1
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Stekelenburg C, Blouin JL, Santoni F, Zaghloul N, O'Hare EA, Dusaulcy R, Maechler P, Schwitzgebel VM. Loss of Nexmif results in the expression of phenotypic variability and loss of genomic integrity. Sci Rep 2022; 12:13815. [PMID: 35970867 PMCID: PMC9378738 DOI: 10.1038/s41598-022-17845-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
We identified two NEXMIF variants in two unrelated individuals with non-autoimmune diabetes and autistic traits, and investigated the expression of Nexmif in mouse and human pancreas and its function in pancreatic beta cells in vitro and in vivo. In insulin-secreting INS-1E cells, Nexmif expression increased strongly in response to oxidative stress. CRISPR Cas9-generated Nexmif knockout mice exhibited a reduced number of proliferating beta cells in pancreatic islets. RNA sequencing of pancreatic islets showed that the downregulated genes in Nexmif mutant islets are involved in stress response and the deposition of epigenetic marks. They include H3f3b, encoding histone H3.3, which is associated with the regulation of beta-cell proliferation and maintains genomic integrity by silencing transposable elements, particularly LINE1 elements. LINE1 activity has been associated with autism and neurodevelopmental disorders in which patients share characteristics with NEXMIF patients, and can cause genomic instability and genetic variation through retrotransposition. Nexmif knockout mice exhibited various other phenotypes. Mortality and phenotypic abnormalities increased in each generation in both Nexmif mutant and non-mutant littermates. In Nexmif mutant mice, LINE1 element expression was upregulated in the pancreas, brain, and testis, possibly inducing genomic instability in Nexmif mutant mice and causing phenotypic variability in their progeny.
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Affiliation(s)
- Caroline Stekelenburg
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland.,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Louis Blouin
- Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, 1211, Geneva, Switzerland.,Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Norann Zaghloul
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, USA
| | - Elisabeth A O'Hare
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, USA
| | - Rodolphe Dusaulcy
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland.,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pierre Maechler
- Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Cell Physiology and Metabolism, University of Geneva Medical Center, 1206, Geneva, Switzerland
| | - Valerie M Schwitzgebel
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland. .,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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2
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Biallelic truncation variants in ATP9A are associated with a novel autosomal recessive neurodevelopmental disorder. NPJ Genom Med 2021; 6:94. [PMID: 34764295 PMCID: PMC8586153 DOI: 10.1038/s41525-021-00255-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Intellectual disability (ID) is a highly heterogeneous disorder with hundreds of associated genes. Despite progress in the identification of the genetic causes of ID following the introduction of high-throughput sequencing, about half of affected individuals still remain without a molecular diagnosis. Consanguineous families with affected individuals provide a unique opportunity to identify novel recessive causative genes. In this report, we describe a novel autosomal recessive neurodevelopmental disorder. We identified two consanguineous families with homozygous variants predicted to alter the splicing of ATP9A which encodes a transmembrane lipid flippase of the class II P4-ATPases. The three individuals homozygous for these putatively truncating variants presented with severe ID, motor and speech impairment, and behavioral anomalies. Consistent with a causative role of ATP9A in these patients, a previously described Atp9a−/− mouse model showed behavioral changes.
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3
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Antonarakis SE, Holoubek A, Rapti M, Rademaker J, Meylan J, Iwaszkiewicz J, Zoete V, Wilson C, Taylor J, Ansar M, Borel C, Menzel O, Kuželová K, Santoni FA. Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2. Hum Mol Genet 2021; 31:1-9. [PMID: 33693784 DOI: 10.1093/hmg/ddab026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/11/2021] [Accepted: 01/31/2021] [Indexed: 11/12/2022] Open
Abstract
Knobloch syndrome is an autosomal recessive phenotype mainly characterized by retinal detachment and encephalocele caused by biallelic pathogenic variants in the COL18A1 gene. However, there are patients clinically diagnosed as Knobloch syndrome with unknown molecular etiology not linked to COL18A1. We studied an historical pedigree (published in 1998) designated as KNO2 (Knobloch type 2 syndrome with intellectual disability, autistic behavior, retinal degeneration, encephalocele). Whole exome sequencing of the two affected siblings and the normal parents resulted in the identification of a PAK2 non-synonymous substitution p.(Glu435Lys) as a causative variant. The variant was monoallelic and apparently de novo in both siblings indicating a likely germline mosaicism in one of the parents; the mosaicism however could not be observed after deep sequencing of blood parental DNA. PAK2 encodes a member of a small group of serine/threonine kinases; these P21-activating kinases (PAKs) are essential in signal transduction and cellular regulation (cytoskeletal dynamics, cell motility, death and survival signaling, and cell cycle progression). Structural analysis of the PAK2 p.(Glu435Lys) variant which is located in the kinase domain of the protein predicts a possible compromise in the kinase activity. Functional analysis of the p.(Glu435Lys) PAK2 variant in transfected HEK293T cells results in a partial loss of the kinase activity. PAK2 has been previously suggested as an autism related gene. Our results show that PAK2 induced phenotypic spectrum is broad and not fully understood. We conclude that the KNO2 syndrome in the studied family is dominant and caused by a deleterious variant in the PAK2 gene.
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Affiliation(s)
- Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva 1211, Switzerland
| | - Ales Holoubek
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Melivoia Rapti
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jesse Rademaker
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jenny Meylan
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Department of Fundamental Oncology, Ludwig Institute for Cancer Research, Lausanne University, Epalinges 1066, Switzerland
| | - Callum Wilson
- National Metabolic Service, Starship Children's Hospital, Auckland 1142, New Zealand
| | - Juliet Taylor
- National Metabolic Service, Starship Children's Hospital, Auckland 1142, New Zealand
| | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology, Basel 4031, Switzerland
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland
| | - Olivier Menzel
- Health 2030 Genome Center, Foundation Campus Biotech Geneva Foundation, Geneva 1202, Switzerland
| | - Kateřina Kuželová
- Department of Proteomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Federico A Santoni
- Department of Endocrinology Diabetes and Metabolism, Lausanne University Hospital, Lausanne 1011, Switzerland.,Faculty of Biology and Medicine, University of Lausanne, Lausanne 1011, Switzerland
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4
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Ali OH, Yurchenko AA, Pavlova O, Sartori A, Bomze D, Higgins R, Ring SS, Hartmann F, Bühler D, Fritzsche FR, Jochum W, Navarini AA, Kim A, French LE, Dermitzakis E, Christiano AM, Hohl D, Bickers DR, Nikolaev SI, Flatz L. Genomic profiling of late-onset basal cell carcinomas from two brothers with nevoid basal cell carcinoma syndrome. J Eur Acad Dermatol Venereol 2021; 35:396-402. [PMID: 32564428 PMCID: PMC7750252 DOI: 10.1111/jdv.16767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 05/29/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant genetic disorder. It is commonly caused by mutations in PTCH1 and chiefly characterized by multiple basal cell carcinomas (BCCs) developing prior to the age of 30 years. In rare cases, NBCCS presents with a late onset of BCC development. OBJECTIVE To investigate BCC tumorigenesis in two brothers, who showed characteristic features of NBCCS but developed their first BCCs only after the age of 40 years. Two other siblings did not show signs of NBCCS. RESULTS We obtained blood samples from four siblings and nine BCCs from the two brothers with NBCCS. Whole exome sequencing and RNA sequencing revealed loss of heterozygosity (LOH) of PTCH1 in eight out of nine tumours that consistently involved the same haplotype on chromosome 9. This haplotype contained a germinal splice site mutation in PTCH1 (NM_001083605:exon9:c.763-6C>A). Analysis of germline DNA confirmed segregation of this mutation with the disease. All BCCs harboured additional somatic loss-of-function (LoF) mutations in the remaining PTCH1 allele which are not typically seen in other cases of NBCCS. This suggests a hypomorphic nature of the germinal PTCH1 mutation in this family. Furthermore, all BCCs had a similar tumour mutational burden compared to BCCs of unrelated NBCCS patients while harbouring a higher number of damaging PTCH1 mutations. CONCLUSIONS Our data suggest that a sequence of three genetic hits leads to the late development of BCCs in two brothers with NBCCS: a hypomorphic germline mutation, followed by somatic LOH and additional mutations that complete PTCH1 inactivation. These genetic events are in line with the late occurrence of the first BCC and with the higher number of damaging PTCH1 mutations compared to usual cases of NBCCS.
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Affiliation(s)
- Omar Hasan Ali
- Department of Dermatology, University Hospital Zurich,
Zurich, Switzerland
- Institute of Immunobiology, Kantonsspital St. Gallen, St.
