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Kalfakakou D, Fostira F, Papathanasiou A, Apostolou P, Dellatola V, Gavra IE, Vlachos IS, Scouras ZG, Drosopoulou E, Yannoukakos D, Konstantopoulou I. CanVaS: Documenting the genetic variation spectrum of Greek cancer patients. Hum Mutat 2021; 42:1081-1093. [PMID: 34174131 DOI: 10.1002/humu.24249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/13/2021] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
National genetic variation registries vastly increase the level of detail for the relevant population, while directly affecting patient management. Herein, we report CanVaS, a Cancer Variation reSource aiming to document the genetic variation of cancer patients in Greece. CanVaS comprises germline genetic data from 7,363 Greek individuals with a personal and/or family history of malignancy. The data set incorporates approximately 24,000 functionally annotated rare variants in 97 established or suspected cancer susceptibility genes. For each variant, allele frequency for the Greek population, interpretation for clinical significance, anonymized family and segregation information, as well as phenotypic traits of the carriers, are included. Moreover, information on the geographic distribution of the variants across the country is provided, enabling the study of Greek population isolates. Direct comparisons between Greek (sub)populations with relevant genetic resources are supported, allowing fine-grain localized adjustment of guidelines and clinical decision-making. Most importantly, anonymized data are available for download, while the Leiden Open Variation Database schema is adopted, enabling integration/interconnection with central resources. CanVaS could become a stepping-stone for a countrywide effort to characterize the cancer genetic variation landscape, concurrently supporting national and international cancer research. The database can be accessed at: http://ithaka.rrp.demokritos.gr/CanVaS.
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Affiliation(s)
- Despoina Kalfakakou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Athanasios Papathanasiou
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Vasiliki Dellatola
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Ioanna E Gavra
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Ioannis S Vlachos
- Department of Pathology, Cancer Research Institute, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Zacharias G Scouras
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Drosopoulou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, Institute of Nuclear & Radiological Sciences and Technology, Energy & Safety, National Center for Scientific Research "Demokritos", Athens, Greece
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2
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Pavlovsky M, Peled A, Samuelov L, Malki L, Malovitski K, Assaf S, Mohamad J, Meijers O, Eskin-Schwartz M, Sarig O, Sprecher E. Molecular epidemiology of pachyonychia congenita in the Israeli population. Clin Exp Dermatol 2020; 46:663-668. [PMID: 33190296 DOI: 10.1111/ced.14509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pachyonychia congenita (PC) is a rare autosomal dominant disorder featuring palmoplantar keratoderma, nail dystrophy, oral leucokeratosis, pilosebaceous cysts and natal teeth. PC results from dominant mutations in one of five genes (KRT6A, KRT6B, KRT6C, KRT16, KRT17) encoding keratin proteins. AIM To delineate the clinical and genetic features of PC in a series of Israeli patients. METHODS We used direct sequencing of genomic DNA, and also used cDNA sequencing where applicable. RESULTS We collected clinical information and molecular data in a cohort of Israeli families diagnosed with PC (n = 16). Most of the patients were Ashkenazi Jews and had a family history of PC. The most common clinical findings were painful focal plantar keratoderma (94%) accompanied by nail dystrophy (81%), pilosebaceous cysts (31%) and prenatal/natal teeth (13%). In contrast to the high prevalence of KRT6A mutations in other populations, we found that KRT16 mutations were the most common type among Israeli patients with PC (56%). Most (77%) of the Israeli patients with PC with KRT16 mutation carried the same variant (c.380G>A; p.R127H) and shared the same haplotype around the KRT16 locus, suggestive of a founder effect. CONCLUSION The data gleaned from this study emphasizes the importance of population-specific tailored diagnostic strategies.
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Affiliation(s)
- M Pavlovsky
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - A Peled
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - L Samuelov
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L Malki
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - K Malovitski
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - S Assaf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - J Mohamad
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - O Meijers
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - M Eskin-Schwartz
- Genetics Institute at Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - O Sarig
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - E Sprecher
- Division of Dermatology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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3
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Rets AV, Reading NS, Agarwal AM. δ-Globin Chain Variants Associated with Decreased Hb A 2 Levels: A National Reference Laboratory Experience. Hemoglobin 2020; 44:438-441. [PMID: 33054450 DOI: 10.1080/03630269.2020.1831531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
High prevalence of hemoglobin (Hb) disorders mandates national programs for screening and genetic counseling in many countries. Increased Hb A2 levels are commonly associated with β-thalassemias, however, various disorders including alteration of δ chains may result in decreased production of Hb A2, thus hindering the diagnosis of β-thalassemias. The reported data reflect the experience of a large reference laboratory in the United States. In the current study, we have attempted to assess the prevalence and also tried to characterize the identified mutations in the HBD gene resulting in decreased Hb A2 levels. In our cohort, 1.6% of 6486 patients were found to have Hb A2 values of <1.9%. Bidirectional sequencing of the HBD gene demonstrated mutations in 20 cases (19.0% of the individuals with decreased Hb A2). In addition to the previously reported variants, one novel mutation (Hb A2-Utah or HBD: c.46T>C).
