein OS, Gulati N, Peckham-Gregory EC, Ozuah NW, Lubega J, El-Mallawany NK, Agrusa JE, Poli MC, Vogel TP, Chaimowitz NS, Rider NL, Mace EM, Orange JS, Caldwell JW, Aldave-Becerra JC, Jolles S, Saettini F, Chong HJ, Stray-Pedersen A, Heslop HE, Kamdar KY, Rouce RH, Muzny DM, Jhangiani SN, Gibbs RA, Coban-Akdemir ZH, Lupski JR, McClain KL, Allen CE, Chinn IK. Genetic errors of immunity distinguish pediatric nonmalignant lymphoproliferative disorders. J Allergy Clin Immunol 2022; 149:758-766. [PMID: 34329649 PMCID: PMC8795244 DOI: 10.1016/j.jaci.2021.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/02/2021] [Accepted: 07/14/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Pediatric nonmalignant lymphoproliferative disorders (PLPDs) are clinically and genetically heterogeneous. Long-standing immune dysregulation and lymphoproliferation in children may be life-threatening, and a paucity of data exists to guide evaluation and treatment of children with PLPD. OBJECTIVE The primary objective of this study was to ascertain the spectrum of genomic immunologic defects in PLPD. Secondary objectives included characterization of clinical outcomes and associations between genetic diagnoses and those outcomes. METHODS PLPD was defined by persistent lymphadenopathy, lymph organ involvement, or lymphocytic infiltration for more than 3 months, with or without chronic or significant Epstein-Barr virus (EBV) infection. Fifty-one subjects from 47 different families with PLPD were analyzed using whole exome sequencing. RESULTS Whole exome sequencing identified likely genetic errors of immunity in 51% to 62% of families (53% to 65% of affected children). Presence of a genetic etiology was associated with younger age and hemophagocytic lymphohistiocytosis. Ten-year survival for the cohort was 72.4%, and patients with viable genetic diagnoses had a higher survival rate (82%) compared to children without a genetic explanation (48%, P = .03). Survival outcomes for individuals with EBV-associated disease and no genetic explanation were particularly worse than outcomes for subjects with EBV-associated disease and a genetic explanation (17% vs 90%; P = .002). Ascertainment of a molecular diagnosis provided targetable treatment options for up to 18 individuals and led to active management changes for 12 patients. CONCLUSIONS PLPD defines children at high risk for mortality, and whole exome sequencing informs clinical risks and therapeutic opportunities for this diagnosis.
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Affiliation(s)
- Lisa R Forbes
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Immunology/Allergy/Retrovirology, Texas Children's Hospital, Houston, Tex
| | - Olive S Eckstein
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - Nitya Gulati
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - Erin C Peckham-Gregory
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - Nmazuo W Ozuah
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - Joseph Lubega
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - Nader K El-Mallawany
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - Jennifer E Agrusa
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - M Cecilia Poli
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Universidad del Desarrollo, Clínica Alemana de Santiago, Santiago, Chile
| | - Tiphanie P Vogel
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Natalia S Chaimowitz
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Immunology/Allergy/Retrovirology, Texas Children's Hospital, Houston, Tex
| | - Nicholas L Rider
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Immunology/Allergy/Retrovirology, Texas Children's Hospital, Houston, Tex
| | - Emily M Mace
- New York Presbyterian Morgan Stanley Children's Hospital, Columbia University College of Physicians and Surgeons, Department of Pediatrics, New York, NY
| | - Jordan S Orange
- New York Presbyterian Morgan Stanley Children's Hospital, Columbia University College of Physicians and Surgeons, Department of Pediatrics, New York, NY
| | - Jason W Caldwell
- Section of Pulmonary, Critical Care, Allergic and Immunologic Diseases, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Juan C Aldave-Becerra
- Division of Allergy and Immunology, Hospital Nacional Edgardo Rebagliati Martins, Lima, Peru
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, United Kingdom
| | - Francesco Saettini
- Department of Pediatric Hematology, Fondazione MBBM, University of Milan-Bicocca, Monza, Italy
| | - Hey J Chong
- Division of Pediatric Allergy and Immunology, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Asbjorg Stray-Pedersen
- Department of Pediatric and Adolescent Medicine, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Helen E Heslop
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Tex
| | - Kala Y Kamdar
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - R Helen Rouce
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Tex
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Baylor-Hopkins Center for Mendelian Genomics, Houston, Tex
| | - Zeynep H Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Baylor-Hopkins Center for Mendelian Genomics, Houston, Tex
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Baylor-Hopkins Center for Mendelian Genomics, Houston, Tex
| | - Kenneth L McClain
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex
| | - Carl E Allen
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, Tex.
| | - Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Texas Children's Hospital, Houston, Tex; Division of Pediatric Immunology/Allergy/Retrovirology, Texas Children's Hospital, Houston, Tex.
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9
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Mahmoud M, Doddapaneni H, Timp W, Sedlazeck FJ. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol 2021; 22:268. [PMID: 34521442 PMCID: PMC8442460 DOI: 10.1186/s13059-021-02486-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/02/2021] [Indexed: 12/11/2022] Open
Abstract
Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive insight into the sample and thus enables novel findings in biology or medicine. PRINCESS is a structured workflow that takes raw sequence reads and generates a fully phased SNV, SV, and methylation call set within a few hours. PRINCESS achieves high accuracy and long phasing even on low coverage datasets and can resolve repetitive, complex medical relevant genes that often escape detection. PRINCESS is publicly available at https://github.com/MeHelmy/princess under the MIT license.
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Affiliation(s)
- Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | | | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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10
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Cananzi M, Wohler E, Marzollo A, Colavito D, You J, Jing H, Bresolin S, Gaio P, Martin R, Mescoli C, Bade S, Posey JE, Dalle Carbonare M, Tung W, Jhangiani SN, Bosa L, Zhang Y, Filho JS, Gabelli M, Kellermayer R, Kader HA, Oliva-Hemker M, Perilongo G, Lupski JR, Biffi A, Valle D, Leon A, de Macena Sobreira NL, Su HC, Guerrerio AL. IFIH1 loss-of-function variants contribute to very early-onset inflammatory bowel disease. Hum Genet 2021; 140:1299-1312. [PMID: 34185153 PMCID: PMC8423350 DOI: 10.1007/s00439-021-02300-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Genetic defects of innate immunity impairing intestinal bacterial sensing are linked to the development of Inflammatory Bowel Disease (IBD). Although much evidence supports a role of the intestinal virome in gut homeostasis, most studies focus on intestinal viral composition rather than on host intestinal viral sensitivity. To demonstrate the association between the development of Very Early Onset IBD (VEOIBD) and variants in the IFIH1 gene which encodes MDA5, a key cytosolic sensor for viral nucleic acids. Whole exome sequencing (WES) was performed in two independent cohorts of children with VEOIBD enrolled in Italy (n = 18) and USA (n = 24). Luciferase reporter assays were employed to assess MDA5 activity. An enrichment analysis was performed on IFIH1 comparing 42 VEOIBD probands with 1527 unrelated individuals without gastrointestinal or immunological issues. We identified rare, likely loss-of-function (LoF), IFIH1 variants in eight patients with VEOIBD from a combined cohort of 42 children. One subject, carrying a homozygous truncating variant resulting in complete LoF, experienced neonatal-onset, pan-gastrointestinal, IBD-like enteropathy plus multiple infectious episodes. The remaining seven subjects, affected by VEOIBD without immunodeficiency, were carriers of one LoF variant in IFIH1. Among these, two patients also carried a second hypomorphic variant, with partial function apparent when MDA5 was weakly stimulated. Furthermore, IFIH1 variants were significantly enriched in children with VEOIBD as compared to controls (p = 0.007). Complete and partial MDA5 deficiency is associated with VEOIBD with variable penetrance and expressivity, suggesting a role for impaired intestinal viral sensing in IBD pathogenesis.
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Affiliation(s)
- Mara Cananzi
- Unit of Pediatric Gastroenterology, Digestive Endoscopy, Hepatology and Care of the Child with Liver Transplantation, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy.
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Antonio Marzollo
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
- Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, Padova, Italy
| | - Davide Colavito
- Research & Innovation (R&I Genetics) Srl, C.so Stati Uniti 4, Padova, Italy
| | - Jing You
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Huie Jing
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Silvia Bresolin
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
- Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, Padova, Italy
| | - Paola Gaio
- Unit of Pediatric Gastroenterology, Digestive Endoscopy, Hepatology and Care of the Child with Liver Transplantation, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - Renan Martin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Claudia Mescoli
- Surgical Pathology and Cytopathology Unit, Department of Medicine (DIMED), University Hospital of Padova, Padova, Italy
| | - Sangeeta Bade
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Wesley Tung
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Luca Bosa
- Unit of Pediatric Gastroenterology, Digestive Endoscopy, Hepatology and Care of the Child with Liver Transplantation, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joselito Sobreira Filho
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Maria Gabelli
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Howard A Kader
- Department of Pediatrics, Division of Pediatric Gastroenterology & Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maria Oliva-Hemker
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Giorgio Perilongo
- Unit of Pediatric Gastroenterology, Digestive Endoscopy, Hepatology and Care of the Child with Liver Transplantation, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - 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
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Alessandra Biffi
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Alberta Leon
- Research & Innovation (R&I Genetics) Srl, C.so Stati Uniti 4, Padova, Italy
| | | | - Helen C Su
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anthony L Guerrerio
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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11
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Claes KBM, Rosseel T, De Leeneer K. Dealing with Pseudogenes in Molecular Diagnostics in the Next Generation Sequencing Era. Methods Mol Biol 2021; 2324:363-381. [PMID: 34165726 DOI: 10.1007/978-1-0716-1503-4_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.
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Affiliation(s)
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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12
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Mwesigwa S, Williams L, Retshabile G, Katagirya E, Mboowa G, Mlotshwa B, Kyobe S, Kateete DP, Wampande EM, Wayengera M, Mpoloka SW, Mirembe AN, Kasvosve I, Morapedi K, Kisitu GP, Kekitiinwa AR, Anabwani G, Joloba ML, Matovu E, Mulindwa J, Noyes H, Botha G, Brown CW, Mardon G, Matshaba M, Hanchard NA. Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression. NPJ Genom Med 2021; 6:24. [PMID: 33741997 PMCID: PMC7979878 DOI: 10.1038/s41525-021-00185-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection remains a significant public health burden globally. The role of viral co-infection in the rate of progression of HIV infection has been suggested but not empirically tested, particularly among children. We extracted and classified 42 viral species from whole-exome sequencing (WES) data of 813 HIV-infected children in Botswana and Uganda categorised as either long-term non-progressors (LTNPs) or rapid progressors (RPs). The Ugandan participants had a higher viral community diversity index compared to Batswana (p = 4.6 × 10-13), and viral sequences were more frequently detected among LTNPs than RPs (24% vs 16%; p = 0.008; OR, 1.9; 95% CI, 1.6-2.3), with Anelloviridae showing strong association with LTNP status (p = 3 × 10-4; q = 0.004, OR, 3.99; 95% CI, 1.74-10.25). This trend was still evident when stratified by country, sex, and sequencing platform, and after a logistic regression analysis adjusting for age, sex, country, and the sequencing platform (p = 0.02; q = 0.03; OR, 7.3; 95% CI, 1.6-40.5). Torque teno virus (TTV), which made up 95% of the Anelloviridae reads, has been associated with reduced immune activation. We identify an association between viral co-infection and prolonged AIDs-free survival status that may have utility as a biomarker of LTNP and could provide mechanistic insights to HIV progression in children, demonstrating the added value of interrogating off-target WES reads in cohort studies.
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Affiliation(s)
| | | | | | - Eric Katagirya
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Samuel Kyobe
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - David P Kateete
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Misaki Wayengera
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Angella N Mirembe
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | | | | | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | - Adeodata R Kekitiinwa
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Moses L Joloba
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius Mulindwa
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Harry Noyes
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gerrit Botha
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Chester W Brown
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- 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.
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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13
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Variants in FLRT3 and SLC35E2B identified using exome sequencing in seven high myopia families from Central Europe. Adv Med Sci 2021; 66:192-198. [PMID: 33711669 DOI: 10.1016/j.advms.2021.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/09/2021] [Accepted: 02/26/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE High myopia (HM) is an eye disorder with both environmental and genetic factors involved. Many genetic factors responsible for HM were recognized worldwide, but little is known about genetic variants underlying HM in Central Europe. Thus, the aim of this study was to identify rare sequence variants involved in HM in families from Central Europe to better understand the genetic basis of HM. MATERIALS AND METHODS We assessed 17 individuals from 7 unrelated Central European families with hereditary HM using exome sequencing (ES). Segregation of selected variants in other available family members was performed using Sanger sequencing. RESULTS Detected 73 rare variants were selected for verification. We observed 2 missense variants, c.938C>T in SLC35E2B - encoding solute carrier family 35 member E2B, and c.1642G>C in FLRT3 - encoding fibronectin leucine rich transmembrane protein, segregating with HM in one family. CONCLUSIONS FLRT3 and/or SLC35E2B could represent disease candidate genes and identified sequence variants might be responsible for HM in the studied family.
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14
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Liu Y, Xia J, McKay J, Tsavachidis S, Xiao X, Spitz MR, Cheng C, Byun J, Hong W, Li Y, Zhu D, Song Z, Rosenberg SM, Scheurer ME, Kheradmand F, Pikielny CW, Lusk CM, Schwartz AG, Wistuba II, Cho MH, Silverman EK, Bailey-Wilson J, Pinney SM, Anderson M, Kupert E, Gaba C, Mandal D, You M, de Andrade M, Yang P, Liloglou T, Davies MPA, Lissowska J, Swiatkowska B, Zaridze D, Mukeria A, Janout V, Holcatova I, Mates D, Stojsic J, Scelo G, Brennan P, Liu G, Field JK, Hung RJ, Christiani DC, Amos CI. Rare deleterious germline variants and risk of lung cancer. NPJ Precis Oncol 2021; 5:12. [PMID: 33594163 PMCID: PMC7887261 DOI: 10.1038/s41698-021-00146-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Recent studies suggest that rare variants exhibit stronger effect sizes and might play a crucial role in the etiology of lung cancers (LC). Whole exome plus targeted sequencing of germline DNA was performed on 1045 LC cases and 885 controls in the discovery set. To unveil the inherited causal variants, we focused on rare and predicted deleterious variants and small indels enriched in cases or controls. Promising candidates were further validated in a series of 26,803 LCs and 555,107 controls. During discovery, we identified 25 rare deleterious variants associated with LC susceptibility, including 13 reported in ClinVar. Of the five validated candidates, we discovered two pathogenic variants in known LC susceptibility loci, ATM p.V2716A (Odds Ratio [OR] 19.55, 95%CI 5.04-75.6) and MPZL2 p.I24M frameshift deletion (OR 3.88, 95%CI 1.71-8.8); and three in novel LC susceptibility genes, POMC c.*28delT at 3' UTR (OR 4.33, 95%CI 2.03-9.24), STAU2 p.N364M frameshift deletion (OR 4.48, 95%CI 1.73-11.55), and MLNR p.Q334V frameshift deletion (OR 2.69, 95%CI 1.33-5.43). The potential cancer-promoting role of selected candidate genes and variants was further supported by endogenous DNA damage assays. Our analyses led to the identification of new rare deleterious variants with LC susceptibility. However, in-depth mechanistic studies are still needed to evaluate the pathogenic effects of these specific alleles.
