<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Salgado, David</style></author><author><style face="normal" font="default" size="100%">Armean, Irina M</style></author><author><style face="normal" font="default" size="100%">Baudis, Michael</style></author><author><style face="normal" font="default" size="100%">Beltran, Sergi</style></author><author><style face="normal" font="default" size="100%">Capella-Gutíerrez, Salvador</style></author><author><style face="normal" font="default" size="100%">Carvalho-Silva, Denise</style></author><author><style face="normal" font="default" size="100%">Dominguez Del Angel, Victoria</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Furlong, Laura I</style></author><author><style face="normal" font="default" size="100%">Gao, Bo</style></author><author><style face="normal" font="default" size="100%">Garcia, Leyla</style></author><author><style face="normal" font="default" size="100%">Gerloff, Dietlind</style></author><author><style face="normal" font="default" size="100%">Gut, Ivo</style></author><author><style face="normal" font="default" size="100%">Gyenesei, Attila</style></author><author><style face="normal" font="default" size="100%">Habermann, Nina</style></author><author><style face="normal" font="default" size="100%">Hancock, John M</style></author><author><style face="normal" font="default" size="100%">Hanauer, Marc</style></author><author><style face="normal" font="default" size="100%">Hovig, Eivind</style></author><author><style face="normal" font="default" size="100%">Johansson, Lennart F</style></author><author><style face="normal" font="default" size="100%">Keane, Thomas</style></author><author><style face="normal" font="default" size="100%">Korbel, Jan</style></author><author><style face="normal" font="default" size="100%">Lauer, Katharina B</style></author><author><style face="normal" font="default" size="100%">Laurie, Steve</style></author><author><style face="normal" font="default" size="100%">Leskošek, Brane</style></author><author><style face="normal" font="default" size="100%">Lloyd, David</style></author><author><style face="normal" font="default" size="100%">Marqués-Bonet, Tomás</style></author><author><style face="normal" font="default" size="100%">Mei, Hailiang</style></author><author><style face="normal" font="default" size="100%">Monostory, Katalin</style></author><author><style face="normal" font="default" size="100%">Piñero, Janet</style></author><author><style face="normal" font="default" size="100%">Poterlowicz, Krzysztof</style></author><author><style face="normal" font="default" size="100%">Rath, Ana</style></author><author><style face="normal" font="default" size="100%">Samarakoon, Pubudu</style></author><author><style face="normal" font="default" size="100%">Sanz, Ferran</style></author><author><style face="normal" font="default" size="100%">Saunders, Gary</style></author><author><style face="normal" font="default" size="100%">Sie, Daoud</style></author><author><style face="normal" font="default" size="100%">Swertz, Morris A</style></author><author><style face="normal" font="default" size="100%">Tsukanov, Kirill</style></author><author><style face="normal" font="default" size="100%">Valencia, Alfonso</style></author><author><style face="normal" font="default" size="100%">Vidak, Marko</style></author><author><style face="normal" font="default" size="100%">Yenyxe González, Cristina</style></author><author><style face="normal" font="default" size="100%">Ylstra, Bauke</style></author><author><style face="normal" font="default" size="100%">Béroud, Christophe</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research.</style></title><secondary-title><style face="normal" font="default" size="100%">F1000Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">F1000Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Copy Number Variations</style></keyword><keyword><style  face="normal" font="default" size="100%">High-Throughput Nucleotide Sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While &quot;High-Throughput&quot; sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR's recently established   with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.&lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/34367618?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bogliolo, Massimo</style></author><author><style face="normal" font="default" size="100%">Pujol, Roser</style></author><author><style face="normal" font="default" size="100%">Aza-Carmona, Miriam</style></author><author><style face="normal" font="default" size="100%">Muñoz-Subirana, Núria</style></author><author><style face="normal" font="default" size="100%">Rodriguez-Santiago, Benjamin</style></author><author><style face="normal" font="default" size="100%">Casado, José Antonio</style></author><author><style face="normal" font="default" size="100%">Rio, Paula</style></author><author><style face="normal" font="default" size="100%">Bauser, Christopher</style></author><author><style face="normal" font="default" size="100%">Reina-Castillón, Judith</style></author><author><style face="normal" font="default" size="100%">Lopez-Sanchez, Marcos</style></author><author><style face="normal" font="default" size="100%">Gonzalez-Quereda, Lidia</style></author><author><style face="normal" font="default" size="100%">Gallano, Pia</style></author><author><style face="normal" font="default" size="100%">Catalá, Albert</style></author><author><style face="normal" font="default" size="100%">Ruiz-Llobet, Ana</style></author><author><style face="normal" font="default" size="100%">Badell, Isabel</style></author><author><style face="normal" font="default" size="100%">Diaz-Heredia, Cristina</style></author><author><style face="normal" font="default" size="100%">Hladun, Raquel</style></author><author><style face="normal" font="default" size="100%">Senent, Leonort</style></author><author><style face="normal" font="default" size="100%">Argiles, Bienvenida</style></author><author><style face="normal" font="default" size="100%">Bergua Burgues, Juan Miguel</style></author><author><style face="normal" font="default" size="100%">Bañez, Fatima</style></author><author><style face="normal" font="default" size="100%">Arrizabalaga, Beatriz</style></author><author><style face="normal" font="default" size="100%">López