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Affiliation(s)
- Anton V Rets
- Hematopathology Division, Associated Regional University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA.,Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT, USA
| | - Noel Scott Reading
- Hematopathology Division, Associated Regional University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA.,Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT, USA.,Department of Internal Medicine, Division of Hematology, University of Utah Health, Salt Lake City, UT, USA
| | - Archana M Agarwal
- Hematopathology Division, Associated Regional University Pathologists (ARUP) Laboratories, Salt Lake City, UT, USA.,Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT, USA
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4
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Bittles AH. Population structure and inherited genetic disorders in the Bedouin of the Negev. J Community Genet 2019; 11:11-12. [PMID: 31346959 DOI: 10.1007/s12687-019-00432-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022] Open
Affiliation(s)
- A H Bittles
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, 6027, Australia. .,Centre for Comparative Genomics, Murdoch University, Perth, WA, 6051, Australia.
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5
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Zlotogora J, Patrinos GP, Meiner V. Ashkenazi Jewish genomic variants: integrating data from the Israeli National Genetic Database and gnomAD. Genet Med 2017; 20:867-871. [PMID: 29144512 DOI: 10.1038/gim.2017.193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 10/03/2017] [Indexed: 01/07/2023] Open
Abstract
PURPOSE The aim of the study was to compare the data for mutations related to clinical disorders reported among Ashkenazi Jewish patients in the Israeli National Genetic Database (INGD) with variants included in the Genome Aggregation Database (gnomAD). METHODS We extracted data for mutations claimed to cause disorders reported among Ashkenazi Jews from the INGD and searched gnomAD for each of them. We compared the allele frequency of each variant in Ashkenazi Jews with that of other delineated populations. RESULTS Of the 58 INGD-reported mutations related to autosomal-dominant disorders, 19 were present in gnomAD (32.8%). Of the 309 mutations related to autosomal-recessive disorders, 240 (77.7%) were variants found in gnomAD. Of these variants, 202 (84.2%) were documented among one or more Ashkenazi individuals. At this point in the INGD, there are 168 Ashkenazi assumed founder mutations in 128 different genes corresponding to 111 autosomal-recessive disorders. CONCLUSION Integration of information on mutations among Ashkenazi Jews extracted from the INGD with their population frequency recorded in gnomAD is important for effective straightforward molecular diagnosis as well as for targeted carrier screening either for reproductive decision-making or for implementation of disease-modifying behavior.
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Affiliation(s)
- Joël Zlotogora
- Faculty of Medicine, Hebrew University, Jerusalem, Israel.
| | - George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece.,Department of Bioinformatics, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vardiella Meiner
- Faculty of Medicine, Hebrew University, Jerusalem, Israel.,Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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6
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Zlotogora J, Patrinos GP. The Israeli National Genetic database: a 10-year experience. Hum Genomics 2017; 11:5. [PMID: 28302154 PMCID: PMC5356354 DOI: 10.1186/s40246-017-0100-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/06/2017] [Indexed: 11/10/2022] Open
Abstract
Background The Israeli National and Ethnic Mutation database (http://server.goldenhelix.org/israeli) was launched in September 2006 on the ETHNOS software to include clinically relevant genomic variants reported among Jewish and Arab Israeli patients. In 2016, the database was reviewed and corrected according to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar) and ExAC (http://exac.broadinstitute.org) database entries. The present article summarizes some key aspects from the development and continuous update of the database over a 10-year period, which could serve as a paradigm of successful database curation for other similar resources. Results In September 2016, there were 2444 entries in the database, 890 among Jews, 1376 among Israeli Arabs, and 178 entries among Palestinian Arabs, corresponding to an ~4× data content increase compared to when originally launched. While the Israeli Arab population is much smaller than the Jewish population, the number of pathogenic variants causing recessive disorders reported in the database is higher among Arabs (934) than among Jews (648). Nevertheless, the number of pathogenic variants classified as founder mutations in the database is smaller among Arabs (175) than among Jews (192). In 2016, the entire database content was compared to that of other databases such as ClinVar and ExAC. We show that a significant difference in the percentage of pathogenic variants from the Israeli genetic database that were present in ExAC was observed between the Jewish population (31.8%) and the Israeli Arab population (20.6%). Conclusions The Israeli genetic database was launched in 2006 on the ETHNOS software and is available online ever since. It allows querying the database according to the disorder and the ethnicity; however, many other features are not available, in particular the possibility to search according to the name of the gene. In addition, due to the technical limitations of the previous ETHNOS software, new features and data are not included in the present online version of the database and upgrade is currently ongoing.
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Affiliation(s)
- Joël Zlotogora
- Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, University Campus, Rion, 26504, Patras, Greece. .,Department of Bioinformatics, School of Medicine and Health Sciences, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands.