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Grants
- R01 CA060691 NCI NIH HHS
- U19 CA203654 NCI NIH HHS
- R01 CA084354 NCI NIH HHS
- R01 HL110883 NHLBI NIH HHS
- U01 CA076293 NCI NIH HHS
- R01 CA080127 NCI NIH HHS
- R01 CA141769 NCI NIH HHS
- P30 ES006096 NIEHS NIH HHS
- P50 CA090578 NCI NIH HHS
- P30 CA022453 NCI NIH HHS
- S10 RR024574 NCRR NIH HHS
- HHSN261201300011C NCI NIH HHS
- R01 CA134682 NCI NIH HHS
- R01 CA134433 NCI NIH HHS
- R01 HL113264 NHLBI NIH HHS
- R01 HL082487 NHLBI NIH HHS
- R01 CA250905 NCI NIH HHS
- U19 CA148127 NCI NIH HHS
- P20 GM103534 NIGMS NIH HHS
- R01 CA092824 NCI NIH HHS
- R01 CA087895 NCI NIH HHS
- U01 HL089897 NHLBI NIH HHS
- K07 CA181480 NCI NIH HHS
- HHSN268201100011I NHLBI NIH HHS
- HHSN268201100011C NHLBI NIH HHS
- R01 CA127219 NCI NIH HHS
- R01 CA074386 NCI NIH HHS
- P30 CA023108 NCI NIH HHS
- U01 HL089856 NHLBI NIH HHS
- P30 ES030285 NIEHS NIH HHS
- P30 CA125123 NCI NIH HHS
- DP1 AG072751 NIA NIH HHS
- U01 CA243483 NCI NIH HHS
- HHSN268200782096C NHLBI NIH HHS
- HHSN268201200007C NHLBI NIH HHS
- N01HG65404 NHGRI NIH HHS
- R35 GM122598 NIGMS NIH HHS
- U01 CA209414 NCI NIH HHS
- R03 CA077118 NCI NIH HHS
- 001 World Health Organization
- DP1 CA174424 NCI NIH HHS
- This work was supported by grants from the National Institutes of Health (R01CA127219, R01CA141769, R01CA060691, R01CA87895, R01CA80127, R01CA84354, R01CA134682, R01CA134433, R01CA074386, R01CA092824, R01CA250905, R01HL113264, R01HL082487, R01HL110883, R03CA77118, P20GM103534, P30CA125123, P30CA023108, P30CA022453, P30ES006096, P50CA090578, U01CA243483, U01HL089856, U01HL089897, U01CA76293, U19CA148127, U01CA209414, K07CA181480, N01-HG-65404, HHSN268200782096C, HHSN261201300011I, HHSN268201100011, HHSN268201 200007C, DP1-CA174424, DP1-AG072751, CA125123, RR024574, Intramural Research Program of the National Human Genome Research Institute (JEB-W), and Herrick Foundation. Dr. Amos is an Established Research Scholar of the Cancer Prevention Research Institute of Texas (RR170048). We also want to acknowledge the Cytometry and Cell Sorting Core support by the Cancer Prevention and Research Institute of Texas Core Facility (RP180672). At Toronto, the study is supported by The Canadian Cancer Society Research Institute (# 020214) to R. H., Ontario Institute for Cancer Research to R. H, and the Alan Brown Chair to G. L. and Lusi Wong Programs at the Princess Margaret Hospital Foundation. The Liverpool Lung Project is supported by Roy Castle Lung Cancer Foundation.
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Affiliation(s)
- Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Margaret R Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Wei Hong
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Scheurer
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Farrah Kheradmand
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Claudio W Pikielny
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Christine M Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Susan M Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Elena Kupert
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Colette Gaba
- The University of Toledo College of Medicine, Toledo, OH, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Ping Yang
- Mayo Clinic College of Medicine, Scottsdale, AZ, USA
| | - Triantafillos Liloglou
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Michael P A Davies
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Jolanta Lissowska
- M. Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Anush Mukeria
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Jelena Stojsic
- Department of Thoracopulmonary Pathology, Service of Pathology, Clinical Center of Serbia, Belgrade, Serbia
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | - John K Field
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | | | - Christopher I Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
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15
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Saettini F, Poli C, Vengoechea J, Bonanomi S, Orellana JC, Fazio G, Rodriguez FH, Noguera LP, Booth C, Jarur-Chamy V, Shams M, Iascone M, Vukic M, Gasperini S, Quadri M, Barroeta Seijas A, Rivers E, Mauri M, Badolato R, Cazzaniga G, Bugarin C, Gaipa G, Kroes WGM, Moratto D, van Oostaijen-Ten Dam MM, Baas F, van der Maarel S, Piazza R, Coban-Akdemir ZH, Lupski JR, Yuan B, Chinn IK, Daxinger L, Biondi A. Absent B cells, agammaglobulinemia, and hypertrophic cardiomyopathy in folliculin-interacting protein 1 deficiency. Blood 2021; 137:493-499. [PMID: 32905580 PMCID: PMC7845007 DOI: 10.1182/blood.2020006441] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/22/2020] [Indexed: 12/30/2022] Open
Abstract
Agammaglobulinemia is the most profound primary antibody deficiency that can occur due to an early termination of B-cell development. We here investigated 3 novel patients, including the first known adult, from unrelated families with agammaglobulinemia, recurrent infections, and hypertrophic cardiomyopathy (HCM). Two of them also presented with intermittent or severe chronic neutropenia. We identified homozygous or compound-heterozygous variants in the gene for folliculin interacting protein 1 (FNIP1), leading to loss of the FNIP1 protein. B-cell metabolism, including mitochondrial numbers and activity and phosphatidylinositol 3-kinase/AKT pathway, was impaired. These defects recapitulated the Fnip1-/- animal model. Moreover, we identified either uniparental disomy or copy-number variants (CNVs) in 2 patients, expanding the variant spectrum of this novel inborn error of immunity. The results indicate that FNIP1 deficiency can be caused by complex genetic mechanisms and support the clinical utility of exome sequencing and CNV analysis in patients with broad phenotypes, including agammaglobulinemia and HCM. FNIP1 deficiency is a novel inborn error of immunity characterized by early and severe B-cell development defect, agammaglobulinemia, variable neutropenia, and HCM. Our findings elucidate a functional and relevant role of FNIP1 in B-cell development and metabolism and potentially neutrophil activity.
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Affiliation(s)
- Francesco Saettini
- Pediatric Hematology Department, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), University of Milano Bicocca, Monza, Italy
| | - Cecilia Poli
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Facultad de Medicina Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago, Chile
| | - Jaime Vengoechea
- Department of Human Genetics, Emory University, Atlanta, GA
- Department of Medicine, Emory University, Atlanta, GA
| | - Sonia Bonanomi
- Pediatric Hematology Department, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), University of Milano Bicocca, Monza, Italy
| | - Julio C Orellana
- Division Alergia e Inmunología Clínica, Hospital de Niños de la Santísima Trinidad, Córdoba, Argentina
| | - Grazia Fazio
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Fred H Rodriguez
- Section of Cardiology, Department of Medicine, and
- Section of Cardiology, Department of Pediatrics, Emory University, Atlanta, GA
| | - Loreani P Noguera
- Facultad de Medicina Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago, Chile
| | - Claire Booth
- Molecular and Cellular Immunology Section, UCL Institute of Child Health, London, United Kingdom
| | - Valentina Jarur-Chamy
- Facultad de Medicina Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago, Chile
| | - Marissa Shams
- Department of Medicine, Emory University, Atlanta, GA
| | - Maria Iascone
- Molecular Genetics Laboratory, Università Settore Scientifico-Disciplinare Laboratorio di Genetica Medica (USSD LGM), Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Maja Vukic
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Serena Gasperini
- Metabolic Rare Disease Unit, Pediatric Department, Fondazione MBBM, University of Milano Bicocca, Monza, Italy
| | - Manuel Quadri
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
| | | | - Elizabeth Rivers
- Molecular and Cellular Immunology Section, UCL Institute of Child Health, London, United Kingdom
| | - Mario Mauri
- Department of Medicine and Surgery, University of Milano Bicocca-San Gerardo Hospital, Monza, Italy
| | - Raffaele Badolato
- Pediatrics Clinic and Institute of Molecular Medicine A. Novicelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
- Department of Medicine and Surgery, University of Milano Bicocca-San Gerardo Hospital, Monza, Italy
| | - Cristina Bugarin
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Giuseppe Gaipa
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Wilma G M Kroes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniele Moratto
- Flow Cytometry Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | | | - Frank Baas
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano Bicocca-San Gerardo Hospital, Monza, Italy
| | - Zeynep H Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Genetics Laboratory, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor-Hopkins Center for Mendelian Genomics, Houston, TX; and
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Genetics Laboratory, Houston, TX
| | - Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrea Biondi
- Pediatric Hematology Department, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), University of Milano Bicocca, Monza, Italy
- Centro Ricerca Tettamanti, University of Milano Bicocca, Monza, Italy
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16
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Weinfurter JT, Graham ME, Ericsen AJ, Matschke LM, Llewellyn-Lacey S, Price DA, Wiseman RW, Reynolds MR. Identifying a Minor Histocompatibility Antigen in Mauritian Cynomolgus Macaques Encoded by APOBEC3C. Front Immunol 2020; 11:586251. [PMID: 33193411 PMCID: PMC7649366 DOI: 10.3389/fimmu.2020.586251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/08/2020] [Indexed: 11/29/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplants can lead to dramatic reductions in human immunodeficiency virus (HIV) reservoirs. This effect is partially mediated by donor T cells recognizing lymphocyte-expressed minor histocompatibility antigens (mHAgs). The potential to mark malignant and latently infected cells for destruction makes mHAgs attractive targets for cellular immunotherapies. However, testing such HIV reservoir reduction strategies will likely require preclinical studies in non-human primates (NHPs). In this study, we used a combination of alloimmunization, whole exome sequencing, and bioinformatics to identify an mHAg in Mauritian cynomolgus macaques (MCMs). We mapped the minimal optimal epitope to a 10-mer peptide (SW10) in apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3C (APOBEC3C) and determined the major histocompatibility complex class I restriction element as Mafa-A1∗063, which is expressed in almost 90% of MCMs. APOBEC3C SW10-specific CD8+ T cells recognized immortalized B cells but not fibroblasts from an mHAg-positive MCM. These results provide a framework for identifying mHAgs in a non-transplant setting and suggest that APOBEC3C SW10 could be used as a model antigen to test mHAg-targeted therapies in NHPs.
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Affiliation(s)
- Jason T. Weinfurter
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael E. Graham
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Adam J. Ericsen
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Lea M. Matschke
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David A. Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Roger W. Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Matthew R. Reynolds
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States
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17
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Mace EM, Paust S, Conte MI, Baxley RM, Schmit MM, Patil SL, Guilz NC, Mukherjee M, Pezzi AE, Chmielowiec J, Tatineni S, Chinn IK, Akdemir ZC, Jhangiani SN, Muzny DM, Stray-Pedersen A, Bradley RE, Moody M, Connor PP, Heaps AG, Steward C, Banerjee PP, Gibbs RA, Borowiak M, Lupski JR, Jolles S, Bielinsky AK, Orange JS. Human NK cell deficiency as a result of biallelic mutations in MCM10. J Clin Invest 2020; 130:5272-5286. [PMID: 32865517 PMCID: PMC7524476 DOI: 10.1172/jci134966] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Human natural killer cell deficiency (NKD) arises from inborn errors of immunity that lead to impaired NK cell development, function, or both. Through the understanding of the biological perturbations in individuals with NKD, requirements for the generation of terminally mature functional innate effector cells can be elucidated. Here, we report a cause of NKD resulting from compound heterozygous mutations in minichromosomal maintenance complex member 10 (MCM10) that impaired NK cell maturation in a child with fatal susceptibility to CMV. MCM10 has not been previously associated with monogenic disease and plays a critical role in the activation and function of the eukaryotic DNA replisome. Through evaluation of patient primary fibroblasts, modeling patient mutations in fibroblast cell lines, and MCM10 knockdown in human NK cell lines, we have shown that loss of MCM10 function leads to impaired cell cycle progression and induction of DNA damage-response pathways. By modeling MCM10 deficiency in primary NK cell precursors, including patient-derived induced pluripotent stem cells, we further demonstrated that MCM10 is required for NK cell terminal maturation and acquisition of immunological system function. Together, these data define MCM10 as an NKD gene and provide biological insight into the requirement for the DNA replisome in human NK cell maturation and function.
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Affiliation(s)
- Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Silke Paust
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, California, USA
| | - Matilde I. Conte
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Megan M. Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sagar L. Patil
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Nicole C. Guilz
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Malini Mukherjee
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Ashley E. Pezzi
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Jolanta Chmielowiec
- Center for Cell and Gene Therapy, and
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Swetha Tatineni
- Department of Pediatrics
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Ivan K. Chinn
- Department of Pediatrics
- Department of Molecular and Human Genetics and
| | | | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M. Muzny
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo, Norway
| | - Rachel E. Bradley
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Mo Moody
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Philip P. Connor
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Adrian G. Heaps
- Department of Virology and Immunology, North Cumbria University Hospitals, Carlisle, United Kingdom
| | - Colin Steward
- Department of Paediatric Haematology, Oncology and Bone Marrow Transplantation, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Pinaki P. Banerjee
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Malgorzata Borowiak
- Center for Cell and Gene Therapy, and
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas, USA
- Adam Mickiewicz University, Poznan, Poland
- McNair Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Department of Pediatrics
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Anja K. Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jordan S. Orange
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
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18
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Shi LE, Shang X, Nie KC, Xu Q, Chen NB, Zhu ZZ. Identification of potential crucial genes associated with the pathogenesis and prognosis of pancreatic adenocarcinoma. Oncol Lett 2020; 20:60. [PMID: 32793313 PMCID: PMC7418510 DOI: 10.3892/ol.2020.11921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is a type of malignant tumor with the highest mortality rate among all neoplasms worldwide, and its exact pathogenesis is still poorly understood. Timely diagnosis and treatment are of great importance in order to decrease the mortality rate of PAAD. Therefore, identifying new biomarkers for diagnosis and prognosis is essential to enable early detection of PAAD and to improve the overall survival (OS) rate. In order to screen and integrate differentially expressed genes (DEGs) between PAAD and normal tissues, a total of seven datasets were downloaded from the Gene Expression Omnibus database and the ‘limma’ and ‘robustrankggreg’ packages in R software were used. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of the DEGs was performed using the Database for Annotation, Visualization and Integrated Discovery website, and the protein-protein interaction network analysis was performed using the Search Tool for the Retrieval of Interacting Genes/Proteins database. A gene prognostic signature was constructed using the Cox regression model. A total of 10 genes (CDK1, CCNB1, CDC20, ASPM, UBE2C, TPX2, TOP2A, NUSAP1, KIF20A and DLGAP5) that may be associated with pancreatic adenocarcinoma were identified. According to the differentially expressed genes in The Cancer Genome Atlas, the present study set up four prognostic signatures (matrix metalloproteinase 12, sodium voltage-gated channel α subunit 11, tetraspanin 1 and SH3 domain and tetratricopeptide repeats-containing 2), which effectively predicted OS. The hub genes that were highly associated with the occurrence, development and prognosis of PAAD were identified, which may be helpful to further understand the molecular basis of pancreatic cancer and guide the synthesis of drugs for PPAD.