Gallen, Switzerland
- Department of Dermatology, Venerology and Allergology,
Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Andrey A. Yurchenko
- Inserm U981, Gustave Roussy Cancer Campus,
Université Paris Saclay, Villejuif, France
| | - Olesya Pavlova
- Service of Dermatology and Venerology, CHUV, Lausanne,
Switzerland
| | - Ambra Sartori
- Department of Genetic Medicine and Development, University
of Geneva Medical School, Geneva, Switzerland
| | - David Bomze
- Institute of Immunobiology, Kantonsspital St. Gallen, St.
Gallen, Switzerland
| | - Rebecca Higgins
- Department of Dermatology, University Hospital Zurich,
Zurich, Switzerland
| | - Sandra S. Ring
- Institute of Immunobiology, Kantonsspital St. Gallen, St.
Gallen, Switzerland
| | - Fabienne Hartmann
- Institute of Immunobiology, Kantonsspital St. Gallen, St.
Gallen, Switzerland
| | | | | | - Wolfram Jochum
- Institute of Pathology, Kantonsspital St. Gallen, St.
Gallen, Switzerland
| | | | - Arianna Kim
- Department of Dermatology, Columbia University Irving
Medical Center, New York, USA
| | - Lars E. French
- Department of Dermatology and Allergology,
Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Emmanouil Dermitzakis
- Department of Genetic Medicine and Development, University
of Geneva Medical School, Geneva, Switzerland
| | - Angela M. Christiano
- Department of Dermatology, Columbia University Irving
Medical Center, New York, USA
- Department of Genetics & Development, Columbia
University Irving Medical Center, New York, USA
| | - Daniel Hohl
- Service of Dermatology and Venerology, CHUV, Lausanne,
Switzerland
| | - David R. Bickers
- Department of Dermatology, Columbia University Irving
Medical Center, New York, USA
| | - Sergey I. Nikolaev
- Inserm U981, Gustave Roussy Cancer Campus,
Université Paris Saclay, Villejuif, France
- University Paris 7, Saint Louis Hospital, Paris,
France
| | - Lukas Flatz
- Department of Dermatology, University Hospital Zurich,
Zurich, Switzerland
- Institute of Immunobiology, Kantonsspital St. Gallen, St.
Gallen, Switzerland
- Department of Dermatology, Venerology and Allergology,
Kantonsspital St. Gallen, St. Gallen, Switzerland
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5
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Ilaslan E, Markosyan R, Sproll P, Stevenson BJ, Sajek M, Sajek MP, Hayrapetyan H, Sarkisian T, Livshits L, Nef S, Jaruzelska J, Kusz-Zamelczyk K. The FKBP4 Gene, Encoding a Regulator of the Androgen Receptor Signaling Pathway, Is a Novel Candidate Gene for Androgen Insensitivity Syndrome. Int J Mol Sci 2020; 21:ijms21218403. [PMID: 33182400 PMCID: PMC7664851 DOI: 10.3390/ijms21218403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022] Open
Abstract
Androgen insensitivity syndrome (AIS), manifesting incomplete virilization in 46,XY individuals, is caused mostly by androgen receptor (AR) gene mutations. Therefore, a search for AR mutations is a routine approach in AIS diagnosis. However, some AIS patients lack AR mutations, which complicates the diagnosis. Here, we describe a patient suffering from partial androgen insensitivity syndrome (PAIS) and lacking AR mutations. The whole exome sequencing of the patient and his family members identified a heterozygous FKBP4 gene mutation, c.956T>C (p.Leu319Pro), inherited from the mother. The gene encodes FKBP prolyl isomerase 4, a positive regulator of the AR signaling pathway. This is the first report describing a FKBP4 gene mutation in association with a human disorder of sexual development (DSD). Importantly, the dysfunction of a homologous gene was previously reported in mice, resulting in a phenotype corresponding to PAIS. Moreover, the Leu319Pro amino acid substitution occurred in a highly conserved position of the FKBP4 region, responsible for interaction with other proteins that are crucial for the AR functional heterocomplex formation and therefore the substitution is predicted to cause the disease. We proposed the FKBP4 gene as a candidate AIS gene and suggest screening that gene for the molecular diagnosis of AIS patients lacking AR gene mutations.
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Affiliation(s)
- Erkut Ilaslan
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (E.I.); (M.P.S.); (J.J.)
| | - Renata Markosyan
- Endocrinology Department, “Muratsan” University Hospital, Endocrinology Clinic, Yerevan State Medical University, 0025 Yerevan, Armenia;
| | - Patrick Sproll
- Division of Endocrinology, University of Fribourg, 1700 Fribourg, Switzerland;
| | | | - Malgorzata Sajek
- Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, 61-614 Poznan, Poland;
| | - Marcin P. Sajek
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (E.I.); (M.P.S.); (J.J.)
| | - Hasmik Hayrapetyan
- Department of Medical Genetics, Yerevan State Medical University, 0025 Yerevan, Armenia; (H.H.); (T.S.)
- Center of Medical Genetics and Primary Health Care, 375010 Yerevan, Armenia
| | - Tamara Sarkisian
- Department of Medical Genetics, Yerevan State Medical University, 0025 Yerevan, Armenia; (H.H.); (T.S.)
- Center of Medical Genetics and Primary Health Care, 375010 Yerevan, Armenia
| | - Ludmila Livshits
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine;
| | - Serge Nef
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, CH-1211 Genève 4, Switzerland
- Correspondence: (S.N.); (K.K.-Z.)
| | - Jadwiga Jaruzelska
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (E.I.); (M.P.S.); (J.J.)
| | - Kamila Kusz-Zamelczyk
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (E.I.); (M.P.S.); (J.J.)
- Correspondence: (S.N.); (K.K.-Z.)
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6
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Pathogenic mosaic variants in congenital hypogonadotropic hypogonadism. Genet Med 2020; 22:1759-1767. [DOI: 10.1038/s41436-020-0896-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 01/13/2023] Open
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7
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Ilie A, Boucher A, Park J, Berghuis AM, McKinney RA, Orlowski J. Assorted dysfunctions of endosomal alkali cation/proton exchanger SLC9A6 variants linked to Christianson syndrome. J Biol Chem 2020; 295:7075-7095. [PMID: 32277048 PMCID: PMC7242699 DOI: 10.1074/jbc.ra120.012614] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic screening has identified numerous variants of the endosomal solute carrier family 9 member A6 (SLC9A6)/(Na+,K+)/H+ exchanger 6 (NHE6) gene that cause Christianson syndrome, a debilitating X-linked developmental disorder associated with a range of neurological, somatic, and behavioral symptoms. Many of these variants cause complete loss of NHE6 expression, but how subtler missense substitutions or nonsense mutations that partially truncate its C-terminal cytoplasmic regulatory domain impair NHE6 activity and endosomal function are poorly understood. Here, we describe the molecular and cellular consequences of six unique mutations located in the N-terminal cytoplasmic segment (A9S), the membrane ion translocation domain (L188P and G383D), and the C-terminal regulatory domain (E547*, R568Q, and W570*) of human NHE6 that purportedly cause disease. Using a heterologous NHE6-deficient cell expression system, we show that the biochemical, catalytic, and cellular properties of the A9S and R568Q variants were largely indistinguishable from those of the WT transporter, which obscured their disease significance. By contrast, the L188P, G383D, E547*, and W570* mutants exhibited variable deficiencies in biosynthetic post-translational maturation, membrane sorting, pH homeostasis in recycling endosomes, and cargo trafficking, and they also triggered apoptosis. These findings broaden our understanding of the molecular dysfunctions of distinct NHE6 variants associated with Christianson syndrome.
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Affiliation(s)
- Alina Ilie
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Annie Boucher
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | | | - R Anne McKinney
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - John Orlowski
- Department of Physiology, McGill University, Montreal, Quebec H3G 0B1, Canada
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8
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Pagel KA, Kim R, Moad K, Busby B, Zheng L, Tokheim C, Ryan M, Karchin R. Integrated Informatics Analysis of Cancer-Related Variants. JCO Clin Cancer Inform 2020; 4:310-317. [PMID: 32228266 PMCID: PMC7113103 DOI: 10.1200/cci.19.00132] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 01/03/2023] Open
Abstract
PURPOSE The modern researcher is confronted with hundreds of published methods to interpret genetic variants. There are databases of genes and variants, phenotype-genotype relationships, algorithms that score and rank genes, and in silico variant effect prediction tools. Because variant prioritization is a multifactorial problem, a welcome development in the field has been the emergence of decision support frameworks, which make it easier to integrate multiple resources in an interactive environment. Current decision support frameworks are typically limited by closed proprietary architectures, access to a restricted set of tools, lack of customizability, Web dependencies that expose protected data, or limited scalability. METHODS We present the Open Custom Ranked Analysis of Variants Toolkit1 (OpenCRAVAT) a new open-source, scalable decision support system for variant and gene prioritization. We have designed the resource catalog to be open and modular to maximize community and developer involvement, and as a result, the catalog is being actively developed and growing every month. Resources made available via the store are well suited for analysis of cancer, as well as Mendelian and complex diseases. RESULTS OpenCRAVAT offers both command-line utility and dynamic graphical user interface, allowing users to install with a single command, easily download tools from an extensive resource catalog, create customized pipelines, and explore results in a richly detailed viewing environment. We present several case studies to illustrate the design of custom workflows to prioritize genes and variants. CONCLUSION OpenCRAVAT is distinguished from similar tools by its capabilities to access and integrate an unprecedented amount of diverse data resources and computational prediction methods, which span germline, somatic, common, rare, coding, and noncoding variants.