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7
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Gal M, Khermesh K, Barak M, Lin M, Lahat H, Reznik Wolf H, Lin M, Pras E, Levanon EY. Expanding preconception carrier screening for the Jewish population using high throughput microfluidics technology and next generation sequencing. BMC Med Genomics 2016; 9:24. [PMID: 27175728 PMCID: PMC4865987 DOI: 10.1186/s12920-016-0184-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 05/02/2016] [Indexed: 11/15/2022] Open
Abstract
Background Genetic screening to identify carriers of autosomal recessive diseases has become an integral part of routine prenatal care. In spite of the rapid growth of known mutations, most current screening programs include only a small subset of these mutations, and are performed using diverse molecular techniques, which are generally labor-intensive and time consuming. We examine the implementation of the combined high-throughput technologies of specific target amplification and next generation sequencing (NGS), for expanding the carrier screening program in the Israeli Jewish population as a test case. Methods We compiled a panel of 370 germline mutations, causing 120 disorders, previously identified in affected Jewish individuals from different ethnicities. This mutation panel was simultaneously captured in 48 samples using a multiplex PCR-based microfluidics approach followed by NGS, thereby performing 17,760 individual assays in a single experiment. Results The sensitivity (measured with depth of at least 50×) and specificity of the target capture was 98 and 95 % respectively, leaving minimal rate of inconclusive tests per sample tested. 97 % of the targeted mutations present in the samples were correctly identified and validated. Conclusion Our methodology was shown to successfully combine multiplexing of target specific primers, samples indexing and NGS technology for population genetic screens. Moreover, it’s relatively ease of use and flexibility of updating the targets screened, makes it highly suitable for clinical implementation. This protocol was demonstrated in pre-conceptional screening for pan-Jewish individuals, but can be applied to any other population or different sets of mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0184-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Moran Gal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Khen Khermesh
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Michal Barak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Min Lin
- Fluidigm corporation, South San Francisco, California
| | - Hadas Lahat
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Haike Reznik Wolf
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Michael Lin
- Fluidigm corporation, South San Francisco, California
| | - Elon Pras
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel.
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8
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Affiliation(s)
- Joël Zlotogora
- Department of Community Genetics, Public Health Services, Ministry of Health and the Hebrew University Jerusalem, Israel
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9
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Israeli S, Sarig O, Garty BZ, Indelman M, Bergman R, Sprecher E, Goldberg I. Molecular Analysis of a Series of Israeli Families with Comèl-Netherton Syndrome. Dermatology 2014; 228:183-8. [DOI: 10.1159/000357560] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 11/26/2013] [Indexed: 11/19/2022] Open
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10
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Abstract
UNLABELLED Quantification of the T cell receptor excision circles (TRECs) has recently emerged as a useful non-invasive clinical and research tool to investigate thymic activity. It allows the identification of T cell production by the thymus. Quantification of TREC copies has recently been implemented as the preferred test to screen neonates with severe combined immunodeficiency (SCID) or significant lymphopenia. Neonatal genetic screening for SCID is highly important in countries with high rates of consanguinous marriages, such as Israel, and can be used for early diagnosis, enabling prompt therapeutic intervention that will save lives and improve the outcome of these patients. TREC measurement is also applicable in clinical settings where T cell immunity is involved, including any T cell immunodeficiencies, HIV infection, the aging process, autoimmune diseases, and immune reconstitution after bone marrow transplantation. TAKE-HOME MESSAGES Severe combined immunodeficiency, a life-threatening condition, can be detected by neonatal screening.The earlier the detection and the quicker the implementation of appropriate treatment, the greater the likelihood for improved outcome, even cure, for the affected children.TRECs and KRECs quantification are useful screening tests for severe T and B cell immunodeficiency and can be used also to evaluate every medical condition involving T and B cell immunity.
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Affiliation(s)
- Raz Somech
- Pediatric Department B North, Pediatric Immunology Service, Jeffrey Modell Foundation (JMF) Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel Hashomer, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- To whom correspondence should be addressed. E-mail:
| | - Amos Etzioni
- Meyer Children’s Hospital, Rappaport Faculty of Medicine, The Technion – Israel Institute of Technology, Haifa, Israel
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11
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Papadopoulos P, Viennas E, Gkantouna V, Pavlidis C, Bartsakoulia M, Ioannou ZM, Ratbi I, Sefiani A, Tsaknakis J, Poulas K, Tzimas G, Patrinos GP. Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies. Nucleic Acids Res 2013; 42:D1020-6. [PMID: 24234438 PMCID: PMC3964978 DOI: 10.1093/nar/gkt1125] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
FINDbase (http://www.findbase.org) aims to document frequencies of clinically relevant genomic variations, namely causative mutations and pharmacogenomic markers, worldwide. Each database record includes the population, ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related databases and the genetic variation together with its frequency in that population. Here, we report, in addition to the regular data content updates, significant developments in FINDbase, related to data visualization and querying, data submission, interrelation with other resources and a new module for genetic disease summaries. In particular, (i) we have developed new data visualization tools that facilitate data querying and comparison among different populations, (ii) we have generated a new FINDbase module, built around Microsoft’s PivotViewer (http://www.getpivot.com) software, based on Microsoft Silverlight technology (http://www.silverlight.net), that includes 259 genetic disease summaries from five populations, systematically collected from the literature representing the documented genetic makeup of these populations and (iii) the implementation of a generic data submission tool for every module currently available in FINDbase.