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Affiliation(s)
- Lan-Er Shi
- Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
| | - Xin Shang
- Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
| | - Ke-Chao Nie
- Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
| | - Qiang Xu
- Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
| | - Na-Bei Chen
- Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
| | - Zhang-Zhi Zhu
- Department of Endocrinology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510405, P.R. China
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19
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Gonzaga-Jauregui C, Yesil G, Nistala H, Gezdirici A, Bayram Y, Nannuru KC, Pehlivan D, Yuan B, Jimenez J, Sahin Y, Paine IS, Akdemir ZC, Rajamani S, Staples J, Dronzek J, Howell K, Fatih JM, Smaldone S, Schlesinger AE, Ramírez N, Cornier AS, Kelly MA, Haber R, Chim SM, Nieman K, Wu N, Walls J, Poueymirou W, Siao CJ, Sutton VR, Williams MS, Posey JE, Gibbs RA, Carlo S, Tegay DH, Economides AN, Lupski JR. Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide. Eur J Hum Genet 2020; 28:1243-1264. [PMID: 32376988 PMCID: PMC7608441 DOI: 10.1038/s41431-020-0632-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 01/20/2023] Open
Abstract
Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles identified in unrelated consanguineous Turkish kindreds suggesting Clan Genomics and identity-by-descent homozygosity contributing to disease in this population. The hypothesis that carrier states for this autosomal recessive osteochondrodysplasia may contribute to common complex traits is further explored in a large clinical population cohort. Our findings augment our understanding of COL27A1 biology and its role in skeletal development; and expand the functional allelic architecture in this gene underlying both rare and common disease phenotypes.
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Affiliation(s)
| | - Gozde Yesil
- Istanbul Faculty of Medicine Department of Medical Genetics, Istanbul University, 34093, Istanbul, Turkey
| | - Harikiran Nistala
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303, Istanbul, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Division of Pediatric Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, 06570, Ankara, Turkey
| | - Ingrid S Paine
- Department of Molecular and Human Genetics, 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
| | | | - Jeffrey Staples
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - John Dronzek
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Kristen Howell
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Alan E Schlesinger
- Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Radiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Alberto S Cornier
- Genetics Section, San Jorge Children's Hospital, San Juan, PR, 00912, USA.,Ponce Health Sciences University, Ponce, PR, 00716, USA.,Department of Pediatrics, Universidad Central del Caribe School of Medicine, Bayamon, PR, 00960, USA
| | | | - Robert Haber
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Shek Man Chim
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Kristy Nieman
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, and Medical Research Center of Orthopedics, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, 100730, Beijing, China
| | | | | | | | - Chia-Jen Siao
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Jennifer E Posey
- Department of Molecular and Human Genetics, 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
| | - Simon Carlo
- Mayagüez Medical Center, Mayagüez, PR, 00681, USA.,Ponce Health Sciences University, Ponce, PR, 00716, USA
| | - David H Tegay
- Department of Pediatrics, Division of Medical Genetics, Cohen Children's Medical Center of Northwell Health, New Hyde Park, NY, 11040, USA
| | - Aris N Economides
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA.,Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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20
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Assia Batzir N, Kishor Bhagwat P, Larson A, Coban Akdemir Z, Bagłaj M, Bofferding L, Bosanko KB, Bouassida S, Callewaert B, Cannon A, Enchautegui Colon Y, Garnica AD, Harr MH, Heck S, Hurst ACE, Jhangiani SN, Isidor B, Littlejohn RO, Liu P, Magoulas P, Mar Fan H, Marom R, McLean S, Nezarati MM, Nugent KM, Petersen MB, Rocha ML, Roeder E, Smigiel R, Tully I, Weisfeld-Adams J, Wells KO, Posey JE, Lupski JR, Beaudet AL, Wangler MF. Recurrent arginine substitutions in the ACTG2 gene are the primary driver of disease burden and severity in visceral myopathy. Hum Mutat 2020; 41:641-654. [PMID: 31769566 PMCID: PMC7720429 DOI: 10.1002/humu.23960] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/04/2019] [Accepted: 11/06/2019] [Indexed: 02/06/2023]
Abstract
Visceral myopathy with abnormal intestinal and bladder peristalsis includes a clinical spectrum with megacystis-microcolon intestinal hypoperistalsis syndrome and chronic intestinal pseudo-obstruction. The vast majority of cases are caused by dominant variants in ACTG2; however, the overall genetic architecture of visceral myopathy has not been well-characterized. We ascertained 53 families, with visceral myopathy based on megacystis, functional bladder/gastrointestinal obstruction, or microcolon. A combination of targeted ACTG2 sequencing and exome sequencing was used. We report a molecular diagnostic rate of 64% (34/53), of which 97% (33/34) is attributed to ACTG2. Strikingly, missense mutations in five conserved arginine residues involving CpG dinucleotides accounted for 49% (26/53) of disease in the cohort. As a group, the ACTG2-negative cases had a more favorable clinical outcome and more restricted disease. Within the ACTG2-positive group, poor outcomes (characterized by total parenteral nutrition dependence, death, or transplantation) were invariably due to one of the arginine missense alleles. Analysis of specific residues suggests a severity spectrum of p.Arg178>p.Arg257>p.Arg40 along with other less-frequently reported sites p.Arg63 and p.Arg211. These results provide genotype-phenotype correlation for ACTG2-related disease and demonstrate the importance of arginine missense changes in visceral myopathy.
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Affiliation(s)
- Nurit Assia Batzir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
| | - Pranjali Kishor Bhagwat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Austin Larson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, Colorado
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Maciej Bagłaj
- Department of Pediatric Surgery and Urology, Wroclaw Medical University, Wroclaw, Poland
| | - Leon Bofferding
- Département de Pédiatrie Néonatologie, Kannerklinik, Centre Hospitalier de Luxembourg, Luxembourg City, Luxembourg
| | - Katherine B Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Skander Bouassida
- Humboldt Clinic, Vivantes Health Network GmbH, Charité Academic Teaching Hospital, Medical University of Berlin, Berlin, Germany
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ashley Cannon
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yazmin Enchautegui Colon
- Inherited Metabolic Diseases Clinic, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, Colorado
| | - Adolfo D Garnica
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Margaret H Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sandra Heck
- Département de Pédiatrie Néonatologie, Kannerklinik, Centre Hospitalier de Luxembourg, Luxembourg City, Luxembourg
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Bertrand Isidor
- CHU de Nantes, Service de Génétique Médicale, Nantes 44093 Cedex 1, Nantes, France
| | - Rebecca O Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
| | - Helen Mar Fan
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
| | - Scott McLean
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | - Marjan M Nezarati
- Genetics Program, North York General Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | | | - Maria L Rocha
- Humboldt Clinic, Vivantes Health Network GmbH, Charité Academic Teaching Hospital, Medical University of Berlin, Berlin, Germany
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | - Robert Smigiel
- Department of Pediatrics, Division of Pediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland
| | - Ian Tully
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - James Weisfeld-Adams
- Inherited Metabolic Diseases Clinic, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, Colorado
| | - Katerina O Wells
- Department of Surgery, Division of Colorectal Surgery, Baylor University Medical Center, Dallas, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
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21
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Blackburn ATM, Bekheirnia N, Uma VC, Corkins ME, Xu Y, Rosenfeld JA, Bainbridge MN, Yang Y, Liu P, Madan-Khetarpal S, Delgado MR, Hudgins L, Krantz I, Rodriguez-Buritica D, Wheeler PG, Al-Gazali L, Mohamed Saeed Mohamed Al Shamsi A, Gomez-Ospina N, Chao HT, Mirzaa GM, Scheuerle AE, Kukolich MK, Scaglia F, Eng C, Willsey HR, Braun MC, Lamb DJ, Miller RK, Bekheirnia MR. DYRK1A-related intellectual disability: a syndrome associated with congenital anomalies of the kidney and urinary tract. Genet Med 2019; 21:2755-2764. [PMID: 31263215 PMCID: PMC6895419 DOI: 10.1038/s41436-019-0576-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/29/2019] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Haploinsufficiency of DYRK1A causes a recognizable clinical syndrome. The goal of this paper is to investigate congenital anomalies of the kidney and urinary tract (CAKUT) and genital defects (GD) in patients with DYRK1A variants. METHODS A large database of clinical exome sequencing (ES) was queried for de novo DYRK1A variants and CAKUT/GD phenotypes were characterized. Xenopus laevis (frog) was chosen as a model organism to assess Dyrk1a's role in renal development. RESULTS Phenotypic details and variants of 19 patients were compiled after an initial observation that one patient with a de novo pathogenic variant in DYRK1A had GD. CAKUT/GD data were available from 15 patients, 11 of whom presented with CAKUT/GD. Studies in Xenopus embryos demonstrated that knockdown of Dyrk1a, which is expressed in forming nephrons, disrupts the development of segments of embryonic nephrons, which ultimately give rise to the entire genitourinary (GU) tract. These defects could be rescued by coinjecting wild-type human DYRK1A RNA, but not with DYRK1AR205* or DYRK1AL245R RNA. CONCLUSION Evidence supports routine GU screening of all individuals with de novo DYRK1A pathogenic variants to ensure optimized clinical management. Collectively, the reported clinical data and loss-of-function studies in Xenopus substantiate a novel role for DYRK1A in GU development.
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Affiliation(s)
- Alexandria T M Blackburn
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center, McGovern Medical School, Houston, TX, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Nasim Bekheirnia
- Renal Section, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | | | - Mark E Corkins
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center, McGovern Medical School, Houston, TX, USA
| | - Yuxiao Xu
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew N Bainbridge
- Codified Genomics, LLC, Houston, TX, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Suneeta Madan-Khetarpal
- Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mauricio R Delgado
- Department of neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Louanne Hudgins
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Stanford, CA, USA
| | - Ian Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia and the Department of Pediatrics, Perelman School of medicine at University of Pennsylvania, Philadelphia, PA, USA
| | - David Rodriguez-Buritica
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Lihadh Al-Gazali
- College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | | | - Natalia Gomez-Ospina
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Stanford, CA, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- McNair Medical Institute at The Robert and Janice McNair Foundation, Houston, TX, USA
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Angela E Scheuerle
- Department of Pediatrics (Genetics and Metabolism), The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mary K Kukolich
- Clinical Genetics, Cook Children's Medical Center, Fort Worth, TX, USA
| | - Fernando Scaglia
- Texas Children's Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, Hong Kong SAR
| | - Christine Eng
- Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Helen Rankin Willsey
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Michael C Braun
- Renal Section, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
| | - Dolores J Lamb
- Department of Urology and Center for Reproductive Genomics, Weill Cornell Medicine, New York, NY, USA
| | - Rachel K Miller
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center, McGovern Medical School, Houston, TX, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, TX, USA.
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Program in Biochemistry and Cell Biology, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, TX, USA.
| | - Mir Reza Bekheirnia
- Renal Section, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Houston, TX, USA.
- Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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22
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Link N, Chung H, Jolly A, Withers M, Tepe B, Arenkiel BR, Shah PS, Krogan NJ, Aydin H, Geckinli BB, Tos T, Isikay S, Tuysuz B, Mochida GH, Thomas AX, Clark RD, Mirzaa GM, Lupski JR, Bellen HJ. Mutations in ANKLE2, a ZIKA Virus Target, Disrupt an Asymmetric Cell Division Pathway in Drosophila Neuroblasts to Cause Microcephaly. Dev Cell 2019; 51:713-729.e6. [PMID: 31735666 DOI: 10.1016/j.devcel.2019.10.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/19/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022]
Abstract
The apical Par complex, which contains atypical protein kinase C (aPKC), Bazooka (Par-3), and Par-6, is required for establishing polarity during asymmetric division of neuroblasts in Drosophila, and its activity depends on L(2)gl. We show that loss of Ankle2, a protein associated with microcephaly in humans and known to interact with Zika protein NS4A, reduces brain volume in flies and impacts the function of the Par complex. Reducing Ankle2 levels disrupts endoplasmic reticulum (ER) and nuclear envelope morphology, releasing the kinase Ballchen-VRK1 into the cytosol. These defects are associated with reduced phosphorylation of aPKC, disruption of Par-complex localization, and spindle alignment defects. Importantly, removal of one copy of ballchen or l(2)gl suppresses Ankle2 mutant phenotypes and restores viability and brain size. Human mutational studies implicate the above-mentioned genes in microcephaly and motor neuron disease. We suggest that NS4A, ANKLE2, VRK1, and LLGL1 define a pathway impinging on asymmetric determinants of neural stem cell division.
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Affiliation(s)
- Nichole Link
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hyunglok Chung
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; MD/PhD Medical Scientist Training Program and MHG Graduate program, BCM, Houston, TX 77030, USA
| | - Marjorie Withers
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Burak Tepe
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Benjamin R Arenkiel
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Priya S Shah
- Department of Chemical Engineering and Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA 95616, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hatip Aydin
- Center of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey
| | - Bilgen B Geckinli
- Department of Medical Genetics, Marmara University School of Medicine, Istanbul, Turkey
| | - Tulay Tos
- Department of Medical Genetics, Dr. Sami Ulus Research and Training Hospital of Women's and Children's Health and Diseases, Ankara, Turkey
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep, Turkey
| | - Beyhan Tuysuz
- Department of Pediatrics, Istanbul University-Cerrahpasa, Medical Faculty, Istanbul, Turkey
| | - Ganesh H Mochida
- Division of Genetics and Genomics, Department of Pediatrics and Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ajay X Thomas
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, BCM, Houston, TX 77030, USA; Section of Child Neurology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Robin D Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University Medical Center, Loma Linda, CA 92354, USA
| | - Ghayda M Mirzaa
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hugo J Bellen
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; MD/PhD Medical Scientist Training Program and MHG Graduate program, BCM, Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA.
