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      High frequency of CHD7 mutations in congenital hypogonadotropic hypogonadism

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          Abstract

          Congenital hypogonadotropic hypogonadism (CHH) is characterized by lack of normal pubertal development due to deficient gonadotropin-releasing hormone (GnRH) secretion or action, and is caused by genetic defects in several genes. Mutations in the CHD7 gene cause CHARGE syndrome (Coloboma of the eye, Heart defects, Atresia of the choanae, Retardation of growth and development, Genital hypoplasia and Ear abnormalities), but have also been found in patients with isolated CHH. The aim of this study was to identify CHD7 mutations in patients with CHH. Fifty Portuguese patients with CHH were screened for mutations in the CHD7 gene by DNA sequencing. Eight (16%) patients had CHD7 rare sequence variants that consisted of six missense (p.Gly388Glu, p.His903Pro, p.Thr1082Ile, p.Val1452Leu, p.Asp1854Gly, and p.Arg2065His) and two synonymous (p.Ser559Ser, and p.Ala2785Ala) mutations. Five of these mutations have never been reported before. Three CHD7 mutations occurred in patients that had mutations in additional CHH-genes. This study uncovered novel genetic variants that expand the known spectrum of mutations associated with CHH. The frequency of CHD7 mutations in this cohort was higher than that of other major CHH-genes and confirms the importance of including CHD7 in the genetic testing of CHH, even in the absence of additional CHARGE features.

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          Primer3Plus, an enhanced web interface to Primer3

          Here we present Primer3Plus, a new web interface to the popular Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. Primer3 consists of a command line program and a web interface. The web interface is one large form showing all of the possible options. This makes the interface powerful, but at the same time confusing for occasional users. Primer3Plus provides an intuitive user interface using present-day web technologies and has been developed in close collaboration with molecular biologists and technicians regularly designing primers. It focuses on the task at hand, and hides detailed settings from the user until these are needed. We also added functionality to automate specific tasks like designing primers for cloning or step-wise sequencing. Settings and designed primer sequences can be stored locally for later use. Primer3Plus supports a range of common sequence formats, such as FASTA. Finally, primers selected by Primer3Plus can be sent to an order form, allowing tight integration into laboratory ordering systems. Moreover, the open architecture of Primer3Plus allows easy expansion or integration of external software packages. The Primer3Plus Perl source code is available under GPL license from SourceForge. Primer3Plus is available at http://www.bioinformatics.nl/primer3plus.
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            Nomenclature for the description of human sequence variations.

            A nomenclature system has recently been suggested for the description of changes (mutations and polymorphisms) in DNA and protein sequences. These nomenclature recommendations have now been largely accepted. However, current rules do not yet cover all types of mutations, nor do they cover more complex mutations. This document lists the existing recommendations and summarizes suggestions for the description of additional, more complex changes. Another version of this paper has been published in Hum Mut 15:7-12, 2000.
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              Oligogenic basis of isolated gonadotropin-releasing hormone deficiency.

              Between the genetic extremes of rare monogenic and common polygenic diseases lie diverse oligogenic disorders involving mutations in more than one locus in each affected individual. Elucidating the principles of oligogenic inheritance and mechanisms of genetic interactions could help unravel the newly appreciated role of rare sequence variants in polygenic disorders. With few exceptions, however, the precise genetic architecture of oligogenic diseases remains unknown. Isolated gonadotropin-releasing hormone (GnRH) deficiency caused by defective secretion or action of hypothalamic GnRH is a rare genetic disease that manifests as sexual immaturity and infertility. Recent reports of patients who harbor pathogenic rare variants in more than one gene have challenged the long-held view that the disorder is strictly monogenic, yet the frequency and extent of oligogenicity in isolated GnRH deficiency have not been investigated. By systematically defining genetic variants in large cohorts of well-phenotyped patients (n = 397), family members, and unaffected subjects (n = 179) for the majority of known disease genes, this study suggests a significant role of oligogenicity in this disease. Remarkably, oligogenicity in isolated GnRH deficiency was as frequent as homozygosity/compound heterozygosity at a single locus (2.5%). Among the 22% of patients with detectable rare protein-altering variants, the likelihood of oligogenicity was 11.3%. No oligogenicity was detected among controls (P < 0.05), even though deleterious variants were present. Viewing isolated GnRH deficiency as an oligogenic condition has implications for understanding the pathogenesis of its reproductive and nonreproductive phenotypes; deciphering the etiology of common GnRH-related disorders; and modeling the genetic architecture of other oligogenic and multifactorial diseases.
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                Author and article information

                Contributors
                mclemos@fcsaude.ubi.pt
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                7 February 2019
                7 February 2019
                2019
                : 9
                : 1597
                Affiliations
                [1 ]ISNI 0000 0001 2220 7094, GRID grid.7427.6, CICS-UBI, Health Sciences Research Centre, , University of Beira Interior, ; 6200-506 Covilhã, Portugal
                [2 ]ISNI 0000 0001 2295 9747, GRID grid.411265.5, Serviço de Endocrinologia, Diabetes e Metabolismo, , Hospital de Santa Maria, ; 1649-035 Lisboa, Portugal
                [3 ]ISNI 0000 0001 1503 7226, GRID grid.5808.5, Serviço de Endocrinologia, Diabetes e Metabolismo, Centro Hospitalar de São João and Faculty of Medicine and Instituto de Investigação e Inovação em Saúde, , University of Porto, ; 4200-319 Porto, Portugal
                [4 ]ISNI 0000 0000 9647 1835, GRID grid.413362.1, Serviço de Endocrinologia, Diabetes e Metabolismo, , Hospital de Curry Cabral, ; 1069-166 Lisboa, Portugal
                [5 ]Unidade de Endocrinologia Pediátrica, Serviço de Pediatria, Hospital de Braga, 4710-243 Braga, Portugal
                [6 ]Serviço de Endocrinologia, Hospital de Braga, 4710-243 Braga, Portugal
                [7 ]ISNI 0000 0000 8563 4416, GRID grid.414708.e, Serviço de Endocrinologia e Diabetes, Hospital Garcia de Orta, ; 2805-267 Almada, Portugal
                Author information
                http://orcid.org/0000-0001-9326-8900
                Article
                38178
                10.1038/s41598-018-38178-y
                6367338
                30733481
                d6e24002-a71d-4add-9e78-c283b15ac84b
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 14 August 2018
                : 17 December 2018
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100001871, Ministry of Education and Science | Funda&amp;#x00E7;&amp;#x00E3;o para a Ci&amp;#x00EA;ncia e a Tecnologia (Portuguese Science and Technology Foundation);
                Award ID: PTDC/SAU-GMG/098419/2008
                Award ID: PTDC/SAU-GMG/098419/2008
                Award Recipient :
                Funded by: Programa Operacional do Centro, Centro 2020, CENTRO-01-0145-FEDER-000013
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