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Affiliation(s)
- Kymberleigh A. Pagel
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD
| | - Rick Kim
- In Silico Solutions, Falls Church, VA
| | - Kyle Moad
- In Silico Solutions, Falls Church, VA
| | | | - Lily Zheng
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD
- Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | - Rachel Karchin
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD
- Departments of Biomedical Engineering, Oncology, and Computer Science, The Johns Hopkins University, Baltimore, MD
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9
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Liang Y, He L, Zhao Y, Hao Y, Zhou Y, Li M, Li C, Pu X, Wen Z. Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting the de novo Mutations in Humans. Front Pharmacol 2019; 10:358. [PMID: 31105557 PMCID: PMC6499170 DOI: 10.3389/fphar.2019.00358] [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: 12/11/2018] [Accepted: 03/21/2019] [Indexed: 01/22/2023] Open
Abstract
Despite of the low occurrence rate in the entire genomes, de novo mutation is proved to be deleterious and will lead to severe genetic diseases via impacting on the gene function. Considering the fact that the traditional family based linkage approaches and the genome-wide association studies are unsuitable for identifying the de novo mutations, in recent years, several pipelines have been proposed to detect them based on the whole-genome or whole-exome sequencing data and were used for calling them in the rare diseases. However, how the performance of these variant calling pipelines on detecting the de novo mutations is still unexplored. For the purpose of facilitating the appropriate choice of the pipelines and reducing the false positive rate, in this study, we thoroughly evaluated the performance of the commonly used trio calling methods on the detection of the de novo single-nucleotide variants (DNSNVs) by conducting a comparative analysis for the calling results. Our results exhibited that different pipelines have a specific tendency to detect the DNSNVs in the genomic regions with different GC contents. Additionally, to refine the calling results for a single pipeline, our proposed filter achieved satisfied results, indicating that the read coverage at the mutation positions can be used as an effective index to identify the high-confidence DNSNVs. Our findings should be good support for the committees to choose an appropriate way to explore the de novo mutations for the rare diseases.
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Affiliation(s)
- Yu Liang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Li He
- Biogas Appliance Quality Supervision and Inspection Center, Biogas Institute of Ministry of Agriculture, Chengdu, China
| | - Yiru Zhao
- College of Computer Science, Sichuan University, Chengdu, China
| | - Yinyi Hao
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yifan Zhou
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Chuan Li
- College of Computer Science, Sichuan University, Chengdu, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, China
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, China
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10
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Ilaslan E, Calvel P, Nowak D, Szarras-Czapnik M, Slowikowska-Hilczer J, Spik A, Sararols P, Nef S, Jaruzelska J, Kusz-Zamelczyk K. A Case of Two Sisters Suffering from 46,XY Gonadal Dysgenesis and Carrying a Mutation of a Novel Candidate Sex-Determining Gene STARD8 on the X Chromosome. Sex Dev 2018; 12:191-195. [PMID: 29886504 DOI: 10.1159/000489692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2018] [Indexed: 11/19/2022] Open
Abstract
Identification of novel genes involved in sexual development is crucial for understanding disorders of sex development (DSD). Here, we propose a member of the START domain family, the X chromosome STARD8, as a DSD candidate gene. We have identified a missense mutation of this gene in 2 sisters with 46,XY gonadal dysgenesis, inherited from their heterozygous mother. Gonadal tissue of one of the sisters contained Leydig cells overloaded with cholesterol droplets, i.e., structures previously identified in 46,XY DSD patients carrying mutations in the STAR gene encoding another START domain family member, which is crucial for steroidogenesis. Based on the phenotypes of our patients, we propose a dual role of STARD8 in sexual development, namely in testes determination and testosterone synthesis. However, further studies are needed to confirm the involvement of STARD8 in sexual development.
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11
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Andrianova MA, Chetan GK, Sibin MK, Mckee T, Merkler D, Narasinga RK, Ribaux P, Blouin JL, Makrythanasis P, Seplyarskiy VB, Antonarakis SE, Nikolaev SI. Germline PMS2 and somatic POLE exonuclease mutations cause hypermutability of the leading DNA strand in biallelic mismatch repair deficiency syndrome brain tumours. J Pathol 2017; 243:331-341. [PMID: 28805995 DOI: 10.1002/path.4957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 08/02/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022]
Abstract
Biallelic mismatch repair deficiency (bMMRD) in tumours is frequently associated with somatic mutations in the exonuclease domains of DNA polymerases POLE or POLD1, and results in a characteristic mutational profile. In this article, we describe the genetic basis of ultramutated high-grade brain tumours in the context of bMMRD. We performed exome sequencing of two second-cousin patients from a large consanguineous family of Indian origin with early onset of high-grade glioblastoma and astrocytoma. We identified a germline homozygous nonsense variant, p.R802*, in the PMS2 gene. Additionally, by genome sequencing of these tumours, we found extremely high somatic mutation rates (237/Mb and 123/Mb), as well as somatic mutations in the proofreading domain of POLE polymerase (p.P436H and p.L424V), which replicates the leading DNA strand. Most interestingly, we found, in both cancers, that the vast majority of mutations were consistent with the signature of POLE exo- , i.e. an abundance of C>A and C>T mutations, particularly in special contexts, on the leading strand. We showed that the fraction of mutations under positive selection among mutations in tumour suppressor genes is more than two-fold lower in ultramutated tumours than in other glioblastomas. Genetic analyses enabled the diagnosis of the two consanguineous childhood brain tumours as being due to a combination of PMS2 germline and POLE somatic variants, and confirmed them as bMMRD/POLE exo- disorders. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Ghati Kasturirangan Chetan
- Department of Human Genetics, National Institute of Mental Health & Neurosciences (NIMHANS), Bangalore, India
| | - Madathan Kandi Sibin
- Department of Human Genetics, National Institute of Mental Health & Neurosciences (NIMHANS), Bangalore, India
| | - Thomas Mckee
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - Doron Merkler
- Department of Pathology and Immunology, Université de Genève (UNIGE), Geneva, Switzerland
| | - Rao Kvl Narasinga
- Department of Neuro-surgery, National Institute of Mental Health & Neurosciences (NIMHANS), Bangalore, India
| | - Pascale Ribaux
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Jean-Louis Blouin
- Service of Genetic Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Moscow, Russia.,Moscow State University, Moscow, Russia.,Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
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12
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Huang AY, Zhang Z, Ye AY, Dou Y, Yan L, Yang X, Zhang Y, Wei L. MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples. Nucleic Acids Res 2017; 45:e76. [PMID: 28132024 PMCID: PMC5449543 DOI: 10.1093/nar/gkx024] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/24/2016] [Accepted: 01/26/2017] [Indexed: 02/07/2023] Open
Abstract
Genomic mosaicism arising from postzygotic mutations has long been associated with cancer and more recently with non-cancer diseases. It has also been detected in healthy individuals including healthy parents of children affected with genetic disorders, highlighting its critical role in the origin of genetic mutations. However, most existing software for the genome-wide identification of single-nucleotide mosaicisms (SNMs) requires a paired control tissue obtained from the same individual which is often unavailable for non-cancer individuals and sometimes missing in cancer studies. Here, we present MosaicHunter (http://mosaichunter.cbi.pku.edu.cn), a bioinformatics tool that can identify SNMs in whole-genome and whole-exome sequencing data of unpaired samples without matched controls using Bayesian genotypers. We evaluate the accuracy of MosaicHunter on both simulated and real data and demonstrate that it has improved performance compared with other somatic mutation callers. We further demonstrate that incorporating sequencing data of the parents can be an effective approach to significantly improve the accuracy of detecting SNMs in an individual when a matched control sample is unavailable. Finally, MosaicHunter also has a paired mode that can take advantage of matched control samples when available, making it a useful tool for detecting SNMs in both non-cancer and cancer studies.