Almaraz, Ricardo</style></author><author><style face="normal" font="default" size="100%">Lopez, Monica</style></author><author><style face="normal" font="default" size="100%">Figuera, Ángela</style></author><author><style face="normal" font="default" size="100%">Molinés, Antonio</style></author><author><style face="normal" font="default" size="100%">Pérez de Soto, Inmaculada</style></author><author><style face="normal" font="default" size="100%">Hernando, Inés</style></author><author><style face="normal" font="default" size="100%">Muñoz, Juan Antonio</style></author><author><style face="normal" font="default" size="100%">Del Rosario Marin, Maria</style></author><author><style face="normal" font="default" size="100%">Balmaña, Judith</style></author><author><style face="normal" font="default" size="100%">Stjepanovic, Neda</style></author><author><style face="normal" font="default" size="100%">Carrasco, Estela</style></author><author><style face="normal" font="default" size="100%">Cuesta, Isabel</style></author><author><style face="normal" font="default" size="100%">Cosuelo, José Miguel</style></author><author><style face="normal" font="default" size="100%">Regueiro, Alexandra</style></author><author><style face="normal" font="default" size="100%">Moraleda Jimenez, José</style></author><author><style face="normal" font="default" size="100%">Galera-Miñarro, Ana Maria</style></author><author><style face="normal" font="default" size="100%">Rosiñol, Laura</style></author><author><style face="normal" font="default" size="100%">Carrió, Anna</style></author><author><style face="normal" font="default" size="100%">Beléndez-Bieler, Cristina</style></author><author><style face="normal" font="default" size="100%">Escudero Soto, Antonio</style></author><author><style face="normal" font="default" size="100%">Cela, Elena</style></author><author><style face="normal" font="default" size="100%">de la Mata, Gregorio</style></author><author><style face="normal" font="default" size="100%">Fernández-Delgado, Rafael</style></author><author><style face="normal" font="default" size="100%">Garcia-Pardos, Maria Carmen</style></author><author><style face="normal" font="default" size="100%">Sáez-Villaverde, Raquel</style></author><author><style face="normal" font="default" size="100%">Barragaño, Marta</style></author><author><style face="normal" font="default" size="100%">Portugal, Raquel</style></author><author><style face="normal" font="default" size="100%">Lendinez, Francisco</style></author><author><style face="normal" font="default" size="100%">Hernadez, Ines</style></author><author><style face="normal" font="default" size="100%">Vagace, José Manue</style></author><author><style face="normal" font="default" size="100%">Tapia, Maria</style></author><author><style face="normal" font="default" size="100%">Nieto, José</style></author><author><style face="normal" font="default" size="100%">Garcia, Marta</style></author><author><style face="normal" font="default" size="100%">Gonzalez, Macarena</style></author><author><style face="normal" font="default" size="100%">Vicho, Cristina</style></author><author><style face="normal" font="default" size="100%">Galvez, Eva</style></author><author><style face="normal" font="default" size="100%">Valiente, Alberto</style></author><author><style face="normal" font="default" size="100%">Antelo, Maria Luisa</style></author><author><style face="normal" font="default" size="100%">Ancliff, Phil</style></author><author><style face="normal" font="default" size="100%">García, Francisco</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Sevilla, Julian</style></author><author><style face="normal" font="default" size="100%">Paprotka, Tobias</style></author><author><style face="normal" font="default" size="100%">Pérez-Jurado, Luis Alberto</style></author><author><style face="normal" font="default" size="100%">Bueren, Juan</style></author><author><style face="normal" font="default" size="100%">Surralles, Jordi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies.</style></title><secondary-title><style face="normal" font="default" size="100%">J Med Genet</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J Med Genet</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Cell Line</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Copy Number Variations</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Repair</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA-Binding Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Fanconi Anemia</style></keyword><keyword><style  face="normal" font="default" size="100%">Fanconi Anemia Complementation Group A Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">Female</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Knockout Techniques</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Predisposition to Disease</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Male</style></keyword><keyword><style  face="normal" font="default" size="100%">Mutation, Missense</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Single Nucleotide</style></keyword><keyword><style  face="normal" font="default" size="100%">whole exome sequencing</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 04</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">57</style></volume><pages><style face="normal" font="default" size="100%">258-268</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;PURPOSE: &lt;/b&gt;Patients with Fanconi anaemia (FA), a rare DNA repair genetic disease, exhibit chromosome fragility, bone marrow failure, malformations and cancer susceptibility. FA molecular diagnosis is challenging since FA is caused by point mutations and large deletions in 22 genes following three heritability patterns. To optimise FA patients' characterisation, we developed a simplified but effective methodology based on whole exome sequencing (WES) and functional studies.&lt;/p&gt;&lt;p&gt;&lt;b&gt;METHODS: &lt;/b&gt;68 patients with FA were analysed by commercial WES services. Copy number variations were evaluated by sequencing data analysis with RStudio. To test  missense variants, wt FANCA cDNA was cloned and variants were introduced by site-directed mutagenesis. Vectors were then tested for their ability to complement DNA repair defects of a FANCA-KO human cell line generated by TALEN technologies.