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Affiliation(s)
- Petros Papadopoulos
- Department of Pharmacy, School of Health Sciences, University of Patras, GR-26504, Patras, Greece, Department of Computer Engineering and Informatics, Faculty of Engineering, University of Patras, GR-26504, Patras, Greece, Faculty of Medicine and Pharmacy, Human Genomic Center, University Mohammed V Souissi, 11400, Rabat, Morocco and Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, GR-26334, Patras, Greece
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12
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Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 407] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
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Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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Sagi M, Uhlmann WR. Genetic counseling services and training of genetic counselors in Israel: an overview. J Genet Couns 2013; 22:890-6. [PMID: 23435755 DOI: 10.1007/s10897-013-9576-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 02/04/2013] [Indexed: 10/27/2022]
Abstract
Genetic counseling services have existed in Israel since 1964 and are available in almost all the major hospitals. Given the socialized healthcare system and small country size, genetic services are generally accessible and often free. The existence of founder mutations in various communities in Israel makes genetic testing easier to perform. Yet, the ethnic, cultural and religious diversity of the population has major implications on the design of the screening programs and the use of genetic services. The Israeli Association of Genetic Counselors (IAGC) was established in 2008 and had existed informally since 1989. There are two Master level genetic counseling training programs (6 students/class, 2 year program): Hebrew University-Hadassah Medical School (established in 1997) and the Technion (established in 2009). Genetic counselors' clinical training is largely observational and 2 years of supervised counseling sessions post degree are required for board exam eligibility. Genetic counselors are licensed and lead counseling sessions individually, but currently must work under medical geneticist supervision. This is the first article to summarize the history and training of Master level genetic counselors in Israel. Genetic services, coverage and regulations are also described.
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Affiliation(s)
- Michal Sagi
- Department of Human Genetics and Metabolic Diseases, Hadassah Hebrew University Medical Center, Jerusalem, 91120, Israel,
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Mitropoulos K, Innocenti F, van Schaik RH, Lezhava A, Tzimas G, Kollia P, Macek M, Fortina P, Patrinos GP. Institutional Profile: Golden Helix Institute of Biomedical Research: interdisciplinary research and educational activities in pharmacogenomics and personalized medicine. Pharmacogenomics 2012; 13:387-92. [PMID: 22379996 DOI: 10.2217/pgs.12.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Golden Helix Institute of Biomedical Research is an international nonprofit scientific organization with interdisciplinary research and educational activities in the field of genome medicine in Europe, Asia and Latin America. These activities are supervised by an international scientific advisory council, consisting of world leaders in the field of genomics and translational medicine. Research activities include the regional coordination of the Pharmacogenomics for Every Nation Initiative in Europe, in an effort to integrate pharmacogenomics in developing countries, the development of several national/ethnic genetic databases and related web services and the critical assessment of the impact of genetics and genomic medicine on society in various countries. Educational activities also include the organization of the Golden Helix Symposia(®), which are high-profile scientific research symposia in the field of personalized medicine and the Golden Helix Pharmacogenomics Days, an international educational activity focused on pharmacogenomics, as part of its international pharmacogenomics education and outreach efforts.