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Affiliation(s)
- August Yue Huang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Zheng Zhang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Adam Yongxin Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- Peking-Tsinghua Center for Life Sciences, Beijing, People's Republic of China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, People's Republic of China
| | - Yanmei Dou
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
- National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Linlin Yan
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaoxu Yang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yuehua Zhang
- Peking University First Hospital, Peking University, Beijing 100034, People's Republic of China
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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13
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Bertoldi L, Forcato C, Vitulo N, Birolo G, De Pascale F, Feltrin E, Schiavon R, Anglani F, Negrisolo S, Zanetti A, D'Avanzo F, Tomanin R, Faulkner G, Vezzi A, Valle G. QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. BMC Bioinformatics 2017; 18:225. [PMID: 28454514 PMCID: PMC5410040 DOI: 10.1186/s12859-017-1654-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/26/2017] [Indexed: 11/21/2022] Open
Abstract
Background Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1654-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Loris Bertoldi
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | - Claudio Forcato
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | - Nicola Vitulo
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy.,Present address: Department of Biotechnology, University of Verona, Verona, Italy
| | - Giovanni Birolo
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | | | - Erika Feltrin
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy
| | | | - Franca Anglani
- Department of Medicine, University of Padua, Padua, Italy
| | - Susanna Negrisolo
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Alessandra Zanetti
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Francesca D'Avanzo
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Rosella Tomanin
- Department of Women's and Children's Health, University of Padua, Padua, Italy
| | | | | | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy. .,Department of Biology, University of Padua, Padua, Italy.
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14
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Feng BJ. PERCH: A Unified Framework for Disease Gene Prioritization. Hum Mutat 2017; 38:243-251. [PMID: 27995669 PMCID: PMC5299048 DOI: 10.1002/humu.23158] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/12/2016] [Indexed: 12/30/2022]
Abstract
To interpret genetic variants discovered from next-generation sequencing, integration of heterogeneous information is vital for success. This article describes a framework named PERCH (Polymorphism Evaluation, Ranking, and Classification for a Heritable trait), available at http://BJFengLab.org/. It can prioritize disease genes by quantitatively unifying a new deleteriousness measure called BayesDel, an improved assessment of the biological relevance of genes to the disease, a modified linkage analysis, a novel rare-variant association test, and a converted variant call quality score. It supports data that contain various combinations of extended pedigrees, trios, and case-controls, and allows for a reduced penetrance, an elevated phenocopy rate, liability classes, and covariates. BayesDel is more accurate than PolyPhen2, SIFT, FATHMM, LRT, Mutation Taster, Mutation Assessor, PhyloP, GERP++, SiPhy, CADD, MetaLR, and MetaSVM. The overall approach is faster and more powerful than the existing quantitative method pVAAST, as shown by the simulations of challenging situations in finding the missing heritability of a complex disease. This framework can also classify variants of unknown significance (variants of uncertain significance) by quantitatively integrating allele frequencies, deleteriousness, association, and co-segregation. PERCH is a versatile tool for gene prioritization in gene discovery research and variant classification in clinical genetic testing.
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Affiliation(s)
- Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, UT 84132, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84132, USA
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15
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Olcese C, Patel MP, Shoemark A, Kiviluoto S, Legendre M, Williams HJ, Vaughan CK, Hayward J, Goldenberg A, Emes RD, Munye MM, Dyer L, Cahill T, Bevillard J, Gehrig C, Guipponi M, Chantot S, Duquesnoy P, Thomas L, Jeanson L, Copin B, Tamalet A, Thauvin-Robinet C, Papon JF, Garin A, Pin I, Vera G, Aurora P, Fassad MR, Jenkins L, Boustred C, Cullup T, Dixon M, Onoufriadis A, Bush A, Chung EMK, Antonarakis SE, Loebinger MR, Wilson R, Armengot M, Escudier E, Hogg C, Amselem S, Sun Z, Bartoloni L, Blouin JL, Mitchison HM. X-linked primary ciliary dyskinesia due to mutations in the cytoplasmic axonemal dynein assembly factor PIH1D3. Nat Commun 2017; 8:14279. [PMID: 28176794 PMCID: PMC5309803 DOI: 10.1038/ncomms14279] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/15/2016] [Indexed: 01/06/2023] Open
Abstract
By moving essential body fluids and molecules, motile cilia and flagella govern respiratory mucociliary clearance, laterality determination and the transport of gametes and cerebrospinal fluid. Primary ciliary dyskinesia (PCD) is an autosomal recessive disorder frequently caused by non-assembly of dynein arm motors into cilia and flagella axonemes. Before their import into cilia and flagella, multi-subunit axonemal dynein arms are thought to be stabilized and pre-assembled in the cytoplasm through a DNAAF2–DNAAF4–HSP90 complex akin to the HSP90 co-chaperone R2TP complex. Here, we demonstrate that large genomic deletions as well as point mutations involving PIH1D3 are responsible for an X-linked form of PCD causing disruption of early axonemal dynein assembly. We propose that PIH1D3, a protein that emerges as a new player of the cytoplasmic pre-assembly pathway, is part of a complementary conserved R2TP-like HSP90 co-chaperone complex, the loss of which affects assembly of a subset of inner arm dyneins. Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disease resulting in reduced mucus clearance and impaired lung function. Here, the authors show that mutations in PIH1D3 are responsible for an X-linked form of PCD, affecting assembly of a subset of inner arm dyneins.
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Affiliation(s)
- Chiara Olcese
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,Department of Life Sciences and Biotechnologies, University of Ferrara, 46-44121 Ferrara, Italy
| | - Mitali P Patel
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Amelia Shoemark
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK
| | - Santeri Kiviluoto
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Marie Legendre
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Hywel J Williams
- GOSgene, Genetics and Genomic Medicine Programme, University College London (UCL) Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Cara K Vaughan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Biological Sciences, Malet Street, London, WC1E 7HX, UK
| | - Jane Hayward
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Alice Goldenberg
- Service de Génétique, CHU de Rouen, INSERM U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Richard D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK.,Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
| | - Mustafa M Munye
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Laura Dyer
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Thomas Cahill
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK
| | - Jeremy Bevillard
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, CH-1211 Geneva, Switzerland
| | - Sandra Chantot
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Philippe Duquesnoy
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Lucie Thomas
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Ludovic Jeanson
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Bruno Copin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Aline Tamalet
- Service de Pneumologie Pédiatrique, Centre National de Référence des Maladies Respiratoires Rares, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Christel Thauvin-Robinet
- Centre de génétique, CHU Dijon Bourgogne, Équipe EA4271 GAD, Université de Bourgogne, Hôpital François Mitterrand, 21000 Dijon, France
| | - Jean-François Papon
- Service d'Oto-Rhino-Laryngologie et de Chirurgie Cervico-Maxillo-Faciale, Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre 94275, France
| | - Antoine Garin
- Service d'Oto-Rhino-Laryngologie et de Chirurgie Cervico-Maxillo-Faciale, Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre 94275, France
| | - Isabelle Pin
- Pédiatrie, CHU Grenoble Alpes, INSERM U 1209, Institut for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - Gabriella Vera
- Service de Génétique, CHU de Rouen, INSERM U1079, Université de Rouen, Centre Normand de Génomique Médicale et Médecine Personnalisée, Rouen, France
| | - Paul Aurora
- Department of Paediatric Respiratory Medicine, Great Ormond Street Hospital for Children, London WC1N 3JH, UK.,Department of Respiratory, Critical Care and Anaesthesia Unit, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Mahmoud R Fassad