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23
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Wang H, Kaçar Bayram A, Sprute R, Ozdemir O, Cooper E, Pergande M, Efthymiou S, Nedic I, Mazaheri N, Stumpfe K, Azizi Malamiri R, Shariati G, Zeighami J, Bayram N, Naghibzadeh SK, Tajik M, Yaşar M, Sami Güven A, Bibi F, Sultan T, Salpietro V, Houlden H, Per H, Galehdari H, Shalbafan B, Jamshidi Y, Cirak S. Genotype-Phenotype Correlations in Charcot-Marie-Tooth Disease Due to MTMR2 Mutations and Implications in Membrane Trafficking. Front Neurosci 2019; 13:974. [PMID: 31680794 PMCID: PMC6807680 DOI: 10.3389/fnins.2019.00974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 08/30/2019] [Indexed: 11/13/2022] Open
Abstract
Charcot-Marie-Tooth type 4 (CMT4) is an autosomal recessive severe form of neuropathy with genetic heterogeneity. CMT4B1 is caused by mutations in the myotubularin-related 2 (MTMR2) gene and as a member of the myotubularin family, the MTMR2 protein is crucial for the modulation of membrane trafficking. To enable future clinical trials, we performed a detailed review of the published cases with MTMR2 mutations and describe four novel cases identified through whole-exome sequencing (WES). The four unrelated families harbor novel homozygous mutations in MTMR2 (NM_016156, Family 1: c.1490dupC; p.Phe498IlefsTer2; Family 2: c.1479+1G>A; Family 3: c.1090C>T; p.Arg364Ter; Family 4: c.883C>T; p.Arg295Ter) and present with CMT4B1-related severe early-onset motor and sensory neuropathy, generalized muscle atrophy, facial and bulbar weakness, and pes cavus deformity. The clinical description of the new mutations reported here overlap with previously reported CMT4B1 phenotypes caused by mutations in the phosphatase domain of MTMR2, suggesting that nonsense MTMR2 mutations, which are predicted to result in loss or disruption of the phosphatase domain, are associated with a severe phenotype and loss of independent ambulation by the early twenties. Whereas the few reported missense mutations and also those truncating mutations occurring at the C-terminus after the phosphatase domain cause a rather mild phenotype and patients were still ambulatory above the age 30 years. Charcot-Marie-Tooth neuropathy and Centronuclear Myopathy causing mutations have been shown to occur in proteins involved in membrane remodeling and trafficking pathway mediated by phosphoinositides. Earlier studies have showing the rescue of MTM1 myopathy by MTMR2 overexpression, emphasize the importance of maintaining the phosphoinositides equilibrium and highlight a potential compensatory mechanism amongst members of this pathway. This proved that the regulation of expression of these proteins involved in the membrane remodeling pathway may compensate each other's loss- or gain-of-function mutations by restoring the phosphoinositides equilibrium. This provides a potential therapeutic strategy for neuromuscular diseases resulting from mutations in the membrane remodeling pathway.
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Affiliation(s)
- Haicui Wang
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Ayşe Kaçar Bayram
- Department of Pediatric Neurology, University of Health Sciences, Kayseri City Hospital, Kayseri, Turkey
| | - Rosanne Sprute
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Ozkan Ozdemir
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Emily Cooper
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's, University of London, London, United Kingdom
| | - Matthias Pergande
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, United Kingdom
| | - Ivana Nedic
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's, University of London, London, United Kingdom
| | - Neda Mazaheri
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Katharina Stumpfe
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany
| | - Reza Azizi Malamiri
- Paediatric Neurology, Department of Paediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Nurettin Bayram
- Department of Ophthalmology, University of Health Sciences, Kayseri City Hospital, Kayseri, Turkey
| | | | - Mohamad Tajik
- Department of Neurology, Firoozgar General Hospital, University of Medical Sciences, Tehran, Iran
| | - Mehmet Yaşar
- Department of Ear Nose and Throat, University of Health Sciences, Kayseri City Hospital, Kayseri, Turkey
| | - Ahmet Sami Güven
- Department of Pediatric Neurology, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Farah Bibi
- Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, Institute of Child Health, The Children's Hospital Lahore, Lahore, Pakistan
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, United Kingdom.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Henry Houlden
- Department of Neuromuscular Disorders, Institute of Neurology, University College London, London, United Kingdom
| | - Hüseyin Per
- Department of Pediatric Neurology, Erciyes University Medical School, Kayseri, Turkey
| | - Hamid Galehdari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Bita Shalbafan
- Iran Social Security Organization, Labafinejad Hospital, Tehran, Iran
| | - Yalda Jamshidi
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's, University of London, London, United Kingdom
| | - Sebahattin Cirak
- Department of Pediatrics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
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24
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Burk CM, Coffey KE, Mace EM, Bostwick BL, Chinn IK, Coban-Akdemir ZH, Jhangiani SN, Lupski JR, Ortiz D, Barnum JL, Allen SW, Robertson LM, Orange JS, Chong HJ. Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome with NK dysfunction and EBV-driven malignancy treated with stem cell transplantation. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2019; 8:1103-1106.e3. [PMID: 31520839 DOI: 10.1016/j.jaip.2019.08.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Caitlin M Burk
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa.
| | - Kara E Coffey
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Emily M Mace
- Columbia University Irving Medical Center, New York, NY
| | - Bret L Bostwick
- Texas Children's Hospital/Baylor College of Medicine, Houston, Texas
| | - Ivan K Chinn
- Texas Children's Hospital/Baylor College of Medicine, Houston, Texas
| | | | | | - James R Lupski
- Texas Children's Hospital/Baylor College of Medicine, Houston, Texas
| | - Damara Ortiz
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Jessie L Barnum
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Steven W Allen
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Leanna-Marie Robertson
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | | | - Hey J Chong
- UPMC Children's Hospital of Pittsburgh/University of Pittsburgh School of Medicine, Pittsburgh, Pa
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25
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Oswiecimska J, Dawidziuk M, Gambin T, Ziora K, Marek M, Rzonca S, Guilbride DL, Jhangiani SN, Obuchowicz A, Sikora A, Lupski JR, Wiszniewski W, Gawlinski P. A Patient with Berardinelli-Seip Syndrome, Novel AGPAT2 Splicesite Mutation and Concomitant Development of Non-diabetic Polyneuropathy. J Clin Res Pediatr Endocrinol 2019; 11:319-326. [PMID: 30563316 PMCID: PMC6745459 DOI: 10.4274/jcrpe.galenos.2018.2018.0227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/17/2018] [Indexed: 12/01/2022] Open
Abstract
Primary polyneuropathy in the context of Seip-Berardinelli type 1 seipinopathy, or congenital generalized lipodystrophy type 1 (CGL1) has not been previously reported. We report the case history of a 27 year old female CGL1 patient presenting with an unusual additional development of non-diabetic peripheral neuropathy and learning disabilities in early adolescence. Whole exome sequencing (WES) of the patient genome identified a novel variant, homozygous for a 52 bp intronic deletion in the AGPAT2 locus, coding for 1-acylglycerol-3-phosphate O-acyltransferase 2, which is uniquely associated with CGL1 seipinopathies, with no molecular evidence for dual diagnosis. Functional studies using RNA isolated from patient peripheral blood leucocytes showed abnormal RNA splicing resulting in the loss of 25 amino acids from the patient AGPAT2 protein coding sequence. Stability and transcription levels for the misspliced AGPAT2 mRNA in our patient nonetheless remained normal. Any AGPAT2 protein produced in our patient is therefore likely to be dysfunctional. However, formal linkage of this deletion to the neuropathy observed remains to be shown. The classical clinical presentation of a patient with AGPAT2-associated lipodystrophy shows normal cognition and no development of polyneuropathy. Cognitive disabilities and polyneuropathy are features associated exclusively with clinical CGL type 2 arising from seipin (BSCL2) gene mutations. This case study suggests that in some genetic contexts, AGPAT2 mutations can also produce phenotypes with primary polyneuropathy.
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Affiliation(s)
- Joanna Oswiecimska
- Medical University of Silesia in Katowice, Department of Pediatrics in Zabrze, Silesia, Poland
| | - Mateusz Dawidziuk
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
| | - Tomasz Gambin
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
- Warsaw University of Technology, Institute of Computer Science, Warsaw, Poland
- Baylor College of Medicine, Department of Molecular and Human Genetics, Texas, USA
| | - Katarzyna Ziora
- Medical University of Silesia in Katowice, Department of Pediatrics in Zabrze, Silesia, Poland
| | - Marta Marek
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - Sylwia Rzonca
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
| | | | | | - Anna Obuchowicz
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - Alicja Sikora
- Medical University of Silesia in Katowice, Department of Pediatrics in Bytom, Silesia, Poland
| | - James R. Lupski
- Baylor College of Medicine, Department of Molecular and Human Genetics, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Texas, USA
- Baylor College of Medicine, Department of Pediatrics, Texas, USA
- Texas Children’s Hospital, Texas, USA
| | - Wojciech Wiszniewski
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
- Oregon Health and Science University, Department of Molecular and Medical Genetics, Portland, USA
| | - Pawel Gawlinski
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland
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26
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Karolak JA, Szafranski P, Kilner D, Patel C, Scurry B, Kinning E, Chandler K, Jhangiani SN, Coban Akdemir ZH, Lupski JR, Popek E, Stankiewicz P. Heterozygous CTNNB1 and TBX4 variants in a patient with abnormal lung growth, pulmonary hypertension, microcephaly, and spasticity. Clin Genet 2019; 96:366-370. [PMID: 31309540 DOI: 10.1111/cge.13605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023]
Abstract
The canonical wingless (Wnt) and fibroblast growth factor (FGF) signaling pathways involving CTNNB1 and TBX4, respectively, are crucial for the regulation of human development. Perturbations of these pathways and disruptions from biological homeostasis have been associated with abnormal morphogenesis of multiple organs, including the lung. The aim of this study was to identify the underlying genetic cause of abnormal lung growth, pulmonary hypertension (PAH), severe microcephaly, and muscle spasticity in a full-term newborn, who died at 4 months of age due to progressively worsening PAH and respiratory failure. Family trio exome sequencing showed a de novo heterozygous nonsense c.1603C>T (p.Arg535*) variant in CTNNB1 and a paternally inherited heterozygous missense c.1198G>A (p.Glu400Lys) variant in TBX4, both predicted to be likely deleterious. We expand the phenotypic spectrum associated with CTNNB1 and TBX4 variants and indicate that they could act synergistically to produce a distinct more severe phenotype. Our findings further support a recently proposed complex compound inheritance model in lethal lung developmental diseases and the contention that dual molecular diagnoses can parsimoniously explain blended phenotypes.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - David Kilner
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, Queensland, Australia.,The University of Queensland, Brisbane, Queensland, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Bonnie Scurry
- Pathology Queensland, Royal Brisbane and Women's Hospital and Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Esther Kinning
- West of Scotland Regional Genetics Service, Queen Elizabeth Hospital, Glasgow, UK
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | | | | | - 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
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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27
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Lerat J, Magdelaine C, Lunati A, Dzugan H, Dejoie C, Rego M, Beze Beyrie P, Bieth E, Calvas P, Cintas P, Delaubrier A, Demurger F, Gilbert-Dussardier B, Goizet C, Journel H, Laffargue F, Magy L, Taithe F, Toutain A, Urtizberea JA, Sturtz F, Lia AS. Implication of the SH3TC2 gene in Charcot-Marie-Tooth disease associated with deafness and/or scoliosis: Illustration with four new pathogenic variants. J Neurol Sci 2019; 406:116376. [PMID: 31634715 DOI: 10.1016/j.jns.2019.06.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/07/2019] [Accepted: 06/24/2019] [Indexed: 11/30/2022]
Abstract
The autosomal recessive demyelinating form of Charcot-Marie-Tooth can be due to SH3TC2 gene pathogenic variants (CMT4C, AR-CMTde-SH3TC2). We report on a series of 13 patients with AR-CMTde-SH3TC2 among a French cohort of 350 patients suffering from all type of inheritance peripheral neuropathy. The SH3TC2 gene appeared to be the most frequently mutated gene for demyelinating neuropathy in this series by NGS. Four new pathogenic variants have been identified: two nonsense variants (p.(Tyr970*), p.(Trp1199*)) and two missense variants (p.(Leu1126Pro), p.(Ala1206Asp)). The recurrent variant p.Arg954* was present in 62%, and seems to be a founder mutation. The phenotype is fairly homogeneous, as all these patients, except the youngest ones, presented scoliosis and/or hearing loss.
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Affiliation(s)
- J Lerat
- Service Oto-Rhino-Laryngologie, Centre Hospitalier Universitaire de Limoges, Limoges, France; EA6309, Université de Limoges, Limoges, France.
| | - C Magdelaine
- EA6309, Université de Limoges, Limoges, France; Service de Biochimie et Génétique Moléculaire, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - A Lunati
- EA6309, Université de Limoges, Limoges, France; Service de Biochimie et Génétique Moléculaire, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - H Dzugan
- EA6309, Université de Limoges, Limoges, France; Service de Biochimie et Génétique Moléculaire, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - C Dejoie
- Service de Biochimie et Génétique Moléculaire, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - M Rego
- Service de Biochimie et Génétique Moléculaire, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | | | - E Bieth
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - P Calvas
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - P Cintas
- Service de Neurologie et d'explorations fonctionnelles, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - A Delaubrier
- Service de Médecine Physique et Rééducation, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
| | - F Demurger
- Service de Génétique Médicale, Centre Hospitalier Bretagne Atlantique, Vannes, France
| | - B Gilbert-Dussardier
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Poitiers, Poitiers, France; EA3808, Université de Poitiers, Poitiers, France
| | - C Goizet
- Service de Neurogénétique, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - H Journel
- Service de Génétique Médicale, Centre Hospitalier Bretagne Atlantique, Vannes, France
| | - F Laffargue
- Service de Génétique médicale, Centre Hospitalier Universitaire de Clermont-Ferrand, Limoges, France
| | - L Magy
- EA6309, Université de Limoges, Limoges, France; Service de Neurologie, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - F Taithe
- Service de Neurologie, Centre Hospitalier Universitaire de Clermont-Ferrand, Limoges, France
| | - A Toutain
- Service de Génétique, Centre Hospitalier Universitaire de Tours, Tours, France
| | - J A Urtizberea
- Centre de Compétence Neuromusculaire, APHP, Filnemus, Centre Hospitalier Hendaye, France
| | - F Sturtz
- EA6309, Université de Limoges, Limoges, France; Service de Biochimie et Génétique Moléculaire, Centre Hospitalier Universitaire de Limoges, Limoges, France
| | - A S Lia
- EA6309, Université de Limoges, Limoges, France; Service de Biochimie et Génétique Moléculaire, Centre Hospitalier Universitaire de Limoges, Limoges, France
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28
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Khani M, Taheri H, Shamshiri H, Houlden H, Efthymiou S, Alavi A, Nafissi S, Elahi E. Continuum of phenotypes in hereditary motor and sensory neuropathy with proximal predominance and Charcot-Marie-Tooth patients with TFG
mutation. Am J Med Genet A 2019; 179:1507-1515. [DOI: 10.1002/ajmg.a.61184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/12/2019] [Accepted: 04/23/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Marzieh Khani
- School of Biology; College of Science, University of Tehran; Tehran Iran
| | - Hanieh Taheri
- School of Biology; College of Science, University of Tehran; Tehran Iran
| | - Hosein Shamshiri
- Department of Neurology; Tehran University of Medical Sciences; Tehran Iran
| | - Henry Houlden
- Department of Molecular Neuroscience; UCL Institute of Neurology; London United Kingdom
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience; UCL Institute of Neurology; London United Kingdom
| | - Afagh Alavi
- Genetics Research Center; University of Social Welfare and Rehabilitation Sciences; Tehran Iran
| | - Shahriar Nafissi
- Department of Neurology; Tehran University of Medical Sciences; Tehran Iran
| | - Elahe Elahi
- School of Biology; College of Science, University of Tehran; Tehran Iran
- Department of Biotechnology; College of Science, University of Tehran; Tehran Iran
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29
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Tian S, Yan H, Klee EW, Kalmbach M, Slager SL. Comparative analysis of de novo assemblers for variation discovery in personal genomes. Brief Bioinform 2019; 19:893-904. [PMID: 28407084 PMCID: PMC6169673 DOI: 10.1093/bib/bbx037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/08/2017] [Indexed: 12/30/2022] Open
Abstract
Current variant discovery approaches often rely on an initial read mapping to the reference sequence. Their effectiveness is limited by the presence of gaps, potential misassemblies, regions of duplicates with a high-sequence similarity and regions of high-sequence divergence in the reference. Also, mapping-based approaches are less sensitive to large INDELs and complex variations and provide little phase information in personal genomes. A few de novo assemblers have been developed to identify variants through direct variant calling from the assembly graph, micro-assembly and whole-genome assembly, but mainly for whole-genome sequencing (WGS) data. We developed SGVar, a de novo assembly workflow for haplotype-based variant discovery from whole-exome sequencing (WES) data. Using simulated human exome data, we compared SGVar with five variation-aware de novo assemblers and with BWA-MEM together with three haplotype- or local de novo assembly-based callers. SGVar outperforms the other assemblers in sensitivity and tolerance of sequencing errors. We recapitulated the findings on whole-genome and exome data from a Utah residents with Northern and Western European ancestry (CEU) trio, showing that SGVar had high sensitivity both in the highly divergent human leukocyte antigen (HLA) region and in non-HLA regions of chromosome 6. In particular, SGVar is robust to sequencing error, k-mer selection, divergence level and coverage depth. Unlike mapping-based approaches, SGVar is capable of resolving long-range phase and identifying large INDELs from WES, more prominently from WGS. We conclude that SGVar represents an ideal platform for WES-based variant discovery in highly divergent regions and across the whole genome.