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15
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Patrinos GP, Cooper DN, van Mulligen E, Gkantouna V, Tzimas G, Tatum Z, Schultes E, Roos M, Mons B. Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain. Hum Mutat 2012; 33:1503-12. [PMID: 22736453 DOI: 10.1002/humu.22144] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/23/2012] [Indexed: 11/07/2022]
Abstract
The advances in bioinformatics required to annotate human genomic variants and to place them in public data repositories have not kept pace with their discovery. Moreover, a law of diminishing returns has begun to operate both in terms of data publication and submission. Although the continued deposition of such data in the public domain is essential to maximize both their scientific and clinical utility, rewards for data sharing are few, representing a serious practical impediment to data submission. To date, two main strategies have been adopted as a means to encourage the submission of human genomic variant data: (1) database journal linkups involving the affiliation of a scientific journal with a publicly available database and (2) microattribution, involving the unambiguous linkage of data to their contributors via a unique identifier. The latter could in principle lead to the establishment of a microcitation-tracking system that acknowledges individual endeavor and achievement. Both approaches could incentivize potential data contributors, thereby encouraging them to share their data with the scientific community. Here, we summarize and critically evaluate approaches that have been proposed to address current deficiencies in data attribution and discuss ways in which they could become more widely adopted as novel scientific publication modalities.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
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Patrinos GP, Smith TD, Howard H, Al-Mulla F, Chouchane L, Hadjisavvas A, Hamed SA, Li XT, Marafie M, Ramesar RS, Ramos FJ, de Ravel T, El-Ruby MO, Shrestha TR, Sobrido MJ, Tadmouri G, Witsch-Baumgartner M, Zilfalil BA, Auerbach AD, Carpenter K, Cutting GR, Dung VC, Grody W, Hasler J, Jorde L, Kaput J, Macek M, Matsubara Y, Padilla C, Robinson H, Rojas-Martinez A, Taylor GR, Vihinen M, Weber T, Burn J, Qi M, Cotton RGH, Rimoin D. Human Variome Project country nodes: documenting genetic information within a country. Hum Mutat 2012; 33:1513-9. [PMID: 22753370 DOI: 10.1002/humu.22147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/04/2012] [Indexed: 11/09/2022]
Abstract
The Human Variome Project (http://www.humanvariomeproject.org) is an international effort aiming to systematically collect and share information on all human genetic variation. The two main pillars of this effort are gene/disease-specific databases and a network of Human Variome Project Country Nodes. The latter are nationwide efforts to document the genomic variation reported within a specific population. The development and successful operation of the Human Variome Project Country Nodes are of utmost importance to the success of Human Variome Project's aims and goals because they not only allow the genetic burden of disease to be quantified in different countries, but also provide diagnosticians and researchers access to an up-to-date resource that will assist them in their daily clinical practice and biomedical research, respectively. Here, we report the discussions and recommendations that resulted from the inaugural meeting of the International Confederation of Countries Advisory Council, held on 12th December 2011, during the 2011 Human Variome Project Beijing Meeting. We discuss the steps necessary to maximize the impact of the Country Node effort for developing regional and country-specific clinical genetics resources and summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
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Patrinos GP, Al Aama J, Al Aqeel A, Al-Mulla F, Borg J, Devereux A, Felice AE, Macrae F, Marafie MJ, Petersen MB, Qi M, Ramesar RS, Zlotogora J, Cotton RGH. Recommendations for genetic variation data capture in developing countries to ensure a comprehensive worldwide data collection. Hum Mutat 2011; 32:2-9. [PMID: 21089065 PMCID: PMC3058135 DOI: 10.1002/humu.21397] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Developing countries have significantly contributed to the elucidation of the genetic basis of both common and rare disorders, providing an invaluable resource of cases due to large family sizes, consanguinity, and potential founder effects. Moreover, the recognized depth of genomic variation in indigenous African populations, reflecting the ancient origins of humanity on the African continent, and the effect of selection pressures on the genome, will be valuable in understanding the range of both pathological and nonpathological variations. The involvement of these populations in accurately documenting the extant genetic heterogeneity is more than essential. Developing nations are regarded as key contributors to the Human Variome Project (HVP; http://www.humanvariomeproject.org), a major effort to systematically collect mutations that contribute to or cause human disease and create a cyber infrastructure to tie databases together. However, biomedical research has not been the primary focus in these countries even though such activities are likely to produce economic and health benefits for all. Here, we propose several recommendations and guidelines to facilitate participation of developing countries in genetic variation data documentation, ensuring an accurate and comprehensive worldwide data collection. We also summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects. Hum Mutat 31:1–8, 2010. © 2010 Wiley-Liss, Inc.
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van Baal S, Zlotogora J, Lagoumintzis G, Gkantouna V, Tzimas I, Poulas K, Tsakalidis A, Romeo G, Patrinos GP. ETHNOS : A versatile electronic tool for the development and curation of national genetic databases. Hum Genomics 2011; 4:361-8. [PMID: 20650823 PMCID: PMC3500166 DOI: 10.1186/1479-7364-4-5-361] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.
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Affiliation(s)
- Sjozef van Baal
- Erasmus MC, MGC-Department of Cell Biology and Genetics, Rotterdam, the Netherlands
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Abstract
PURPOSE Israeli investigators have identified several relatively frequent disorders due to founder point mutations in Persian (Iranian) Jews, who, for nearly three centuries up to the Islamic Revolution of 1979, were completely isolated reproductively. METHODS Using a community-based model previously employed with Tay-Sachs disease prevention, we developed a pilot program for the Persian Jewish community of greater Los Angeles. We screened for mutations responsible for four relatively frequent autosomal recessive conditions in Persian Jews in which effective interventions are available for each: Pseudocholinesterase deficiency (butyryl cholinesterase deficiency); Congenital hypoaldosteronism (corticosterone methyl oxidase II); Autoimmune polyendocrinopathy (autoimmune regulatory element); and Hereditary Inclusion Body myopathy. RESULTS One thousand individuals volunteered. Mutations were assessed in saliva-derived DNA and were positive for 121/1000 butyryl cholinesterase deficiency; 92/1000 Hereditary Inclusion Body myopathy; 38/1000 corticosterone methyl oxidase II; and 37/1000 autoimmune regulatory element. Ten homozygous individuals (9 butyryl cholinesterase deficiency and 1 Hereditary Inclusion Body myopathy) and 10 "at-risk" couples (seven for butyryl cholinesterase deficiency and one each for the other three disorders) were identified. These frequencies are comparable with those in Israel and indicate an extraordinary level of inbreeding, as anticipated. CONCLUSIONS A carefully planned effort can be delivered to an "increased risk" community if detailed attention is given to planning and organization. However, availability of an effective intervention for those found to be "at-risk" or possibly affected, is essential before embarking.