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK.,Human Genetics Department, Medical Research Institute, Alexandria University, El-Hadra Alexandria 21561, Egypt
| | - Lucy Jenkins
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, Queen Square, London WC1N 3BH, UK
| | - Christopher Boustred
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, Queen Square, London WC1N 3BH, UK
| | - Thomas Cullup
- North East Thames Regional Genetics Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, Queen Square, London WC1N 3BH, UK
| | - Mellisa Dixon
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK
| | - Alexandros Onoufriadis
- Department of Medical and Molecular Genetics, Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK
| | - Andrew Bush
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK.,Department of Paediatric Respiratory Medicine, National Heart and Lung Institute, Imperial College London, London SW3 6LR, UK
| | - Eddie M K Chung
- Population, Policy and Practice, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, CH-1211 Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, iGE3, CH-1211 Geneva, Switzerland
| | - Michael R Loebinger
- Host Defence Unit, Respiratory Medicine, Royal Brompton Hospital, London SW3 6NP, UK
| | - Robert Wilson
- Host Defence Unit, Respiratory Medicine, Royal Brompton Hospital, London SW3 6NP, UK
| | - Miguel Armengot
- Rhinology and Primary Ciliary Dyskinesia Unit, General and University Hospital, Medical School, Valencia University, Valencia E-46014, Spain
| | - Estelle Escudier
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Claire Hogg
- Paediatric Department, Royal Brompton Hospital, Sydney Street, London SW3 6NP, UK
| | | | - Serge Amselem
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMR_S933 and Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, AP-HP, Paris 75012, France
| | - Zhaoxia Sun
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Lucia Bartoloni
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,UOSD Laboratorio Analisi Venezia, ULSS12 Veneziana, 30121 Venezia, Italy
| | - Jean-Louis Blouin
- Department of Genetic Medicine and Development, University of Geneva School of Medicine, CH-1211 Geneva, Switzerland.,Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, CH-1211 Geneva, Switzerland
| | - Hannah M Mitchison
- Genetics and Genomic Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, Guilford Street, London WC1N 1EH, UK
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16
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No evidence for the presence of genetic variants predisposing to psychotic disorders on the non-deleted 22q11.2 allele of VCFS patients. Transl Psychiatry 2017; 7:e1039. [PMID: 28221368 PMCID: PMC5438018 DOI: 10.1038/tp.2016.258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/16/2016] [Indexed: 12/13/2022] Open
Abstract
The velo-cardio-facial syndrome (VCFS) is caused by hemizygous deletions on chromosome 22q11.2. The VCFS phenotype is complex and characterized by frequent occurrence of neuropsychiatric symptoms with up to 25-30% of cases suffering from psychotic disorders compared with only ~1% in the general population (odds ratio≈20-25). This makes the 22q11.2 deletion one of the most prominent risk factors for schizophrenia. However, its penetrance for neuropsychiatric phenotypes is incomplete suggesting that additional risk factors are required for disease development. These additional risk factors could lie anywhere on the genome, but by reducing the normal diploid to a haploid state, the 22q11.2 deletion could result in the unmasking of otherwise recessive alleles or functional variants on the non-deleted 22q11.2 allele. To test this hypothesis, we captured and sequenced the whole 22q11.2 non-deleted region in 88 VCFS patients with (n=40) and without (n=48) psychotic disorders to identify genetic variation that could increase the risk for schizophrenia. Single nucleotide variants (SNVs), small insertions/deletions (indels) and copy number variants were called and their distributions were compared between the two diagnostic groups using variant-, gene- and region-based association tests. None of these tests resulted in statistical evidence for the existence of a genetic variation in the non-deleted allele that would increase schizophrenia risk in VCFS patients. Power analysis showed that our study was able to achieve >80% statistical power to detect association of a risk variant with an odd ratio of ⩾22. However, it is certainly under-powered to detect risk variant of smaller effect sizes. Our study did not provide evidence that genetic variants of very large effect size located on the non-deleted 22q1.2 allele in VCFS patients increase the risk for developing psychotic disorders. Variants with smaller effects may be located in the remaining 22q11.2 allele and elsewhere in the genome. Therefore, whole exome or even genome sequencing for larger sample size would appear to be the next logical steps in the search for the genetic modifiers of the 22q11.2-deletion neuropsychiatric phenotype.
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17
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Anderson de la Llana S, Klee P, Santoni F, Stekelenburg C, Blouin JL, Schwitzgebel VM. Gene Variants Associated with Transient Neonatal Diabetes Mellitus in the Very Low Birth Weight Infant. Horm Res Paediatr 2016; 84:283-8. [PMID: 26315042 DOI: 10.1159/000437378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 07/01/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Transient and permanent neonatal diabetes mellitus (NDM), usually defined as diabetes diagnosed within the first 6 months of life, are rare conditions occurring in 1:90,000-260,000 live births. The origin of NDM is rarely related to type 1 diabetes, but rather to single gene defects. METHODS Genetic analysis was performed using targeted parallel sequencing including 323 diabetes genes. Data were filtered by a locally developed program. RESULTS A very low birth weight neonate born at 28 weeks postmenstrual age developed diabetes 13 days after birth. The patient was treated with continuous subcutaneous insulin infusion. After 1 month, insulin treatment could be stopped. At 18 months of age, the child was normoglycemic and developing normally. Genetic analysis revealed a novel variant (p.Pro190Leu) in HNF4A, which is located in the ligand binding domain of the transcription factor, and the p.Glu23Lys variant in KCNJ11, which is associated with type 2 diabetes. CONCLUSION Here, we describe a novel HNF4A variant associated with transient NDM in a premature infant. We hypothesize that the neonatal phenotype previously described in carriers of HNF4A mutations was modified by the additional variant in KCNJ11 and prematurity.
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18
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Calvel P, Kusz-Zamelczyk K, Makrythanasis P, Janecki D, Borel C, Conne B, Vannier A, Béna F, Gimelli S, Fichna P, Antonarakis SE, Nef S, Jaruzelska J. A Case of Wiedemann-Steiner Syndrome Associated with a 46,XY Disorder of Sexual Development and Gonadal Dysgenesis. Sex Dev 2015; 9:289-95. [DOI: 10.1159/000441512] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2015] [Indexed: 11/19/2022] Open
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19
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Onodera K, Arimura Y, Isshiki H, Kawakami K, Nagaishi K, Yamashita K, Yamamoto E, Niinuma T, Naishiro Y, Suzuki H, Imai K, Shinomura Y. Low-Frequency IL23R Coding Variant Associated with Crohn's Disease Susceptibility in Japanese Subjects Identified by Personal Genomics Analysis. PLoS One 2015; 10:e0137801. [PMID: 26375822 PMCID: PMC4574159 DOI: 10.1371/journal.pone.0137801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 08/21/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The common disease-common variant hypothesis is insufficient to explain the complexities of Crohn's disease (CD) genetics; therefore, rare variants are expected to be important in the disease. We explored rare variants associated with susceptibility to CD in Japanese individuals by personal genomic analysis. METHODS Two-step analyses were performed. The first step was a trio analysis with whole-exome sequence (WES) analysis and the second was a follow-up case-control association study. The WES analysis pipeline comprised Burrows-Wheeler Aligner, Picard, Genome Analysis Toolkit, and SAMTOOLS. Single nucleotide variants (SNVs)/indels were annotated and filtered by using programs implemented in ANNOVAR in combination with identity-by-descent (IBD), subsequently were subjected to the linkage based, and de novo based strategies. Finally, we conducted an association study that included 176 unrelated subjects with CD and 358 healthy control subjects. RESULTS In family members, 234,067-297,523 SNVs/indels were detected and they were educed to 106-146 by annotation based filtering. Fifty-four CD variants common to both individuals of the affected sib pair were identified. The linkage based strategy detected five candidate variants whereas the de novo based strategy identified no variants. Consequently, five candidates were analyzed in the case-control association study. CD showed a significant association with one variant in exon 4 of IL23R, G149R [rs76418789, P = 3.9E-5, odds ratio (OR) 0.21, 95% confidence interval (CI) 0.09-0.47 for the dominant model (AA + AG versus GG), and P = 7.3E-5, OR 0.21, 95% CI 0.10-0.48 for AG versus GG, and P = 7.2E-5, OR 0.23, 95% CI 0.10-0.50 for the allele model]. CONCLUSIONS The present study, using personal genomics analysis of a small CD pedigree, is the first to show that the low-frequency non-synonymous variant of IL23R, rs76418789, protects against CD development in Japanese subjects.