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Affiliation(s)
- Shulan Tian
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Huihuang Yan
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine Bioinformatics Program, Mayo Clinic, USA
| | - Michael Kalmbach
- Division of Information Management and Analytics, Department of Information Technology, Mayo Clinic, USA
| | - Susan L Slager
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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30
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Chen A, Tiosano D, Guran T, Baris HN, Bayram Y, Mory A, Shapiro-Kulnane L, Hodges CA, Akdemir ZC, Turan S, Jhangiani SN, van den Akker F, Hoppel CL, Salz HK, Lupski JR, Buchner DA. Mutations in the mitochondrial ribosomal protein MRPS22 lead to primary ovarian insufficiency. Hum Mol Genet 2019; 27:1913-1926. [PMID: 29566152 DOI: 10.1093/hmg/ddy098] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/14/2018] [Indexed: 11/12/2022] Open
Abstract
Primary ovarian insufficiency (POI) is characterized by amenorrhea and loss or dysfunction of ovarian follicles prior to the age of 40. POI has been associated with autosomal recessive mutations in genes involving hormonal signaling and folliculogenesis, however, the genetic etiology of POI most often remains unknown. Here we report MRPS22 homozygous missense variants c.404G>A (p.R135Q) and c.605G>A (p.R202H) identified in four females from two independent consanguineous families as a novel genetic cause of POI in adolescents. Both missense mutations identified in MRPS22 are rare, occurred in highly evolutionarily conserved residues, and are predicted to be deleterious to protein function. In contrast to prior reports of mutations in MRPS22 associated with severe mitochondrial disease, the POI phenotype is far less severe. Consistent with this genotype-phenotype correlation, mitochondrial defects in oxidative phosphorylation or rRNA levels were not detected in fibroblasts derived from the POI patients, suggesting a non-bioenergetic or tissue-specific mitochondrial defect. Furthermore, we demonstrate in a Drosophila model that mRpS22 deficiency specifically in somatic cells of the ovary had no effect on fertility, whereas flies with mRpS22 deficiency specifically in germ cells were infertile and agametic, demonstrating a cell autonomous requirement for mRpS22 in germ cell development. These findings collectively identify that MRPS22, a component of the small mitochondrial ribosome subunit, is critical for ovarian development and may therefore provide insight into the pathophysiology and treatment of ovarian dysfunction.
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Affiliation(s)
- Anlu Chen
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Dov Tiosano
- Division of Pediatric Endocrinology, Ruth Children's Hospital, Rambam Medical Center, Haifa 30196, Israel.,Rappaport Family Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 30196, Israel
| | - Tulay Guran
- Department of Pediatric Endocrinology and Diabetes, Marmara University Hospital, Istanbul 34899, Turkey
| | - Hagit N Baris
- Rappaport Family Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 30196, Israel.,The Genetics Institute, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adi Mory
- The Genetics Institute, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Laura Shapiro-Kulnane
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Craig A Hodges
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Serap Turan
- Department of Pediatric Endocrinology and Diabetes, Marmara University Hospital, Istanbul 34899, Turkey
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Charles L Hoppel
- Department of Pharmacology, Center for Mitochondrial Diseases, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Helen K Salz
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, 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.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Hospital, Houston, TX 77030, USA
| | - David A Buchner
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.,Research Institute for Children's Health, Case Western Reserve University, Cleveland, OH 44106, USA
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31
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Karolak JA, Vincent M, Deutsch G, Gambin T, Cogné B, Pichon O, Vetrini F, Mefford HC, Dines JN, Golden-Grant K, Dipple K, Freed AS, Leppig KA, Dishop M, Mowat D, Bennetts B, Gifford AJ, Weber MA, Lee AF, Boerkoel CF, Bartell TM, Ward-Melver C, Besnard T, Petit F, Bache I, Tümer Z, Denis-Musquer M, Joubert M, Martinovic J, Bénéteau C, Molin A, Carles D, André G, Bieth E, Chassaing N, Devisme L, Chalabreysse L, Pasquier L, Secq V, Don M, Orsaria M, Missirian C, Mortreux J, Sanlaville D, Pons L, Küry S, Bézieau S, Liet JM, Joram N, Bihouée T, Scott DA, Brown CW, Scaglia F, Tsai ACH, Grange DK, Phillips JA, Pfotenhauer JP, Jhangiani SN, Gonzaga-Jauregui CG, Chung WK, Schauer GM, Lipson MH, Mercer CL, van Haeringen A, Liu Q, Popek E, Coban Akdemir ZH, Lupski JR, Szafranski P, Isidor B, Le Caignec C, Stankiewicz P. Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway. Am J Hum Genet 2019; 104:213-228. [PMID: 30639323 DOI: 10.1016/j.ajhg.2018.12.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/13/2018] [Indexed: 12/24/2022] Open
Abstract
Primary defects in lung branching morphogenesis, resulting in neonatal lethal pulmonary hypoplasias, are incompletely understood. To elucidate the pathogenetics of human lung development, we studied a unique collection of samples obtained from deceased individuals with clinically and histopathologically diagnosed interstitial neonatal lung disorders: acinar dysplasia (n = 14), congenital alveolar dysplasia (n = 2), and other lethal lung hypoplasias (n = 10). We identified rare heterozygous copy-number variant deletions or single-nucleotide variants (SNVs) involving TBX4 (n = 8 and n = 2, respectively) or FGF10 (n = 2 and n = 2, respectively) in 16/26 (61%) individuals. In addition to TBX4, the overlapping ∼2 Mb recurrent and nonrecurrent deletions at 17q23.1q23.2 identified in seven individuals with lung hypoplasia also remove a lung-specific enhancer region. Individuals with coding variants involving either TBX4 or FGF10 also harbored at least one non-coding SNV in the predicted lung-specific enhancer region, which was absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. The occurrence of rare coding variants involving TBX4 or FGF10 with the putative hypomorphic non-coding SNVs implies a complex compound inheritance of these pulmonary hypoplasias. Moreover, they support the importance of TBX4-FGF10-FGFR2 epithelial-mesenchymal signaling in human lung organogenesis and help to explain the histopathological continuum observed in these rare lethal developmental disorders of the lung.
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MESH Headings
- DNA Copy Number Variations/genetics
- Female
- Fibroblast Growth Factor 10/genetics
- Fibroblast Growth Factor 10/metabolism
- Gene Expression Regulation
- Gestational Age
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/genetics
- Infant, Newborn, Diseases/metabolism
- Infant, Newborn, Diseases/mortality
- Infant, Newborn, Diseases/pathology
- Lung/embryology
- Lung/growth & development
- Lung Diseases/genetics
- Lung Diseases/metabolism
- Lung Diseases/mortality
- Lung Diseases/pathology
- Male
- Maternal Inheritance
- Organogenesis
- Paternal Inheritance
- Pedigree
- Polymorphism, Single Nucleotide/genetics
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Signal Transduction/genetics
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | - Marie Vincent
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Gail Deutsch
- Department of Pathology, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Tomasz Gambin
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland; Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Olivier Pichon
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | | | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer N Dines
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Katie Golden-Grant
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Amanda S Freed
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA
| | - Kathleen A Leppig
- Genetic Services Kaiser Permanente of Washington, Seattle, WA 98112, USA
| | - Megan Dishop
- Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick Sydney, NSW 2031 Australia; School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Bruce Bennetts
- Discipline of Child & Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; Molecular Genetics Department, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Andrew J Gifford
- School of Women's and Children's Health, The University of New South Wales, Sydney, NSW 2052, Australia; Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Martin A Weber
- Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia; School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Cornelius F Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Tina M Bartell
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | | | - Thomas Besnard
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Florence Petit
- Service de Génétique Clinique, CHU Lille, 59000 Lille, France
| | - Iben Bache
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 N Copenhagen, Denmark; Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Ø Copenhagen, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Copenhagen, Denmark; Deparment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N, Copenhagen, Denmark
| | | | | | - Jelena Martinovic
- Unit of Fetal Pathology, AP-HP, Antoine Beclere Hospital, 75000 Paris, France
| | - Claire Bénéteau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Arnaud Molin
- Service de Génétique Médicale, CHU Caen, 14000 Caen, France
| | - Dominique Carles
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Gwenaelle André
- Service d'anatomo-pathologie, CHU Bordeaux, 33000 Bordeaux, France
| | - Eric Bieth
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | - Nicolas Chassaing
- Service de génétique médicale, CHU Toulouse, France and UDEAR, UMR 1056 Inserm - Université de Toulouse, 31000 Toulouse, France
| | | | | | | | - Véronique Secq
- Aix Marseille Univ, APHM, Hôpital Nord, Service d'anatomo-pathologie, 13000 Marseille, France
| | - Massimiliano Don
- Sant'Antonio General Hospital, Pediatric Care Unit, San Daniele del Friuli, 33100 Udine, Italy
| | - Maria Orsaria
- Department of Medical and Biological Sciences, Pathology Unit, University of Udine, Udine, Italy
| | - Chantal Missirian
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Jérémie Mortreux
- Aix Marseille Univ, APHM, INSERM, MMG, Marseille, Timone Hospital, 13000 Marseille, France
| | - Damien Sanlaville
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Linda Pons
- Hospices Civils de Lyon, GHE, Genetics department, and Lyon University, 69000 Lyon, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | - Jean-Michel Liet
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | - Nicolas Joram
- Service de réanimation pédiatrique, CHU Nantes, 44000 Nantes, France
| | | | - Daryl A Scott
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chester W Brown
- Department of Pediatrics, Genetics Division, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fernando Scaglia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, ShaTin, New Territories, Hong Kong SAR
| | - Anne Chun-Hui Tsai
- Department of Pediatrics, The Children's Hospital, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dorothy K Grange
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO 63110, USA
| | - John A Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jean P Pfotenhauer
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Galen M Schauer
- Department of Pathology, Kaiser Permanente Oakland Medical Center, Oakland, CA 94611, USA
| | - Mark H Lipson
- Department of Genetics, Kaiser Permanente Sacramento Medical Center, Sacramento, CA 95815, USA
| | - Catherine L Mercer
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton SO16 5YA, UK
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Qian Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, 44000 Nantes, France
| | | | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Institute of Mother and Child, 01-211 Warsaw, Poland.
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32
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Liu Y, Lusk CM, Cho MH, Silverman EK, Qiao D, Zhang R, Scheurer ME, Kheradmand F, Wheeler DA, Tsavachidis S, Armstrong G, Zhu D, Wistuba II, Chow CWB, Behrens C, Pikielny CW, Neslund-Dudas C, Pinney SM, Anderson M, Kupert E, Bailey-Wilson J, Gaba C, Mandal D, You M, de Andrade M, Yang P, Field JK, Liloglou T, Davies M, Lissowska J, Swiatkowska B, Zaridze D, Mukeriya A, Janout V, Holcatova I, Mates D, Milosavljevic S, Scelo G, Brennan P, McKay J, Liu G, Hung RJ, Christiani DC, Schwartz AG, Amos CI, Spitz MR. Rare Variants in Known Susceptibility Loci and Their Contribution to Risk of Lung Cancer. J Thorac Oncol 2018; 13:1483-1495. [PMID: 29981437 PMCID: PMC6366341 DOI: 10.1016/j.jtho.2018.06.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/06/2018] [Accepted: 06/17/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Genome-wide association studies are widely used to map genomic regions contributing to lung cancer (LC) susceptibility, but they typically do not identify the precise disease-causing genes/variants. To unveil the inherited genetic variants that cause LC, we performed focused exome-sequencing analyses on genes located in 121 genome-wide association study-identified loci previously implicated in the risk of LC, chronic obstructive pulmonary disease, pulmonary function level, and smoking behavior. METHODS Germline DNA from 260 case patients with LC and 318 controls were sequenced by utilizing VCRome 2.1 exome capture. Filtering was based on enrichment of rare and potential deleterious variants in cases (risk alleles) or controls (protective alleles). Allelic association analyses of single-variant and gene-based burden tests of multiple variants were performed. Promising candidates were tested in two independent validation studies with a total of 1773 case patients and 1123 controls. RESULTS We identified 48 rare variants with deleterious effects in the discovery analysis and validated 12 of the 43 candidates that were covered in the validation platforms. The top validated candidates included one well-established truncating variant, namely, BRCA2, DNA repair associated gene (BRCA2) K3326X (OR = 2.36, 95% confidence interval [CI]: 1.38-3.99), and three newly identified variations, namely, lymphotoxin beta gene (LTB) p.Leu87Phe (OR = 7.52, 95% CI: 1.01-16.56), prolyl 3-hydroxylase 2 gene (P3H2) p.Gln185His (OR = 5.39, 95% CI: 0.75-15.43), and dishevelled associated activator of morphogenesis 2 gene (DAAM2) p.Asp762Gly (OR = 0.25, 95% CI: 0.10-0.79). Burden tests revealed strong associations between zinc finger protein 93 gene (ZNF93), DAAM2, bromodomain containing 9 gene (BRD9), and the gene LTB and LC susceptibility. CONCLUSION Our results extend the catalogue of regions associated with LC and highlight the importance of germline rare coding variants in LC susceptibility.