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Mitropoulou C, Webb AJ, Mitropoulos K, Brookes AJ, Patrinos GP. Locus-specific database domain and data content analysis: evolution and content maturation toward clinical use. Hum Mutat 2011; 31:1109-16. [PMID: 20672379 DOI: 10.1002/humu.21332] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetic variation databases have become indispensable in many areas of health care. In addition, more and more experts are depositing published and unpublished disease-causing variants of particular genes into locus-specific databases (LSDBs). Some of these databases contain such extensive information that they have become known as knowledge bases. Here, we analyzed 1,188 LSDBs and their content for the presence or absence of 44 content criteria related to database features (general presentation, locus-specific information, database structure) and data content (data collection, summary table of variants, database querying). Our analyses revealed that several elements have helped to advance the field and reduce data heterogeneity, such as the development of specialized database management systems and the creation of data querying tools. We also identified a number of deficiencies, namely, the lack of detailed disease and phenotypic descriptions for each genetic variant and links to relevant patient organizations, which, if addressed, would allow LSDBs to better serve the clinical genetics community. We propose a structure, based on LSDBs and closely related repositories (namely, clinical genetics databases), which would contribute to a federated genetic variation browser and also allow the maintenance of variation data.
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Affiliation(s)
- Christina Mitropoulou
- Erasmus MC, Faculty of Medicine and Health Sciences, MGC-Department of Cell Biology and Genetics, Rotterdam, The Netherlands
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Povey S, Al Aqeel AI, Cambon-Thomsen A, Dalgleish R, den Dunnen JT, Firth HV, Greenblatt MS, Barash CI, Parker M, Patrinos GP, Savige J, Sobrido MJ, Winship I, Cotton RGH. Practical guidelines addressing ethical issues pertaining to the curation of human locus-specific variation databases (LSDBs). Hum Mutat 2010; 31:1179-84. [PMID: 20683926 PMCID: PMC2992689 DOI: 10.1002/humu.21339] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
More than 1,000 Web-based locus-specific variation databases (LSDBs) are listed on the Website of the Human Genetic Variation Society (HGVS). These individual efforts, which often relate phenotype to genotype, are a valuable source of information for clinicians, patients, and their families, as well as for basic research. The initiators of the Human Variome Project recently recognized that having access to some of the immense resources of unpublished information already present in diagnostic laboratories would provide critical data to help manage genetic disorders. However, there are significant ethical issues involved in sharing these data worldwide. An international working group presents second-generation guidelines addressing ethical issues relating to the curation of human LSDBs that provide information via a Web-based interface. It is intended that these should help current and future curators and may also inform the future decisions of ethics committees and legislators. These guidelines have been reviewed by the Ethics Committee of the Human Genome Organization (HUGO). Hum Mutat 31:–6, 2010. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Sue Povey
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
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Pradhan S, Sengupta M, Dutta A, Bhattacharyya K, Bag SK, Dutta C, Ray K. Indian genetic disease database. Nucleic Acids Res 2010; 39:D933-8. [PMID: 21037256 PMCID: PMC3013653 DOI: 10.1093/nar/gkq1025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Indians, representing about one-sixth of the world population, consist of several thousands of endogamous groups with strong potential for excess of recessive diseases. However, no database is available on Indian population with comprehensive information on the diseases common in the country. To address this issue, we present Indian Genetic Disease Database (IGDD) release 1.0 (http://www.igdd.iicb.res.in)—an integrated and curated repository of growing number of mutation data on common genetic diseases afflicting the Indian populations. Currently the database covers 52 diseases with information on 5760 individuals carrying the mutant alleles of causal genes. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database is currently designed to work best with Internet Explorer 8 (optimal resolution 1440 × 900) and it can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers. Provisions have been made for deposition of new data and logistics for regular updation of the database. The IGDD web portal, planned to be made freely available, contains user-friendly interfaces and is expected to be highly useful to the geneticists, clinicians, biologists and patient support groups of various genetic diseases.