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Affiliation(s)
- Kei Onodera
- Department of Gastroenterology, Rheumatology, and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Yoshiaki Arimura
- Department of Gastroenterology, Rheumatology, and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Hiroyuki Isshiki
- Department of Gastroenterology, Rheumatology, and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Kentaro Kawakami
- Department of Gastroenterology, Rheumatology, and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Kanna Nagaishi
- Department of Anatomy, Sapporo Medical University, Sapporo, Japan
| | - Kentaro Yamashita
- Department of Gastroenterology, Rheumatology, and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Eiichiro Yamamoto
- Department of Gastroenterology, Rheumatology, and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Takeshi Niinuma
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Yasuyoshi Naishiro
- Department of Educational Development, Sapporo Medical University, Sapporo, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Kohzoh Imai
- Center for Antibody and Vaccine Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasuhisa Shinomura
- Department of Gastroenterology, Rheumatology, and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
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Guipponi M, Chentouf A, Webling KE, Freimann K, Crespel A, Nobile C, Lemke JR, Hansen J, Dorn T, Lesca G, Ryvlin P, Hirsch E, Rudolf G, Rosenberg DS, Weber Y, Becker F, Helbig I, Muhle H, Salzmann A, Chaouch M, Oubaiche ML, Ziglio S, Gehrig C, Santoni F, Pizzato M, Langel Ü, Antonarakis SE. Galanin pathogenic mutations in temporal lobe epilepsy. Hum Mol Genet 2015; 24:3082-91. [DOI: 10.1093/hmg/ddv060] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/11/2015] [Indexed: 12/18/2022] Open
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21
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Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J. mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing. J Med Genet 2015; 52:275-81. [PMID: 25596308 DOI: 10.1136/jmedgenet-2014-102656] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Recently, several studies documented that de novo mutations (DNMs) play important roles in the aetiology of sporadic diseases. Next-generation sequencing (NGS) enables variant calling at single-base resolution on a genome-wide scale. However, accurate identification of DNMs from NGS data still remains a major challenge. We developed mirTrios, a web server, to accurately detect DNMs and rare inherited mutations from NGS data in sporadic diseases. METHODS The expectation-maximisation (EM) model was adopted to accurately identify DNMs from variant call files of a trio generated by GATK (Genome Analysis Toolkit). The GATK results, which contain certain basic properties (such as PL, PRT and PART), are iteratively integrated into the EM model to strike a threshold for DNMs detection. Training sets of true and false positive DNMs in the EM model were built from whole genome sequencing data of 64 trios. RESULTS With our in-house whole exome sequencing datasets from 20 trios, mirTrios totally identified 27 DNMs in the coding region, 25 of which (92.6%) are validated as true positives. In addition, to facilitate the interpretation of diverse mutations, mirTrios can also be employed in the identification of rare inherited mutations. Embedded with abundant annotation of DNMs and rare inherited mutations, mirTrios also supports known diagnostic variants and causative gene identification, as well as the prioritisation of novel and promising candidate genes. CONCLUSIONS mirTrios provides an intuitive interface for the general geneticist and clinician, and can be widely used for detection of DNMs and rare inherited mutations, and annotation in sporadic diseases. mirTrios is freely available at http://centre.bioinformatics.zj.cn/mirTrios/.
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Affiliation(s)
- Jinchen Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Tao Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Huiqian Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qing Xie
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qianzhi Shao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xia Ran
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
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22
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Guipponi M, Santoni FA, Setola V, Gehrig C, Rotharmel M, Cuenca M, Guillin O, Dikeos D, Georgantopoulos G, Papadimitriou G, Curtis L, Méary A, Schürhoff F, Jamain S, Avramopoulos D, Leboyer M, Rujescu D, Pulver A, Campion D, Siderovski DP, Antonarakis SE. Exome sequencing in 53 sporadic cases of schizophrenia identifies 18 putative candidate genes. PLoS One 2014; 9:e112745. [PMID: 25420024 PMCID: PMC4242613 DOI: 10.1371/journal.pone.0112745] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/09/2014] [Indexed: 11/18/2022] Open
Abstract
Schizophrenia (SCZ) is a severe, debilitating mental illness which has a significant genetic component. The identification of genetic factors related to SCZ has been challenging and these factors remain largely unknown. To evaluate the contribution of de novo variants (DNVs) to SCZ, we sequenced the exomes of 53 individuals with sporadic SCZ and of their non-affected parents. We identified 49 DNVs, 18 of which were predicted to alter gene function, including 13 damaging missense mutations, 2 conserved splice site mutations, 2 nonsense mutations, and 1 frameshift deletion. The average number of exonic DNV per proband was 0.88, which corresponds to an exonic point mutation rate of 1.7×10−8 per nucleotide per generation. The non-synonymous-to-synonymous mutation ratio of 2.06 did not differ from neutral expectations. Overall, this study provides a list of 18 putative candidate genes for sporadic SCZ, and when combined with the results of similar reports, identifies a second proband carrying a non-synonymous DNV in the RGS12 gene.
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Affiliation(s)
- Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Switzerland
- * E-mail:
| | - Federico A. Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Switzerland
| | - Vincent Setola
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, West Virginia, United States of America
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Switzerland
| | - Maud Rotharmel
- Centre Hospitalier du Rouvray, Sotteville les Rouen et INSERM U1079, France
| | - Macarena Cuenca
- Centre Hospitalier du Rouvray, Sotteville les Rouen et INSERM U1079, France
| | - Olivier Guillin
- Centre Hospitalier du Rouvray, Sotteville les Rouen et INSERM U1079, France
| | - Dimitris Dikeos
- 1st Department of Psychiatry at the Athens University Medical School, Athens, Greece
| | | | - George Papadimitriou
- 1st Department of Psychiatry at the Athens University Medical School, Athens, Greece
| | - Logos Curtis
- Department of Mental Health and Psychiatry, Geneva, Switzerland
| | - Alexandre Méary
- Inserm U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Hôpital A. Chenevier - H. Mondor, Pôle de Psychiatrie, Créteil, France
- Fondation Fondamental, Créteil, France
| | - Franck Schürhoff
- Inserm U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Hôpital A. Chenevier - H. Mondor, Pôle de Psychiatrie, Créteil, France
- Fondation Fondamental, Créteil, France
| | - Stéphane Jamain
- Inserm U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Hôpital A. Chenevier - H. Mondor, Pôle de Psychiatrie, Créteil, France
- Fondation Fondamental, Créteil, France
| | - Dimitri Avramopoulos
- Epidemiology and Genetics Program in Psychiatry, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Marion Leboyer
- Inserm U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Hôpital A. Chenevier - H. Mondor, Pôle de Psychiatrie, Créteil, France
- Fondation Fondamental, Créteil, France
| | - Dan Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
| | - Ann Pulver
- Epidemiology and Genetics Program in Psychiatry, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Dominique Campion
- Centre Hospitalier du Rouvray, Sotteville les Rouen et INSERM U1079, France
| | - David P. Siderovski
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, West Virginia, United States of America
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
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23
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Guipponi M, Santoni FA, Setola V, Gehrig C, Rotharmel M, Cuenca M, Guillin O, Dikeos D, Georgantopoulos G, Papadimitriou G, Curtis L, Méary A, Schürhoff F, Jamain S, Avramopoulos D, Leboyer M, Rujescu D, Pulver A, Campion D, Siderovski DP, Antonarakis SE. Exome sequencing in 53 sporadic cases of schizophrenia identifies 18 putative candidate genes. PLoS One 2014; 9:e112745. [PMID: 25420024 PMCID: PMC4242613 DOI: 10.1371/journal.pone.0112745 10.1371/journal.pone.0141630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Schizophrenia (SCZ) is a severe, debilitating mental illness which has a significant genetic component. The identification of genetic factors related to SCZ has been challenging and these factors remain largely unknown. To evaluate the contribution of de novo variants (DNVs) to SCZ, we sequenced the exomes of 53 individuals with sporadic SCZ and of their non-affected parents. We identified 49 DNVs, 18 of which were predicted to alter gene function, including 13 damaging missense mutations, 2 conserved splice site mutations, 2 nonsense mutations, and 1 frameshift deletion. The average number of exonic DNV per proband was 0.88, which corresponds to an exonic point mutation rate of 1.7×10(-8) per nucleotide per generation. The non-synonymous-to-synonymous mutation ratio of 2.06 did not differ from neutral expectations. Overall, this study provides a list of 18 putative candidate genes for sporadic SCZ, and when combined with the results of similar reports, identifies a second proband carrying a non-synonymous DNV in the RGS12 gene.
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Affiliation(s)
- Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Switzerland
- * E-mail:
| | - Federico A. Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Switzerland
| | - Vincent Setola
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, West Virginia, United States of America
| | - Corinne Gehrig
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Switzerland
| | - Maud Rotharmel
- Centre Hospitalier du Rouvray, Sotteville les Rouen et INSERM U1079, France
| | - Macarena Cuenca
- Centre Hospitalier du Rouvray, Sotteville les Rouen et INSERM U1079, France
| | - Olivier Guillin
- Centre Hospitalier du Rouvray, Sotteville les Rouen et INSERM U1079, France
| | - Dimitris Dikeos
- 1st Department of Psychiatry at the Athens University Medical School, Athens, Greece
| | | | - George Papadimitriou
- 1st Department of Psychiatry at the Athens University Medical School, Athens, Greece
| | - Logos Curtis
- Department of Mental Health and Psychiatry, Geneva, Switzerland
| | - Alexandre Méary
- Inserm U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Hôpital A. Chenevier - H. Mondor, Pôle de Psychiatrie, Créteil, France
- Fondation Fondamental, Créteil, France
| | - Franck Schürhoff
- Inserm U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Hôpital A. Chenevier - H. Mondor, Pôle de Psychiatrie, Créteil, France
- Fondation Fondamental, Créteil, France
| | - Stéphane Jamain
- Inserm U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Hôpital A. Chenevier - H. Mondor, Pôle de Psychiatrie, Créteil, France
- Fondation Fondamental, Créteil, France
| | - Dimitri Avramopoulos
- Epidemiology and Genetics Program in Psychiatry, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Marion Leboyer
- Inserm U955, Psychiatrie Génétique, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Hôpital A. Chenevier - H. Mondor, Pôle de Psychiatrie, Créteil, France
- Fondation Fondamental, Créteil, France
| | - Dan Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
| | - Ann Pulver
- Epidemiology and Genetics Program in Psychiatry, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Dominique Campion
- Centre Hospitalier du Rouvray, Sotteville les Rouen et INSERM U1079, France
| | - David P. Siderovski
- Department of Physiology and Pharmacology, West Virginia University School of Medicine, West Virginia, United States of America
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School and University Hospitals of Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
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24
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Vandeweyer G, Van Laer L, Loeys B, Van den Bulcke T, Kooy RF. VariantDB: a flexible annotation and filtering portal for next generation sequencing data. Genome Med 2014; 6:74. [PMID: 25352915 PMCID: PMC4210545 DOI: 10.1186/s13073-014-0074-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/15/2014] [Indexed: 12/30/2022] Open
Abstract
Interpretation of the multitude of variants obtained from next generation sequencing (NGS) is labor intensive and complex. Web-based interfaces such as Galaxy streamline the generation of variant lists but lack flexibility in the downstream annotation and filtering that are necessary to identify causative variants in medical genomics. To this end, we built VariantDB, a web-based interactive annotation and filtering platform that automatically annotates variants with allele frequencies, functional impact, pathogenicity predictions and pathway information. VariantDB allows filtering by all annotations, under dominant, recessive or de novo inheritance models and is freely available at http://www.biomina.be/app/variantdb/.