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Affiliation(s)
- Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M. Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ruyang Zhang
- Harvard University School of Public Health, Boston, MA 02115, USA
| | - Michael E. Scheurer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Farrah Kheradmand
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Michael E. DeBakey Veterans Affairs Medical Center; Houston, TX 77030, USA
| | - David A. Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequence Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Georgina Armstrong
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dakai Zhu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chi-Wan B. Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Claudio W. Pikielny
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03755, USA
| | | | - Susan M. Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Marshall Anderson
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Elena Kupert
- University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | | | - Colette Gaba
- The University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Ping Yang
- Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - John K. Field
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Triantafillos Liloglou
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Michael Davies
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Jolanta Lissowska
- The M. Sklodowska-Curie Institute of Oncology Center, Warsaw 02781, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz 91348, Poland
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow 115478, Russian Federation
| | - Anush Mukeriya
- Russian N.N. Blokhin Cancer Research Centre, Moscow 115478, Russian Federation
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc 77515, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague 12800, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest 050463, Romania
| | - Sasa Milosavljevic
- International Organization for Cancer Prevention and Research (IOCPR), Belgrade, Serbia
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, M5G 2M9, Canada
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5 Canada
| | | | | | - Ann G. Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Christopher I Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret R. Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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33
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Lumaka A, Race V, Peeters H, Corveleyn A, Coban-Akdemir Z, Jhangiani SN, Song X, Mubungu G, Posey J, Lupski JR, Vermeesch JR, Lukusa P, Devriendt K. A comprehensive clinical and genetic study in 127 patients with ID in Kinshasa, DR Congo. Am J Med Genet A 2018; 176:1897-1909. [PMID: 30088852 DOI: 10.1002/ajmg.a.40382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 06/06/2018] [Indexed: 12/21/2022]
Abstract
Pathogenic variants account for 4 to 41% of patients with intellectual disability (ID) or developmental delay (DD). In Sub-Saharan Africa, the prevalence of ID is thought to be higher, but data in Central Africa are limited to some case reports. In addition, clinical descriptions of some syndromes are not available for this population. This study aimed at providing an estimate for the fraction of ID/DD for which an underlying etiological genetic cause may be elucidated and provide insights into their clinical presentation in special institutions in a Central African country. A total of 127 patients (33 females and 94 males, mean age 10.03 ± 4.68 years), were recruited from six institutions across Kinshasa. A clinical diagnosis was achieved in 44 but molecular confirmation was achieved in 21 of the 22 patients with expected genetic defect (95% clinical sensitivity). Identified diseases included Down syndrome (15%), submicroscopic copy number variants (9%), aminoacylase deficiency (0.8%), Partington syndrome in one patient (0.8%) and his similarly affected brother, X-linked syndromic Mental Retardation type 33 (0.8%), and two conditions without clear underlying molecular genetic etiologies (Oculo-Auriculo-Vertebral and Amniotic Bands Sequence). We have shown that genetic etiologies, similar to those reported in Caucasian subjects, are a common etiologic cause of ID in African patients from Africa. We have confirmed the diagnostic utility of clinical characterization prior to genetic testing. Finally, our clinical descriptions provide insights into the presentation of these genetic diseases in African patients.
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Affiliation(s)
- Aimé Lumaka
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Département des Sciences Biomédicales et Précliniques, GIGA-R, Laboratoire de Génétique Humaine, University of Liège, Liège, Belgium.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo
| | - Valerie Race
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Hilde Peeters
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Anniek Corveleyn
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Gerrye Mubungu
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Department of Pediatrics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Jennifer Posey
- Human Genome Sequencing Center, Baylor College of Medicine, 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.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Genetics Clinic service, Texas Children's Hospital, Houston, Texas
| | - Joris R Vermeesch
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Prosper Lukusa
- Centre for Human Genetics, Faculty of Medicine, University of Kinshasa, Kinshasa, DR, Congo.,Département des Sciences Biomédicales et Précliniques, GIGA-R, Laboratoire de Génétique Humaine, University of Liège, Liège, Belgium.,Institut National de Recherche Biomédicale, Kinshasa, DR, Congo.,Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, University Hospital, University of Leuven, Leuven, Belgium
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34
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Li L, Jiao X, D’Atri I, Ono F, Nelson R, Chan CC, Nakaya N, Ma Z, Ma Y, Cai X, Zhang L, Lin S, Hameed A, Chioza BA, Hardy H, Arno G, Hull S, Khan MI, Fasham J, Harlalka GV, Michaelides M, Moore AT, Coban Akdemir ZH, Jhangiani S, Lupski JR, Cremers FPM, Qamar R, Salman A, Chilton J, Self J, Ayyagari R, Kabir F, Naeem MA, Ali M, Akram J, Sieving PA, Riazuddin S, Baple EL, Riazuddin SA, Crosby AH, Hejtmancik JF. Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa. PLoS Genet 2018; 14:e1007504. [PMID: 30157172 PMCID: PMC6133373 DOI: 10.1371/journal.pgen.1007504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/11/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post fertilization. The depressed electroretinogram (ERG) cone response and cone spectral sensitivity of 5 dpf KO zebrafish and reduced eye size, retinal thickness, and expression of rod and cone opsins could be rescued by injection of wild type CLCC1 mRNA. Clcc1+/- KO mice showed decreased ERGs and photoreceptor number. Together these results strongly suggest that intracellular chloride transport by CLCC1 is a critical process in maintaining retinal integrity, and CLCC1 is crucial for survival and function of retinal cells.
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Affiliation(s)
- Lin Li
- Department of Ophthalmology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ilaria D’Atri
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Fumihito Ono
- Section on Model Synaptic Systems, Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Physiology, Osaka Medical College, Takatsuki, Japan
| | - Ralph Nelson
- Unit on Neural Circuits, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Chao Chan
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Naoki Nakaya
- Section of Molecular Mechanisms of Glaucoma, Laboratory of Molecular and Developmental Biology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Zhiwei Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yan Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaoying Cai
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P.R. China
| | - Longhua Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P.R. China
| | - Siying Lin
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Abdul Hameed
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
| | - Barry A. Chioza
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Holly Hardy
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Gavin Arno
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Sarah Hull
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Muhammad Imran Khan
- Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - James Fasham
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Department of Clinical Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Gaurav V. Harlalka
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Michel Michaelides
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Anthony T. Moore
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
- Ophthalmology Department, UCSF School of Medicine, San Francisco, California, United States of America
| | - Zeynep Hande Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
| | - Frans P. M. Cremers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Raheel Qamar
- Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Ahmed Salman
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - John Chilton
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Jay Self
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Firoz Kabir
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ali
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Javed Akram
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
- National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Paul A. Sieving
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
- National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Emma L. Baple
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Department of Clinical Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - S. Amer Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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35
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Chinn IK, Eckstein OS, Peckham-Gregory EC, Goldberg BR, Forbes LR, Nicholas SK, Mace EM, Vogel TP, Abhyankar HA, Diaz MI, Heslop HE, Krance RA, Martinez CA, Nguyen TC, Bashir DA, Goldman JR, Stray-Pedersen A, Pedroza LA, Poli MC, Aldave-Becerra JC, McGhee SA, Al-Herz W, Chamdin A, Coban-Akdemir ZH, Jhangiani SN, Muzny DM, Cao TN, Hong DN, Gibbs RA, Lupski JR, Orange JS, McClain KL, Allen CE. Genetic and mechanistic diversity in pediatric hemophagocytic lymphohistiocytosis. Blood 2018; 132:89-100. [PMID: 29632024 PMCID: PMC6034641 DOI: 10.1182/blood-2017-11-814244] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/03/2018] [Indexed: 11/20/2022] Open
Abstract
The HLH-2004 criteria are used to diagnose hemophagocytic lymphohistiocytosis (HLH), yet concern exists for their misapplication, resulting in suboptimal treatment of some patients. We sought to define the genomic spectrum and associated outcomes of a diverse cohort of children who met the HLH-2004 criteria. Genetic testing was performed clinically or through research-based whole-exome sequencing. Clinical metrics were analyzed with respect to genomic results. Of 122 subjects enrolled over the course of 17 years, 101 subjects received genetic testing. Biallelic familial HLH (fHLH) gene defects were identified in only 19 (19%) and correlated with presentation at younger than 1 year of age (P < .0001). Digenic fHLH variants were observed but lacked statistical support for disease association. In 28 (58%) of 48 subjects, research whole-exome sequencing analyses successfully identified likely molecular explanations, including underlying primary immunodeficiency diseases, dysregulated immune activation and proliferation disorders, and potentially novel genetic conditions. Two-thirds of patients identified by the HLH-2004 criteria had underlying etiologies for HLH, including genetic defects, autoimmunity, and malignancy. Overall survival was 45%, and increased mortality correlated with HLH triggered by infection or malignancy (P < .05). Differences in survival did not correlate with genetic profile or extent of therapy. HLH should be conceptualized as a phenotype of critical illness characterized by toxic activation of immune cells from different underlying mechanisms. In most patients with HLH, targeted sequencing of fHLH genes remains insufficient for identifying pathogenic mechanisms. Whole-exome sequencing, however, may identify specific therapeutic opportunities and affect hematopoietic stem cell transplantation options for these patients.
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Olive S Eckstein
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
| | - Erin C Peckham-Gregory
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
| | - Baruch R Goldberg
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Lisa R Forbes
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Sarah K Nicholas
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Emily M Mace
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Tiphanie P Vogel
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Harshal A Abhyankar
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
| | - Maria I Diaz
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
| | - Helen E Heslop
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX
| | - Robert A Krance
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX
| | - Caridad A Martinez
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX
| | - Trung C Nguyen
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Critical Care Medicine, Texas Children's Hospital, Houston, TX
- Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veteran Affairs Medical Center, Houston, TX
| | - Dalia A Bashir
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Critical Care Medicine, Texas Children's Hospital, Houston, TX
- Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey Veteran Affairs Medical Center, Houston, TX
| | - Jordana R Goldman
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Critical Care Medicine, Texas Children's Hospital, Houston, TX
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Baylor-Hopkins Center for Mendelian Genomics, Houston, TX
| | - Luis A Pedroza
- Universidad San Francisco de Quito, Colegio de Ciencias de la Salud-Hospital de los Valles, Quito, Ecuador
| | - M Cecilia Poli
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Universidad del Desarrollo, Clinica Alemana de Santiago, Santiago, Chile
| | - Juan C Aldave-Becerra
- Division of Allergy and Immunology, Hospital Nacional Edgardo Rebagliati Martins, Lima, Peru
| | - Sean A McGhee
- Division of Immunology and Allergy, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA
| | - Waleed Al-Herz
- Department of Pediatrics, Kuwait University, Kuwait City, Kuwait
| | - Aghiad Chamdin
- Department of Pediatrics and Human Development, Michigan State University, Lansing, MI; and
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Houston, TX
- Department of Molecular and Human Genetics and
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Donna M Muzny
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Tram N Cao
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Diana N Hong
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics, Houston, TX
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Baylor-Hopkins Center for Mendelian Genomics, Houston, TX
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Jordan S Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Immunology/Allergy/Rheumatology and
| | - Kenneth L McClain
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
| | - Carl E Allen
- Department of Pediatrics, Baylor College of Medicine, Houston, TX
- Department of Pediatrics, Texas Children's Hospital, Houston, TX
- Division of Pediatric Hematology/Oncology, Texas Children's Hospital Cancer Center, Houston, TX
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Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome. Am J Hum Genet 2018. [PMID: 29805043 DOI: 10.1016/j.ajhg.2018.04.010)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The proteasome processes proteins to facilitate immune recognition and host defense. When inherently defective, it can lead to aberrant immunity resulting in a dysregulated response that can cause autoimmunity and/or autoinflammation. Biallelic or digenic loss-of-function variants in some of the proteasome subunits have been described as causing a primary immunodeficiency disease that manifests as a severe dysregulatory syndrome: chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE). Proteasome maturation protein (POMP) is a chaperone for proteasome assembly and is critical for the incorporation of catalytic subunits into the proteasome. Here, we characterize and describe POMP-related autoinflammation and immune dysregulation disease (PRAID) discovered in two unrelated individuals with a unique constellation of early-onset combined immunodeficiency, inflammatory neutrophilic dermatosis, and autoimmunity. We also begin to delineate a complex genetic mechanism whereby de novo heterozygous frameshift variants in the penultimate exon of POMP escape nonsense-mediated mRNA decay (NMD) and result in a truncated protein that perturbs proteasome assembly by a dominant-negative mechanism. To our knowledge, this mechanism has not been reported in any primary immunodeficiencies, autoinflammatory syndromes, or autoimmune diseases. Here, we define a unique hypo- and hyper-immune phenotype and report an immune dysregulation syndrome caused by frameshift mutations that escape NMD.
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37
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Poli MC, Ebstein F, Nicholas SK, de Guzman MM, Forbes LR, Chinn IK, Mace EM, Vogel TP, Carisey AF, Benavides F, Coban-Akdemir ZH, Gibbs RA, Jhangiani SN, Muzny DM, Carvalho CM, Schady DA, Jain M, Rosenfeld JA, Emrick L, Lewis RA, Lee B, Zieba BA, Küry S, Krüger E, Lupski JR, Bostwick BL, Orange JS, Orange JS. Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome. Am J Hum Genet 2018; 102:1126-1142. [PMID: 29805043 DOI: 10.1016/j.ajhg.2018.04.010] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/13/2018] [Indexed: 12/12/2022] Open
Abstract
The proteasome processes proteins to facilitate immune recognition and host defense. When inherently defective, it can lead to aberrant immunity resulting in a dysregulated response that can cause autoimmunity and/or autoinflammation. Biallelic or digenic loss-of-function variants in some of the proteasome subunits have been described as causing a primary immunodeficiency disease that manifests as a severe dysregulatory syndrome: chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE). Proteasome maturation protein (POMP) is a chaperone for proteasome assembly and is critical for the incorporation of catalytic subunits into the proteasome. Here, we characterize and describe POMP-related autoinflammation and immune dysregulation disease (PRAID) discovered in two unrelated individuals with a unique constellation of early-onset combined immunodeficiency, inflammatory neutrophilic dermatosis, and autoimmunity. We also begin to delineate a complex genetic mechanism whereby de novo heterozygous frameshift variants in the penultimate exon of POMP escape nonsense-mediated mRNA decay (NMD) and result in a truncated protein that perturbs proteasome assembly by a dominant-negative mechanism. To our knowledge, this mechanism has not been reported in any primary immunodeficiencies, autoinflammatory syndromes, or autoimmune diseases. Here, we define a unique hypo- and hyper-immune phenotype and report an immune dysregulation syndrome caused by frameshift mutations that escape NMD.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jordan S Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Division of Pediatric Immunology, Allergy, and Rheumatology, Houston, TX 77030, USA.
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38
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Mwesigwa S, Moulds JM, Chen A, Flanagan J, Sheehan VA, George A, Hanchard NA. Whole-exome sequencing of sickle cell disease patients with hyperhemolysis syndrome suggests a role for rare variation in disease predisposition. Transfusion 2018; 58:726-735. [PMID: 29210071 PMCID: PMC5847445 DOI: 10.1111/trf.14431] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Hyperhemolysis syndrome (HHS) is an uncommon, but life-threatening, transfusion-related complication of red blood cell transfusion. HHS has predominantly been described in patients with sickle cell disease (SCD) and is difficult to diagnose and treat. The pathogenesis of HHS, including its occurrence in only a subset of apparently susceptible individuals, is poorly understood. We undertook whole-exome sequencing (WES) of 12 SCD-HHS patients to identify shared genetic variants that might be relevant to the development of HHS. STUDY DESIGN AND METHODS DNA from adults with SCD having at least one previous episode of HHS were subject to WES. High-quality variants were passed through a series of bioinformatics filters to identify variants that were uncommon among African populations represented in public databases. Recurrent, putative loss-of-function variants occurring in biologically plausible genes were prioritized and then genotyped in a larger, ancestry-matched cohort of non-HHS controls. RESULTS A rare, heterozygous stop-gain variant (p.Glu210Ter) in MBL2 was significantly enriched among HHS cases (p = 0.002). This variant is predicted to result in a premature termination codon that escapes nonsense-mediated mRNA decay, potentially leading to a novel phenotype. We also observed a complex insertion-deletion variant in the final exon of KLRC3 that was enriched among cases (p = 0.0019), although neither variant was found among seven pediatric SCD-HHS patients. CONCLUSION Our results suggest a potential role for rare genetic defects in the development of HHS among adult SCD patients. Such enriched variants may ultimately be useful for identifying high-risk individuals and informing therapeutic approaches in HHS.