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Affiliation(s)
- Sanchari Pradhan
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Unit of CSIR, Kolkata, India
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The molecular basis of autosomal recessive diseases among the Arabs and Druze in Israel. Hum Genet 2010; 128:473-9. [PMID: 20852892 DOI: 10.1007/s00439-010-0890-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 09/07/2010] [Indexed: 10/19/2022]
Abstract
The Israeli population mainly includes Jews, Muslim and Christian Arabs, and Druze In the last decade, data on genetic diseases present in the population have been systematically collected and are available online in the Israeli national genetic database ( http://www.goldenhelix.org/server/israeli ). In the non-Jewish population, up to 1 July 2010, the database included molecular data on six diseases relatively frequent in the whole population: thalassemia, familial Mediterranean fever (FMF), cystic fibrosis, deafness, phenylketonuria and congenital adrenal hyperplasia, as well as data on 195 autosomal recessive diseases among Muslim Israeli Arabs, 11 among the Christian Arabs and 31 among Druze. A single mutation was characterized in 149 out of the 238 rare disorders for which the molecular basis was known. In many diseases, mutation had never been observed in any other population and was present in one family only suggesting that it occurred as a de novo event. In other diseases, the mutation was present in more than one community or even in other populations such as Bedouins from the Arab peninsula or Christians from Lebanon. In the 89 other disorders, more than one mutation was characterized either in the same gene or in more than one gene. While it is probable that most of these cases represent random events in some cases such as Bardet Biedl among the Bedouins, the reason may be a selective advantage to the heterozygotes.
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Bandah-Rozenfeld D, Mizrahi-Meissonnier L, Farhy C, Obolensky A, Chowers I, Pe'er J, Merin S, Ben-Yosef T, Ashery-Padan R, Banin E, Sharon D. Homozygosity mapping reveals null mutations in FAM161A as a cause of autosomal-recessive retinitis pigmentosa. Am J Hum Genet 2010; 87:382-91. [PMID: 20705279 DOI: 10.1016/j.ajhg.2010.07.022] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 07/22/2010] [Accepted: 07/29/2010] [Indexed: 01/19/2023] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal degenerations caused by mutations in at least 45 genes. Using homozygosity mapping, we identified a ∼4 Mb homozygous region on chromosome 2p15 in patients with autosomal-recessive RP (arRP). This region partially overlaps with RP28, a previously identified arRP locus. Sequence analysis of 12 candidate genes revealed three null mutations in FAM161A in 20 families. RT-PCR analysis in 21 human tissues revealed high levels of FAM161A expression in the retina and lower levels in the brain and testis. In the human retina, we identified two alternatively spliced transcripts with an intact open reading frame, the major one lacking a highly conserved exon. During mouse embryonic development, low levels of Fam161a transcripts were detected throughout the optic cup. After birth, Fam161a expression was elevated and confined to the photoreceptor layer. FAM161A encodes a protein of unknown function that is moderately conserved in mammals. Clinical manifestations of patients with FAM161A mutations varied but were largely within the spectrum associated with arRP. On funduscopy, pallor of the optic discs and attenuation of blood vessels were common, but bone-spicule-like pigmentation was often mild or lacking. Most patients had nonrecordable electroretinographic responses and constriction of visual fields upon diagnosis. Our data suggest a pivotal role for FAM161A in photoreceptors and reveal that FAM161A loss-of-function mutations are a major cause of arRP, accounting for ∼12% of arRP families in our cohort of patients from Israel and the Palestinian territories.
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Affiliation(s)
- Dikla Bandah-Rozenfeld
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Al-Gazali L, Ali BR. Mutations of a country: a mutation review of single gene disorders in the United Arab Emirates (UAE). Hum Mutat 2010; 31:505-20. [PMID: 20437613 DOI: 10.1002/humu.21232] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The United Arab Emirates inhabitants are ethnically diverse, with ancestries from Arabia, Persia, Baluchistan, and Africa. However, the majority of the current five million inhabitants are expatriates from the Asian subcontinent, Middle Eastern, African, and European countries. Consanguineous marriages within most UAE subpopulations are still the norm, leading to the formation of isolates and higher frequencies of recessive conditions. The UAE is ranked sixth in terms of prevalence of birth defects, with more than 270 genetic disorders reported in the national population. The UAE has high frequencies of blood disorders including thalassemias, sickle cell disease, and G6PD. In addition, certain genetic conditions are relatively common including cystic fibrosis, Joubert, and Meckel syndromes. Furthermore, numerous rare congenital malformations and metabolic disorders have been reported. We review the single gene disorders that have been studied at the molecular level in the UAE (which currently stand at 76) and compile the mutations found. Several novel (p.S2439fs) mutations have been reported including c.7317delA in NF1, c.5C>T (p.A2V) in DKC1, c.1766T>A (p.I589N) in TP63, and c.2117G>T (p.R706L) in VLDLR. We hope that this review will form the basis to establish a UAE mutations database and serve as a model for the collection of mutations of a country.
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Affiliation(s)
- Lihadh Al-Gazali
- Departments of Paediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates.