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Affiliation(s)
- Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, 2650 Edegem, Antwerp Belgium ; Biomedical Informatics Research Center Antwerp, University and University Hospital of Antwerp, 2650 Edegem, Antwerp Belgium
| | - Lut Van Laer
- Department of Medical Genetics, University of Antwerp, 2650 Edegem, Antwerp Belgium ; Department of Medical Genetics, University Hospital of Antwerp, 2650 Edegem, Antwerp Belgium
| | - Bart Loeys
- Department of Medical Genetics, University of Antwerp, 2650 Edegem, Antwerp Belgium ; Department of Medical Genetics, University Hospital of Antwerp, 2650 Edegem, Antwerp Belgium
| | - Tim Van den Bulcke
- Biomedical Informatics Research Center Antwerp, University and University Hospital of Antwerp, 2650 Edegem, Antwerp Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2650 Edegem, Antwerp Belgium
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25
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Bodian DL, Solomon BD, Khromykh A, Thach DC, Iyer RK, Link K, Baker RL, Baveja R, Vockley JG, Niederhuber JE. Diagnosis of an imprinted-gene syndrome by a novel bioinformatics analysis of whole-genome sequences from a family trio. Mol Genet Genomic Med 2014; 2:530-8. [PMID: 25614875 PMCID: PMC4303223 DOI: 10.1002/mgg3.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/02/2014] [Accepted: 07/16/2014] [Indexed: 01/22/2023] Open
Abstract
Whole-genome sequencing and whole-exome sequencing are becoming more widely applied in clinical medicine to help diagnose rare genetic diseases. Identification of the underlying causative mutations by genome-wide sequencing is greatly facilitated by concurrent analysis of multiple family members, most often the mother-father-proband trio, using bioinformatics pipelines that filter genetic variants by mode of inheritance. However, current pipelines are limited to Mendelian inheritance patterns and do not specifically address disorders caused by mutations in imprinted genes, such as forms of Angelman syndrome and Beckwith-Wiedemann syndrome. Using publicly available tools, we implemented a genetic inheritance search mode to identify imprinted-gene mutations. Application of this search mode to whole-genome sequences from a family trio led to a diagnosis for a proband for whom extensive clinical testing and Mendelian inheritance-based sequence analysis were nondiagnostic. The condition in this patient, IMAGe syndrome, is likely caused by the heterozygous mutation c.832A>G (p.Lys278Glu) in the imprinted gene CDKN1C. The genotypes and disease status of six members of the family are consistent with maternal expression of the gene, and allele-biased expression was confirmed by RNA-Seq for the heterozygotes. This analysis demonstrates that an imprinted-gene search mode is a valuable addition to genome sequence analysis pipelines for identifying disease-causative variants.
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Affiliation(s)
- Dale L Bodian
- Inova Translational Medicine Institute, Inova Health System Falls Church, Virginia
| | - Benjamin D Solomon
- Inova Translational Medicine Institute, Inova Health System Falls Church, Virginia
| | - Alina Khromykh
- Inova Translational Medicine Institute, Inova Health System Falls Church, Virginia
| | - Dzung C Thach
- Inova Translational Medicine Institute, Inova Health System Falls Church, Virginia
| | - Ramaswamy K Iyer
- Inova Translational Medicine Institute, Inova Health System Falls Church, Virginia
| | - Kathleen Link
- Department of Pediatric Endocrinology, Inova Children's Hospital Falls Church, Virginia
| | - Robin L Baker
- Fairfax Neonatal Associates PC, Inova Children's Hospital Falls Church, Virginia
| | - Rajiv Baveja
- Fairfax Neonatal Associates PC, Inova Children's Hospital Falls Church, Virginia
| | - Joseph G Vockley
- Inova Translational Medicine Institute, Inova Health System Falls Church, Virginia
| | - John E Niederhuber
- Inova Translational Medicine Institute, Inova Health System Falls Church, Virginia
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26
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Bahlo M, Tankard R, Lukic V, Oliver KL, Smith KR. Using familial information for variant filtering in high-throughput sequencing studies. Hum Genet 2014; 133:1331-41. [PMID: 25129038 PMCID: PMC4185103 DOI: 10.1007/s00439-014-1479-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/07/2014] [Indexed: 12/30/2022]
Abstract
High-throughput sequencing studies (HTS) have been highly successful in identifying the genetic causes of human disease, particularly those following Mendelian inheritance. Many HTS studies to date have been performed without utilizing available family relationships between samples. Here, we discuss the many merits and occasional pitfalls of using identity by descent information in conjunction with HTS studies. These methods are not only applicable to family studies but are also useful in cohorts of apparently unrelated, ‘sporadic’ cases and small families underpowered for linkage and allow inference of relationships between individuals. Incorporating familial/pedigree information not only provides powerful filtering options for the extensive variant lists that are usually produced by HTS but also allows valuable quality control checks, insights into the genetic model and the genotypic status of individuals of interest. In particular, these methods are valuable for challenging discovery scenarios in HTS analysis, such as in the study of populations poorly represented in variant databases typically used for filtering, and in the case of poor-quality HTS data.
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Affiliation(s)
- Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia,
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27
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Smedley D, Köhler S, Czeschik JC, Amberger J, Bocchini C, Hamosh A, Veldboer J, Zemojtel T, Robinson PN. Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases. Bioinformatics 2014; 30:3215-22. [PMID: 25078397 PMCID: PMC4221119 DOI: 10.1093/bioinformatics/btu508] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Motivation: Whole-exome sequencing (WES) has opened up previously unheard of possibilities for identifying novel disease genes in Mendelian disorders, only about half of which have been elucidated to date. However, interpretation of WES data remains challenging. Results: Here, we analyze protein–protein association (PPA) networks to identify candidate genes in the vicinity of genes previously implicated in a disease. The analysis, using a random-walk with restart (RWR) method, is adapted to the setting of WES by developing a composite variant-gene relevance score based on the rarity, location and predicted pathogenicity of variants and the RWR evaluation of genes harboring the variants. Benchmarking using known disease variants from 88 disease-gene families reveals that the correct gene is ranked among the top 10 candidates in ≥50% of cases, a figure which we confirmed using a prospective study of disease genes identified in 2012 and PPA data produced before that date. We implement our method in a freely available Web server, ExomeWalker, that displays a ranked list of candidates together with information on PPAs, frequency and predicted pathogenicity of the variants to allow quick and effective searches for candidates that are likely to reward closer investigation. Availability and implementation: http://compbio.charite.de/ExomeWalker Contact: peter.robinson@charite.de
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Affiliation(s)
- Damian Smedley
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Sebastian Köhler
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Johanna Christina Czeschik
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Joanna Amberger
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Carol Bocchini
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Ada Hamosh
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Julian Veldboer
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Tomasz Zemojtel
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Peter N Robinson
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany Mouse Informatics Group, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Genome Informatics Department, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, McKusick-Nathans Institute of Genetic Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Computer Science, Institute for Bioinformatics, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-701 Poznan, Poland, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin and Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany Mouse Informatics Group, The Wellcome Trust Sang
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Kondapalli KC, Prasad H, Rao R. An inside job: how endosomal Na(+)/H(+) exchangers link to autism and neurological disease. Front Cell Neurosci 2014; 8:172. [PMID: 25002837 PMCID: PMC4066934 DOI: 10.3389/fncel.2014.00172] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/04/2014] [Indexed: 12/02/2022] Open
Abstract
Autism imposes a major impediment to childhood development and a huge emotional and financial burden on society. In recent years, there has been rapidly accumulating genetic evidence that links the eNHE, a subset of Na(+)/H(+) exchangers that localize to intracellular vesicles, to a variety of neurological conditions including autism, attention deficit hyperactivity disorder (ADHD), intellectual disability, and epilepsy. By providing a leak pathway for protons pumped by the V-ATPase, eNHE determine luminal pH and regulate cation (Na(+), K(+)) content in early and recycling endosomal compartments. Loss-of-function mutations in eNHE cause hyperacidification of endosomal lumen, as a result of imbalance in pump and leak pathways. Two isoforms, NHE6 and NHE9 are highly expressed in brain, including hippocampus and cortex. Here, we summarize evidence for the importance of luminal cation content and pH on processing, delivery and fate of cargo. Drawing upon insights from model organisms and mammalian cells we show how eNHE affect surface expression and function of membrane receptors and neurotransmitter transporters. These studies lead to cellular models of eNHE activity in pre- and post-synaptic neurons and astrocytes, where they could impact synapse development and plasticity. The study of eNHE has provided new insight on the mechanism of autism and other debilitating neurological disorders and opened up new possibilities for therapeutic intervention.