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Affiliation(s)
- Savannah Mwesigwa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Collaborative African Genomics Network (CAfGEN), Gaborone, Botswana
- Makerere University, Kampala, Uganda
| | - Joann M Moulds
- Scientific Support Services, LifeShare Blood Centers, Shreveport, Louisiana
| | | | - Jonathan Flanagan
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
| | - Vivien A Sheehan
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
| | | | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Collaborative African Genomics Network (CAfGEN), Gaborone, Botswana
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39
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Ruiz-García R, Vargas-Hernández A, Chinn IK, Angelo LS, Cao TN, Coban-Akdemir Z, Jhangiani SN, Meng Q, Forbes LR, Muzny DM, Allende LM, Ehlayel MS, Gibbs RA, Lupski JR, Uzel G, Orange JS, Mace EM. Mutations in PI3K110δ cause impaired natural killer cell function partially rescued by rapamycin treatment. J Allergy Clin Immunol 2018; 142:605-617.e7. [PMID: 29330011 DOI: 10.1016/j.jaci.2017.11.042] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 10/20/2017] [Accepted: 11/01/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Heterozygous gain-of-function mutations in PI3K110δ lead to lymphadenopathy, lymphoid hyperplasia, EBV and cytomegalovirus viremia, and sinopulmonary infections. OBJECTIVE The known role of natural killer (NK) cell function in the control of EBV and cytomegalovirus prompted us to investigate the functional and phenotypic effects of PI3K110δ mutations on NK cell subsets and cytotoxic function. METHODS Mutations in patients were identified by using whole-exome or targeted sequencing. We performed NK cell phenotyping and functional analysis of patients' cells using flow cytometry, standard Cr51 cytotoxicity assays, and quantitative confocal microscopy. RESULTS PI3K110δ mutations led to an altered NK cell developmental phenotype and cytotoxic dysfunction. Impaired NK cell cytotoxicity was due to decreased conjugate formation with susceptible target cells and abrogated activation of cell machinery required for target cell killing. These defects were restored partially after initiation of treatment with rapamycin in 3 patients. CONCLUSION We describe novel NK cell functional deficiency caused by PI3K110δ mutation, which is a likely contributor to the severe viremia observed in these patients. Rapamycin treatment partially restores NK cell function, providing a further rationale for its use in patients with this disease.
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Affiliation(s)
- Raquel Ruiz-García
- Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Servicio de Immunología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Alexander Vargas-Hernández
- Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Ivan K Chinn
- Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Laura S Angelo
- Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Tram N Cao
- Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Qingchang Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Lisa R Forbes
- Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Luis M Allende
- Servicio de Immunología, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Mohammed S Ehlayel
- Department of Pediatrics, Section of Pediatric Allergy and Immunology, Hamad Medical Corporation, Doha, and Department of Pediatrics, Weill Cornell Medical College, Ar-Rayyan, Qatar
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Gulbu Uzel
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jordan S Orange
- Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Emily M Mace
- Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, Houston, Tex.
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40
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Hampton OA, English AC, Wang M, Salerno WJ, Liu Y, Muzny DM, Han Y, Wheeler DA, Worley KC, Lupski JR, Gibbs RA. SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads. BMC Genomics 2017; 18:691. [PMID: 28984202 PMCID: PMC5629590 DOI: 10.1186/s12864-017-4021-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing. Reliance upon short DNA fragment paired end sequencing has yielded a wealth of single nucleotide variants and internal sequencing read insertions-deletions, at the cost of limited SV detection. Multi-kilobase DNA fragment mate pair sequencing has supplemented the void in SV detection, but introduced new analytic challenges requiring SV detection tools specifically designed for mate pair sequencing data. Here, we introduce SVachra – Structural Variation Assessment of CHRomosomal Aberrations, a breakpoint calling program that identifies large insertions-deletions, inversions, inter- and intra-chromosomal translocations utilizing both inward and outward facing read types generated by mate pair sequencing.
Results We demonstrate SVachra’s utility by executing the program on large-insert (Illumina Nextera) mate pair sequencing data from the personal genome of a single subject (HS1011). An additional data set of long-read (Pacific BioSciences RSII) was also generated to validate SV calls from SVachra and other comparison SV calling programs. SVachra exhibited the highest validation rate and reported the widest distribution of SV types and size ranges when compared to other SV callers. Conclusions SVachra is a highly specific breakpoint calling program that exhibits a more unbiased SV detection methodology than other callers. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4021-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oliver A Hampton
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Adam C English
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Mark Wang
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - William J Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Texas Children's Hospital, 6621 Fanin Street, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
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41
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Gambin T, Akdemir ZC, Yuan B, Gu S, Chiang T, Carvalho CMB, Shaw C, Jhangiani S, Boone PM, Eldomery MK, Karaca E, Bayram Y, Stray-Pedersen A, Muzny D, Charng WL, Bahrambeigi V, Belmont JW, Boerwinkle E, Beaudet AL, Gibbs RA, Lupski JR. Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort. Nucleic Acids Res 2017; 45:1633-1648. [PMID: 27980096 PMCID: PMC5389578 DOI: 10.1093/nar/gkw1237] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/29/2016] [Indexed: 11/14/2022] Open
Abstract
We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor–Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17–50% of pathogenic CNVs in different disease cohorts where 7.1–11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665 Warsaw, Poland
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini 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
| | - Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division for Pediatric and Adolescent Medicine, Oslo University Hospital, N-0424 Oslo, Norway
| | - Donna 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
| | - Wu-Lin Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vahid Bahrambeigi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Arthur L Beaudet
- 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.,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Hospital, Houston, TX 77030, USA
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42
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Gadd S, Huff V, Walz AL, Ooms AH, Armstrong AE, Gerhard DS, Smith MA, Guidry Auvil JM, Meerzaman D, Chen QR, Hsu CH, Yan C, Nguyen C, Hu Y, Hermida LC, Davidsen T, Gesuwan P, Ma Y, Zong Z, Mungall AJ, Moore RA, Marra MA, Dome JS, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Ross N, Gastier-Foster JM, Arold ST, Perlman EJ. A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nat Genet 2017; 49:1487-1494. [PMID: 28825729 PMCID: PMC5712232 DOI: 10.1038/ng.3940] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 07/28/2017] [Indexed: 12/12/2022]
Abstract
We performed genome-wide sequencing and analyzed mRNA and miRNA expression, DNA copy number, and DNA methylation in 117 Wilms tumors, followed by targeted sequencing of 651 Wilms tumors. In addition to genes previously implicated in Wilms tumors (WT1, CTNNB1, AMER1, DROSHA, DGCR8, XPO5, DICER1, SIX1, SIX2, MLLT1, MYCN, and TP53), we identified mutations in genes not previously recognized as recurrently involved in Wilms tumors, the most frequent being BCOR, BCORL1, NONO, MAX, COL6A3, ASXL1, MAP3K4, and ARID1A. DNA copy number changes resulted in recurrent 1q gain, MYCN amplification, LIN28B gain, and MIRLET7A loss. Unexpected germline variants involved PALB2 and CHEK2. Integrated analyses support two major classes of genetic changes that preserve the progenitor state and/or interrupt normal development.
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Affiliation(s)
- Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, 60611, USA
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Amy L. Walz
- Division of Hematology-Oncology and Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - Ariadne H.A.G. Ooms
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, 60611, USA
- Department of Pathology, Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Amy E. Armstrong
- Division of Hematology-Oncology and Transplantation, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Jaime M. Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Qing-Rong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Chih Hao Hsu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Cu Nguyen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Ying Hu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Leandro C. Hermida
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Tanja Davidsen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, V5Z 4S6, Canada
| | - Zusheng Zong
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, V5Z 4S6, Canada
| | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, V5Z 4S6, Canada
| | - Richard A. Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, V5Z 4S6, Canada
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency (BCCA), Vancouver, British Columbia, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Jeffrey S. Dome
- Division of Pediatric Hematology/Oncology, Children's National Medical Center, Washington, DC, 20010, USA
| | - Charles G. Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - David A. Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Oliver A. Hampton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Nicole Ross
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, 43205, USA
| | - Julie M. Gastier-Foster
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, 43205, USA
| | - Stefan T. Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Elizabeth J. Perlman
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, Illinois, 60611, USA
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43
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Vogelaar IP, van der Post RS, van Krieken JHJ, Spruijt L, van Zelst-Stams WA, Kets CM, Lubinski J, Jakubowska A, Teodorczyk U, Aalfs CM, van Hest LP, Pinheiro H, Oliveira C, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, de Ligt J, Vissers LELM, Hoischen A, Gilissen C, van de Vorst M, Goeman JJ, Schackert HK, Ranzani GN, Molinaro V, Gómez García EB, Hes FJ, Holinski-Feder E, Genuardi M, Ausems MGEM, Sijmons RH, Wagner A, van der Kolk LE, Bjørnevoll I, Høberg-Vetti H, van Kessel AG, Kuiper RP, Ligtenberg MJL, Hoogerbrugge N. Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing. Eur J Hum Genet 2017; 25:1246-1252. [PMID: 28875981 PMCID: PMC5643972 DOI: 10.1038/ejhg.2017.138] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 07/07/2017] [Accepted: 07/18/2017] [Indexed: 12/13/2022] Open
Abstract
Recognition of individuals with a genetic predisposition to gastric cancer (GC) enables preventive measures. However, the underlying cause of genetic susceptibility to gastric cancer remains largely unexplained. We performed germline whole-exome sequencing on leukocyte DNA of 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type GC to identify novel GC-predisposing candidate genes. As young age at diagnosis and familial clustering are hallmarks of genetic tumor susceptibility, we selected patients that were diagnosed below the age of 35, patients from families with two cases of GC at or below age 60 and patients from families with three GC cases at or below age 70. All included individuals were tested negative for germline CDH1 mutations before or during the study. Variants that were possibly deleterious according to in silico predictions were filtered using several independent approaches that were based on gene function and gene mutation burden in controls. Despite a rigorous search, no obvious candidate GC predisposition genes were identified. This negative result stresses the importance of future research studies in large, homogeneous cohorts.
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Affiliation(s)
- Ingrid P Vogelaar
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - J Han Jm van Krieken
- Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Liesbeth Spruijt
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | - C Marleen Kets
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Urszula Teodorczyk
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Cora M Aalfs
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Liselotte P van Hest
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Hugo Pinheiro
- Expression Regulation in Cancer Group, Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Carla Oliveira
- Expression Regulation in Cancer Group, Instituto de Investigação e Inovação em Saúde, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Department of Pathology and Oncology, Faculty of Medicine, University of Porto, Al Prof Hernâni Monteiro, Porto, Portugal
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Joep de Ligt
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Jelle J Goeman
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Valeria Molinaro
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Encarna B Gómez García
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, München, Germany
| | - Maurizio Genuardi
- Institute of Genomic Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | | | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lizet E van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Inga Bjørnevoll
- Department of Medical Genetics and Pathology, St. Olavs University Hospital, Trondheim, Norway
| | - Hildegunn Høberg-Vetti
- Western Norway Familial Cancer Center, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands.,Department of Pathology, Radboud university medical center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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44
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Bayram Y, White JJ, Elcioglu N, Cho MT, Zadeh N, Gedikbasi A, Palanduz S, Ozturk S, Cefle K, Kasapcopur O, Coban Akdemir Z, Pehlivan D, Begtrup A, Carvalho CM, Paine IS, Mentes A, Bektas-Kayhan K, Karaca E, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Lupski JR. REST Final-Exon-Truncating Mutations Cause Hereditary Gingival Fibromatosis. Am J Hum Genet 2017; 101:149-156. [PMID: 28686854 DOI: 10.1016/j.ajhg.2017.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/13/2017] [Indexed: 02/04/2023] Open
Abstract
Hereditary gingival fibromatosis (HGF) is the most common genetic form of gingival fibromatosis that develops as a slowly progressive, benign, localized or generalized enlargement of keratinized gingiva. HGF is a genetically heterogeneous disorder and can be transmitted either as an autosomal-dominant or autosomal-recessive trait or appear sporadically. To date, four loci (2p22.1, 2p23.3-p22.3, 5q13-q22, and 11p15) have been mapped to autosomes and one gene (SOS1) has been associated with the HGF trait observed to segregate in a dominant inheritance pattern. Here we report 11 individuals with HGF from three unrelated families. Whole-exome sequencing (WES) revealed three different truncating mutations including two frameshifts and one nonsense variant in RE1-silencing transcription factor (REST) in the probands from all families and further genetic and genomic analyses confirmed the WES-identified findings. REST is a transcriptional repressor that is expressed throughout the body; it has different roles in different cellular contexts, such as oncogenic and tumor-suppressor functions and hematopoietic and cardiac differentiation. Here we show the consequences of germline final-exon-truncating mutations in REST for organismal development and the association with the HGF phenotype.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
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45
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Chinn IK, Sanders RP, Stray-Pedersen A, Coban-Akdemir ZH, Kim VHD, Dadi H, Roifman CM, Quigg T, Lupski JR, Orange JS, Hanson IC. Novel Combined Immune Deficiency and Radiation Sensitivity Blended Phenotype in an Adult with Biallelic Variations in ZAP70 and RNF168. Front Immunol 2017; 8:576. [PMID: 28603521 PMCID: PMC5445153 DOI: 10.3389/fimmu.2017.00576] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/01/2017] [Indexed: 12/11/2022] Open
Abstract
With the advent of high-throughput genomic sequencing techniques, novel genetic etiologies are being uncovered for previously unexplained Mendelian phenotypes, and the underlying genetic architecture of disease is being unraveled. Although most of these “mendelizing” disease traits represent phenotypes caused by single-gene defects, a percentage of patients have blended phenotypes caused by pathogenic variants in multiple genes. We describe an adult patient with susceptibility to bacterial, herpesviral, and fungal infections. Immunologic defects included CD8+ T cell lymphopenia, decreased T cell proliferative responses to mitogens, hypogammaglobulinemia, and radiation sensitivity. Whole-exome sequencing revealed compound heterozygous variants in ZAP70. Biallelic mutations in ZAP70 are known to produce a spectrum of immune deficiency that includes the T cell abnormalities observed in this patient. Analyses for variants in genes associated with radiation sensitivity identified the presence of a homozygous RNF168 variant of unknown significance. RNF168 deficiency causes radiosensitivity, immunodeficiency, dysmorphic features, and learning difficulties syndrome and may account for the radiation sensitivity. Thus, the patient was found to have a novel blended phenotype associated with multilocus genomic variation: i.e., separate and distinct genetic defects. These findings further illustrate the clinical utility of applying genomic testing in patients with primary immunodeficiency diseases.