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Papachatzopoulou A, Kourakli A, Stavrou EF, Fragou E, Vantarakis A, Patrinos GP, Athanassiadou A. Region-Specific Genetic Heterogeneity ofHBBMutation Distribution in South-Western Greece. Hemoglobin 2010; 34:333-42. [DOI: 10.3109/03630269.2010.486354] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Latheef SA. A database for inborn errors of metabolism in the Indian state of Andhra Pradesh. Bioinformation 2010; 4:276-7. [PMID: 20978599 PMCID: PMC2957769 DOI: 10.6026/97320630004276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 12/12/2009] [Indexed: 11/26/2022] Open
Abstract
UNLABELLED A Database for Inborn Errors of Metabolism (IEM) in the Indian State of Andhra Pradesh (DIEMISAP), is a continuously updated literature depository containing the extensive information on the regional prevalence and heterogeneity of Inborn Errors of metabolism. We report the construction of a database, a flat file and secondary data resource developed using Microsoft Front Page as the core engine. The database contains 18 summaries regarding 43 IEM disorders reported in the AP population, both in general and region wise, with references and links to the IEM disorder databases available on web and institutes involved in IEM research, in India. Summaries can be accessed from the reference given against an alphabetically arranged list of IEM disorders. The DIEMISAP is a useful user friendly and extendable online resource for information on prevalence of IEM in AP. AVAILABILITY http://biochem.uohyd.ernet.in.
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Affiliation(s)
- Shaik Abdul Latheef
- Department of Biochemistry, School of Life Sciences University of Hyderabad, Hyderabad, India
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Falik-Zaccai TC, Khayat M, Luder A, Frenkel P, Magen D, Brik R, Gershoni-Baruch R, Mandel H. A broad spectrum of developmental delay in a large cohort of prolidase deficiency patients demonstrates marked interfamilial and intrafamilial phenotypic variability. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:46-56. [PMID: 19308961 DOI: 10.1002/ajmg.b.30945] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Prolidase deficiency (PD) is a rare, pan-ethnic, autosomal recessive disease with a broad phenotypic spectrum. Seventeen causative mutations in the PEPD gene have been reported worldwide. The purpose of this study is to characterize, clinically and molecularly, 20 prolidase deficient patients of Arab Moslem and Druze origin from 10 kindreds residing in northern Israel. All PD patients manifested developmental delay and facial dysmorphism. Typical PD dermatological symptoms, splenomegaly, and recurrent respiratory infections presented in varying degrees. Two patients had systemic lupus erythematosus (SLE), and one a novel cystic fibrosis phenotype. Direct DNA sequencing revealed two novel missense mutations, A212P and L368R. In addition, a previously reported S202F mutation was detected in 17 patients from seven Druze and three Arab Moslem kindreds. Patients homozygous for the S202F mutation manifest considerable interfamilial and intrafamilial phenotypic variability. The high prevalence of this mutation among Arab Moslems and Druze residing in northern Israel, and the presence of an identical haplotype along 500,000 bp in patients and their parents, suggests a founder event tracing back to before the breakaway of the Druze from mainstream Moslem society.
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[Genetic mutation databases: stakes and perspectives for orphan genetic diseases]. PATHOLOGIE-BIOLOGIE 2009; 58:387-95. [PMID: 19954899 DOI: 10.1016/j.patbio.2009.09.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/14/2009] [Indexed: 12/30/2022]
Abstract
New technologies, which constantly become available for mutation detection and gene analysis, have contributed to an exponential rate of discovery of disease genes and variation in the human genome. The task of collecting and documenting this enormous amount of data in genetic databases represents a major challenge for the future of biological and medical science. The Locus Specific Databases (LSDBs) are so far the most efficient mutation databases. This review presents the main types of databases available for the analysis of mutations responsible for genetic disorders, as well as open perspectives for new therapeutic research or challenges for future medicine. Accurate and exhaustive collection of variations in human genomes will be crucial for research and personalized delivery of healthcare.
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Abstract
PURPOSE The Druze community is characterized by consanguinity and endogamy, and by reluctance to genetic testing and technological interventions for the prevention of birth defects. Multiple patients with four rare and severe inborn errors of metabolism cerebrotendinous xanthomatosis, prolidase deficiency, argininosuccinate lyase deficiency, and carbamyl phosphate synthetase I deficiency were identified in an isolated Druze village in northern Israel. The aims of this study were to identify couples at risk for four inherited diseases, and to prevent birth defects in a community presenting religious and cultural obstacles to genetic testing. METHODS A genetic screening and counseling program in a high-risk community. RESULTS The 1425 residents who attended group genetic counseling sessions between 2003 and 2007 consented to genetic testing. We identified 217 carriers for either one or two disease causing mutations. High carrier frequencies for cerebrotendinous xanthomatosis, prolidase deficiency, argininosuccinate lyase deficiency, and carbamyl phosphate synthetase I deficiency were identified as 1:11, 1:21, 1:41, and 1:95, respectively. Fifty-eight percent (125) of the carriers' spouses agreed to genetic counseling and testing. Ten couples at risk for affected offspring were identified and offered prenatal genetic counseling and diagnosis. CONCLUSIONS The genetic screening program, the first of its kind reported in a Druze community, was well received. We expect this program to increase awareness of genetic counseling, to contribute to disease prevention, and to serve as a model for other isolated communities.
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