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Affiliation(s)
| | | | - Rajini Rao
- Department of Physiology, The Johns Hopkins University School of MedicineBaltimore, MD, USA
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29
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Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Nucleic Acids Res 2014; 42:W88-93. [PMID: 24803668 PMCID: PMC4086071 DOI: 10.1093/nar/gku407] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Whole-exome sequencing has become a fundamental tool for the discovery of
disease-related genes of familial diseases and the identification of somatic
driver variants in cancer. However, finding the causal mutation among the
enormous background of individual variability in a small number of samples is
still a big challenge. Here we describe a web-based tool, BiERapp, which
efficiently helps in the identification of causative variants in family and
sporadic genetic diseases. The program reads lists of predicted variants
(nucleotide substitutions and indels) in affected individuals or tumor samples
and controls. In family studies, different modes of inheritance can easily be
defined to filter out variants that do not segregate with the disease along the
family. Moreover, BiERapp integrates additional information such as allelic
frequencies in the general population and the most popular damaging scores to
further narrow down the number of putative variants in successive filtering
steps. BiERapp provides an interactive and user-friendly interface that
implements the filtering strategy used in the context of a large-scale genomic
project carried out by the Spanish Network for Research in Rare Diseases
(CIBERER) in which more than 800 exomes have been analyzed. BiERapp is freely
available at: http://bierapp.babelomics.org/
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Affiliation(s)
- Alejandro Alemán
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia 46010, Spain
| | - Francisco Garcia-Garcia
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain
| | - Francisco Salavert
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia 46010, Spain
| | - Ignacio Medina
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia 46010, Spain Functional Genomics Node, (INB) at CIPF, Valencia 46012, Spain
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30
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Callier P, Calvel P, Matevossian A, Makrythanasis P, Bernard P, Kurosaka H, Vannier A, Thauvin-Robinet C, Borel C, Mazaud-Guittot S, Rolland A, Desdoits-Lethimonier C, Guipponi M, Zimmermann C, Stévant I, Kuhne F, Conne B, Santoni F, Lambert S, Huet F, Mugneret F, Jaruzelska J, Faivre L, Wilhelm D, Jégou B, Trainor PA, Resh MD, Antonarakis SE, Nef S. Loss of function mutation in the palmitoyl-transferase HHAT leads to syndromic 46,XY disorder of sex development by impeding Hedgehog protein palmitoylation and signaling. PLoS Genet 2014; 10:e1004340. [PMID: 24784881 PMCID: PMC4006744 DOI: 10.1371/journal.pgen.1004340] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/07/2014] [Indexed: 12/13/2022] Open
Abstract
The Hedgehog (Hh) family of secreted proteins act as morphogens to control embryonic patterning and development in a variety of organ systems. Post-translational covalent attachment of cholesterol and palmitate to Hh proteins are critical for multimerization and long range signaling potency. However, the biological impact of lipid modifications on Hh ligand distribution and signal reception in humans remains unclear. In the present study, we report a unique case of autosomal recessive syndromic 46,XY Disorder of Sex Development (DSD) with testicular dysgenesis and chondrodysplasia resulting from a homozygous G287V missense mutation in the hedgehog acyl-transferase (HHAT) gene. This mutation occurred in the conserved membrane bound O-acyltransferase (MBOAT) domain and experimentally disrupted the ability of HHAT to palmitoylate Hh proteins such as DHH and SHH. Consistent with the patient phenotype, HHAT was found to be expressed in the somatic cells of both XX and XY gonads at the time of sex determination, and Hhat loss of function in mice recapitulates most of the testicular, skeletal, neuronal and growth defects observed in humans. In the developing testis, HHAT is not required for Sertoli cell commitment but plays a role in proper testis cord formation and the differentiation of fetal Leydig cells. Altogether, these results shed new light on the mechanisms of action of Hh proteins. Furthermore, they provide the first clinical evidence of the essential role played by lipid modification of Hh proteins in human testicular organogenesis and embryonic development. Disorders of gonadal development represent a clinically and genetically heterogeneous class of DSD caused by defects in gonadal development and/or a failure of testis/ovarian differentiation. Unfortunately, in many cases the genetic aetiology of DSD is unknown, indicating that our knowledge of the factors mediating sex determination is limited. Using exome sequencing on a case of autosomal recessive syndromic 46,XY DSD with testicular dysgenesis and chondrodysplasia, we found a homozygous missense mutation (G287V) within the coding sequence of the O-acetyl-transferase HHAT gene. The HHAT gene encodes an enzyme required for the attachment of palmitoyl residues that are critical for multimerization and long range signaling potency of hedgehog secreted proteins. We found that HHAT is widely expressed in human organs during fetal development, including testes and ovaries around the time of sex determination. In vitro assays show that G287V mutation impairs HHAT palmitoyl-transferase activity and mice lacking functional Hhat exhibit testicular dysgenesis as well as other skeletal, neuronal and growth defects that recapitulate most aspects of the syndromic 46,XY DSD patient. These data provide the first clinical evidence of the essential role played by lipid modification of Hedgehog proteins in human testicular organogenesis and embryonic development.
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Affiliation(s)
- Patrick Callier
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; FHU-TRANSLAD, Département de Génétique, Hôpital Le Bocage, CHU, Dijon, France; EA 4271 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Pierre Calvel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Armine Matevossian
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America; Gerstner Sloan-Kettering Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America; Graduate Program in Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Pascal Bernard
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Hiroshi Kurosaka
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Anne Vannier
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Christel Thauvin-Robinet
- FHU-TRANSLAD, Département de Génétique, Hôpital Le Bocage, CHU, Dijon, France; EA 4271 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Séverine Mazaud-Guittot
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1085-IRSET, Université de Rennes 1, Structure Fédérative Recherche Biosit, Campus de Beaulieu, Rennes, France
| | - Antoine Rolland
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1085-IRSET, Université de Rennes 1, Structure Fédérative Recherche Biosit, Campus de Beaulieu, Rennes, France
| | - Christèle Desdoits-Lethimonier
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1085-IRSET, Université de Rennes 1, Structure Fédérative Recherche Biosit, Campus de Beaulieu, Rennes, France
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Céline Zimmermann
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Isabelle Stévant
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Françoise Kuhne
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Béatrice Conne
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Sandy Lambert
- FHU-TRANSLAD, Département de Génétique, Hôpital Le Bocage, CHU, Dijon, France
| | - Frederic Huet
- FHU-TRANSLAD, Département de Génétique, Hôpital Le Bocage, CHU, Dijon, France; EA 4271 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Francine Mugneret
- FHU-TRANSLAD, Département de Génétique, Hôpital Le Bocage, CHU, Dijon, France
| | | | - Laurence Faivre
- FHU-TRANSLAD, Département de Génétique, Hôpital Le Bocage, CHU, Dijon, France; EA 4271 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
| | - Dagmar Wilhelm
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Bernard Jégou
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1085-IRSET, Université de Rennes 1, Structure Fédérative Recherche Biosit, Campus de Beaulieu, Rennes, France; EHESP School of Public Health, Rennes, France
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Marilyn D Resh
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America; Gerstner Sloan-Kettering Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America; Graduate Program in Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
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31
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Tools to exploit familial data. Nat Rev Genet 2014; 15:146. [DOI: 10.1038/nrg3679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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