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX, USA.,Center for Human Immunobiology, Texas Children's Hospital, Houston, TX, USA
| | - Robert P Sanders
- Texas Transplant Institute, Methodist Hospital, San Antonio, TX, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Vy Hong-Diep Kim
- Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Harjit Dadi
- Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,Canadian Centre for Primary Immunodeficiency, The Jeffrey Model Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Chaim M Roifman
- Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,Canadian Centre for Primary Immunodeficiency, The Jeffrey Model Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Troy Quigg
- Texas Transplant Institute, Methodist Hospital, San Antonio, TX, USA
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jordan S Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX, USA.,Center for Human Immunobiology, Texas Children's Hospital, Houston, TX, USA
| | - I Celine Hanson
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX, USA
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46
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Prall TM, Graham ME, Karl JA, Wiseman RW, Ericsen AJ, Raveendran M, Alan Harris R, Muzny DM, Gibbs RA, Rogers J, O'Connor DH. Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics 2017; 69:325-339. [PMID: 28343239 PMCID: PMC5856007 DOI: 10.1007/s00251-017-0977-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/08/2017] [Indexed: 12/25/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS). We also describe a new approach to Macaque Exome Sequencing (MES) and the development of the Rhexome1.0, an adapted target capture reagent that includes macaque-specific capture probe sets. By using sequence reads generated by whole genome sequencing (WGS) and MES to inform primer design, we were able to increase the sensitivity of KIR allele discovery. We demonstrate this increased sensitivity by defining nine novel alleles within a cohort of Mauritian cynomolgus macaques (MCM), a geographically isolated population with restricted KIR genetics that was thought to be completely characterized. Finally, we describe an approach to genotyping KIRs directly from sequence reads generated using WGS/MES reads. The findings presented here expand our understanding of KIR genetics in MCM by associating new genes with all eight KIR haplotypes and demonstrating the existence of at least one KIR3DS gene associated with every haplotype.
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Affiliation(s)
- Trent M Prall
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA
| | - Michael E Graham
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Adam J Ericsen
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA
| | | | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA.
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA.
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47
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Posey JE, Harel T, Liu P, Rosenfeld JA, James RA, Coban Akdemir ZH, Walkiewicz M, Bi W, Xiao R, Ding Y, Xia F, Beaudet AL, Muzny DM, Gibbs RA, Boerwinkle E, Eng CM, Sutton VR, Shaw CA, Plon SE, Yang Y, Lupski JR. Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation. N Engl J Med 2017; 376:21-31. [PMID: 27959697 PMCID: PMC5335876 DOI: 10.1056/nejmoa1516767] [Citation(s) in RCA: 495] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND Whole-exome sequencing can provide insight into the relationship between observed clinical phenotypes and underlying genotypes. METHODS We conducted a retrospective analysis of data from a series of 7374 consecutive unrelated patients who had been referred to a clinical diagnostic laboratory for whole-exome sequencing; our goal was to determine the frequency and clinical characteristics of patients for whom more than one molecular diagnosis was reported. The phenotypic similarity between molecularly diagnosed pairs of diseases was calculated with the use of terms from the Human Phenotype Ontology. RESULTS A molecular diagnosis was rendered for 2076 of 7374 patients (28.2%); among these patients, 101 (4.9%) had diagnoses that involved two or more disease loci. We also analyzed parental samples, when available, and found that de novo variants accounted for 67.8% (61 of 90) of pathogenic variants in autosomal dominant disease genes and 51.7% (15 of 29) of pathogenic variants in X-linked disease genes; both variants were de novo in 44.7% (17 of 38) of patients with two monoallelic variants. Causal copy-number variants were found in 12 patients (11.9%) with multiple diagnoses. Phenotypic similarity scores were significantly lower among patients in whom the phenotype resulted from two distinct mendelian disorders that affected different organ systems (50 patients) than among patients with disorders that had overlapping phenotypic features (30 patients) (median score, 0.21 vs. 0.36; P=1.77×10-7). CONCLUSIONS In our study, we found multiple molecular diagnoses in 4.9% of cases in which whole-exome sequencing was informative. Our results show that structured clinical ontologies can be used to determine the degree of overlap between two mendelian diseases in the same patient; the diseases can be distinct or overlapping. Distinct disease phenotypes affect different organ systems, whereas overlapping disease phenotypes are more likely to be caused by two genes encoding proteins that interact within the same pathway. (Funded by the National Institutes of Health and the Ting Tsung and Wei Fong Chao Foundation.).
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Affiliation(s)
- Jennifer E Posey
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Tamar Harel
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Pengfei Liu
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Jill A Rosenfeld
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Regis A James
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Zeynep H Coban Akdemir
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Magdalena Walkiewicz
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Weimin Bi
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Rui Xiao
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Yan Ding
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Fan Xia
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Arthur L Beaudet
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Donna M Muzny
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Richard A Gibbs
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Eric Boerwinkle
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Christine M Eng
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - V Reid Sutton
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Chad A Shaw
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Sharon E Plon
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - Yaping Yang
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
| | - James R Lupski
- From the Departments of Molecular and Human Genetics (J.E.P., T.H., P.L., J.A.R., Z.H.C.A., M.W., W.B., R.X., F.X., A.L.B., D.M.M., R.A.G., C.M.E., V.R.S., C.A.S., S.E.P., Y.Y., J.R.L.) and Pediatrics (S.E.P., J.R.L.), Baylor Genetics (P.L., M.W., W.B., R.X., Y.D., F.X., R.A.G., C.M.E., Y.Y.), Program in Structural and Computational Biology and Molecular Biophysics (R.A.J.), and Human Genome Sequencing Center (D.M.M., R.A.G., E.B., S.E.P., J.R.L.), Baylor College of Medicine, the Human Genetics Center, University of Texas Health Science Center (E.B.), and the Department of Pediatrics (S.E.P., J.R.L.) and Texas Children's Cancer Center (S.E.P.), Texas Children's Hospital - all in Houston
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Stray-Pedersen A, Sorte HS, Samarakoon P, Gambin T, Chinn IK, Coban Akdemir ZH, Erichsen HC, Forbes LR, Gu S, Yuan B, Jhangiani SN, Muzny DM, Rødningen OK, Sheng Y, Nicholas SK, Noroski LM, Seeborg FO, Davis CM, Canter DL, Mace EM, Vece TJ, Allen CE, Abhyankar HA, Boone PM, Beck CR, Wiszniewski W, Fevang B, Aukrust P, Tjønnfjord GE, Gedde-Dahl T, Hjorth-Hansen H, Dybedal I, Nordøy I, Jørgensen SF, Abrahamsen TG, Øverland T, Bechensteen AG, Skogen V, Osnes LTN, Kulseth MA, Prescott TE, Rustad CF, Heimdal KR, Belmont JW, Rider NL, Chinen J, Cao TN, Smith EA, Caldirola MS, Bezrodnik L, Lugo Reyes SO, Espinosa Rosales FJ, Guerrero-Cursaru ND, Pedroza LA, Poli CM, Franco JL, Trujillo Vargas CM, Aldave Becerra JC, Wright N, Issekutz TB, Issekutz AC, Abbott J, Caldwell JW, Bayer DK, Chan AY, Aiuti A, Cancrini C, Holmberg E, West C, Burstedt M, Karaca E, Yesil G, Artac H, Bayram Y, Atik MM, Eldomery MK, Ehlayel MS, Jolles S, Flatø B, Bertuch AA, Hanson IC, Zhang VW, Wong LJ, Hu J, Walkiewicz M, Yang Y, Eng CM, Boerwinkle E, Gibbs RA, Shearer WT, Lyle R, Orange JS, Lupski JR. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol 2017; 139:232-245. [PMID: 27577878 PMCID: PMC5222743 DOI: 10.1016/j.jaci.2016.05.042] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/10/2016] [Accepted: 05/13/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions. OBJECTIVE We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs. METHODS Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping. RESULTS A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays. CONCLUSION This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.
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Affiliation(s)
- Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Norwegian National Unit for Newborn Screening, Oslo University Hospital, Oslo, Norway; Department of Pediatrics, Oslo University Hospital, Oslo, Norway.
| | - Hanne Sørmo Sorte
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pubudu Samarakoon
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tomasz Gambin
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Ivan K Chinn
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Zeynep H Coban Akdemir
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | | | - Lisa R Forbes
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Shen Gu
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Bo Yuan
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Shalini N Jhangiani
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Donna M Muzny
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Sarah K Nicholas
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Lenora M Noroski
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Filiz O Seeborg
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carla M Davis
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Debra L Canter
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Emily M Mace
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Timothy J Vece
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carl E Allen
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Harshal A Abhyankar
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Philip M Boone
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine R Beck
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Wojciech Wiszniewski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Børre Fevang
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Geir E Tjønnfjord
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Henrik Hjorth-Hansen
- Department of Hematology, St Olavs Hospital, Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Dybedal
- Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Ingvild Nordøy
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Silje F Jørgensen
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Tore G Abrahamsen
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Vegard Skogen
- Department of Infectious Diseases, Medical Clinic, University Hospital of North-Norway, Tromsø, Norway
| | - Liv T N Osnes
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Mari Ann Kulseth
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trine E Prescott
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ketil R Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Nicholas L Rider
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Javier Chinen
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Tram N Cao
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Eric A Smith
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Tex
| | - Maria Soledad Caldirola
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Liliana Bezrodnik
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Saul Oswaldo Lugo Reyes
- Immunodeficiencies Research Unit, National Institute of Pediatrics, Coyoacan, Mexico City, Mexico
| | | | | | | | - Cecilia M Poli
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Hospital Roberto del Rio, Universidad de Chile, Santiago, Chile
| | - Jose L Franco
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Claudia M Trujillo Vargas
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | | | - Nicola Wright
- Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Thomas B Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Andrew C Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Jordan Abbott
- Department of Pediatrics, National Jewish Health, Denver, Colo
| | - Jason W Caldwell
- Section of Pulmonary, Critical Care, Allergic and Immunological Diseases, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston-Salem, NC
| | - Diana K Bayer
- Department of Pediatrics, Division of Pediatric Allergy/Immunology and Pulmonology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Alice Y Chan
- Department of Pediatrics, University of California, San Francisco, Calif
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), and Vita-Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- University Department of Pediatrics, DPUO, Bambino Gesù Children's Hospital, and Tor Vergata University, Rome, Italy
| | - Eva Holmberg
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Christina West
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Magnus Burstedt
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Ender Karaca
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Gözde Yesil
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul, Turkey
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Selcuk University Medical Faculty, Alaeddin Keykubat Kampusu, Konya, Turkey
| | - Yavuz Bayram
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mehmed Musa Atik
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad K Eldomery
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad S Ehlayel
- Department of Pediatrics, Section of Pediatric Allergy and Immunology, Hamad Medical Corporation, Doha, Department of Paediatrics, Weill Cornell Medical College, Ar-Rayyan, Qatar
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Alison A Bertuch
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex
| | - I Celine Hanson
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Victor W Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Eric Boerwinkle
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Human Genetics Center, University of Texas School of Public Health, Houston, Tex
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - William T Shearer
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Jordan S Orange
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex.
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex.
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Mace EM, Bigley V, Gunesch JT, Chinn IK, Angelo LS, Care MA, Maisuria S, Keller MD, Togi S, Watkin LB, LaRosa DF, Jhangiani SN, Muzny DM, Stray-Pedersen A, Coban Akdemir Z, Smith JB, Hernández-Sanabria M, Le DT, Hogg GD, Cao TN, Freud AG, Szymanski EP, Savic S, Collin M, Cant AJ, Gibbs RA, Holland SM, Caligiuri MA, Ozato K, Paust S, Doody GM, Lupski JR, Orange JS. Biallelic mutations in IRF8 impair human NK cell maturation and function. J Clin Invest 2016; 127:306-320. [PMID: 27893462 DOI: 10.1172/jci86276] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 10/18/2016] [Indexed: 12/12/2022] Open
Abstract
Human NK cell deficiencies are rare yet result in severe and often fatal disease, particularly as a result of viral susceptibility. NK cells develop from hematopoietic stem cells, and few monogenic errors that specifically interrupt NK cell development have been reported. Here we have described biallelic mutations in IRF8, which encodes an interferon regulatory factor, as a cause of familial NK cell deficiency that results in fatal and severe viral disease. Compound heterozygous or homozygous mutations in IRF8 in 3 unrelated families resulted in a paucity of mature CD56dim NK cells and an increase in the frequency of the immature CD56bright NK cells, and this impairment in terminal maturation was also observed in Irf8-/-, but not Irf8+/-, mice. We then determined that impaired maturation was NK cell intrinsic, and gene expression analysis of human NK cell developmental subsets showed that multiple genes were dysregulated by IRF8 mutation. The phenotype was accompanied by deficient NK cell function and was stable over time. Together, these data indicate that human NK cells require IRF8 for development and functional maturation and that dysregulation of this function results in severe human disease, thereby emphasizing a critical role for NK cells in human antiviral defense.
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50
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Trujillano D, Bertoli-Avella AM, Kumar Kandaswamy K, Weiss ME, Köster J, Marais A, Paknia O, Schröder R, Garcia-Aznar JM, Werber M, Brandau O, Calvo Del Castillo M, Baldi C, Wessel K, Kishore S, Nahavandi N, Eyaid W, Al Rifai MT, Al-Rumayyan A, Al-Twaijri W, Alothaim A, Alhashem A, Al-Sannaa N, Al-Balwi M, Alfadhel M, Rolfs A, Abou Jamra R. Clinical exome sequencing: results from 2819 samples reflecting 1000 families. Eur J Hum Genet 2016; 25:176-182. [PMID: 27848944 PMCID: PMC5255946 DOI: 10.1038/ejhg.2016.146] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/07/2016] [Accepted: 09/23/2016] [Indexed: 02/01/2023] Open
Abstract
We report our results of 1000 diagnostic WES cases based on 2819 sequenced samples from 54 countries with a wide phenotypic spectrum. Clinical information given by the requesting physicians was translated to HPO terms. WES processes were performed according to standardized settings. We identified the underlying pathogenic or likely pathogenic variants in 307 families (30.7%). In further 253 families (25.3%) a variant of unknown significance, possibly explaining the clinical symptoms of the index patient was identified. WES enabled timely diagnosing of genetic diseases, validation of causality of specific genetic disorders of PTPN23, KCTD3, SCN3A, PPOX, FRMPD4, and SCN1B, and setting dual diagnoses by detecting two causative variants in distinct genes in the same patient. We observed a better diagnostic yield in consanguineous families, in severe and in syndromic phenotypes. Our results suggest that WES has a better yield in patients that present with several symptoms, rather than an isolated abnormality. We also validate the clinical benefit of WES as an effective diagnostic tool, particularly in nonspecific or heterogeneous phenotypes. We recommend WES as a first-line diagnostic in all cases without a clear differential diagnosis, to facilitate personal medical care.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wafaa Eyaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Muhammad Talal Al Rifai
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmed Al-Rumayyan
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Waleed Al-Twaijri
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ali Alothaim
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Department of pathology, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Division of Metabolic and Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Nouriya Al-Sannaa
- Division of Pediatrics, Johns Hopkins Aramco hospital, Dhahran Health Center, Saudi Aramco, Dhahran, Saudi Arabia
| | - Mohammed Al-Balwi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia.,College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Arndt Rolfs
- Centogene AG, Rostock, Germany.,Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
| | - Rami Abou Jamra
- Centogene AG, Rostock, Germany.,Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
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