&lt;/p&gt;&lt;p&gt;&lt;b&gt;RESULTS: &lt;/b&gt;We identified 93.3% of mutated alleles including large deletions. We determined the pathogenicity of three FANCA missense variants and demonstrated that two  variants reported in mutations databases as 'affecting functions' are SNPs. Deep analysis of sequencing data revealed patients' true mutations, highlighting the importance of functional analysis. In one patient, no pathogenic variant could be identified in any of the 22 known FA genes, and in seven patients, only one deleterious variant could be identified (three patients each with FANCA and FANCD2 and one patient with FANCE mutations) CONCLUSION: WES and proper bioinformatics analysis are sufficient to effectively characterise patients with FA regardless of the rarity of their complementation group, type of mutations, mosaic condition and DNA source.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/31586946?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">López-López, Daniel</style></author><author><style face="normal" font="default" size="100%">Loucera, Carlos</style></author><author><style face="normal" font="default" size="100%">Carmona, Rosario</style></author><author><style face="normal" font="default" size="100%">Aquino, Virginia</style></author><author><style face="normal" font="default" size="100%">Salgado, Josefa</style></author><author><style face="normal" font="default" size="100%">Pasalodos, Sara</style></author><author><style face="normal" font="default" size="100%">Miranda, María</style></author><author><style face="normal" font="default" size="100%">Alonso, Ángel</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">SMN1 copy-number and sequence variant analysis from next-generation sequencing data.</style></title><secondary-title><style face="normal" font="default" size="100%">Hum Mutat</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Hum Mutat</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Copy Number Variations</style></keyword><keyword><style  face="normal" font="default" size="100%">High-Throughput Nucleotide Sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Reproducibility of Results</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Survival of Motor Neuron 1 Protein</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2020 12</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">41</style></volume><pages><style face="normal" font="default" size="100%">2073-2077</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Spinal muscular atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy-number by next-generation sequencing (NGS) very difficult. Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy-number using NGS data. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify silent carriers. This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes Project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation. This combination makes it especially suitable to be integrated into production NGS pipelines. Source code and documentation are available at https://www.github.com/babelomics/SMAca.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/33058415?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bravo-Gil, Nereida</style></author><author><style face="normal" font="default" size="100%">Méndez-Vidal, Cristina</style></author><author><style face="normal" font="default" size="100%">Romero-Pérez, Laura</style></author><author><style face="normal" font="default" size="100%">González-del Pozo, María</style></author><author><style face="normal" font="default" size="100%">Rodríguez-de la Rúa, Enrique</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Borrego, Salud</style></author><author><style face="normal" font="default" size="100%">Antiňolo, Guillermo</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel.</style></title><secondary-title><style face="normal" font="default" size="100%">Sci Rep</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Sci Rep</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Alleles</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Simulation</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Copy Number Variations</style></keyword><keyword><style  face="normal" font="default" size="100%">DNA Mutational Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Eye Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Library</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Association Studies</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Heterogeneity</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic Therapy</style></keyword><keyword><style  face="normal" font="default" size="100%">High-Throughput Nucleotide Sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">Phenotype</style></keyword><keyword><style  face="normal" font="default" size="100%">Retinal Dystrophies</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Apr 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">23910</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Next-generation sequencing (NGS) has overcome important limitations to the molecular diagnosis of Inherited Retinal Dystrophies (IRD) such as the high clinical and genetic heterogeneity and the overlapping phenotypes. The purpose of this study was the identification of the genetic defect in 32 Spanish families with different forms of IRD. With that aim, we implemented a custom NGS panel comprising 64 IRD-associated genes in our population, and three disease-associated intronic regions. A total of 37 pathogenic mutations (14 novels) were found in 73% of IRD patients ranging from 50% for autosomal dominant cases, 75% for syndromic cases, 83% for autosomal recessive cases, and 100% for X-linked cases. Additionally, unexpected phenotype-genotype correlations were found in 6 probands, which led to the refinement of their clinical diagnoses. Furthermore, intra- and interfamilial phenotypic variability was observed in two cases. Moreover, two cases unsuccessfully analysed by exome sequencing were resolved by applying this panel. Our results demonstrate that this hypothesis-free approach based on frequently mutated, population-specific loci is highly cost-efficient for the routine diagnosis of this heterogeneous condition and allows the unbiased analysis of a miscellaneous cohort. The molecular information found here has aid clinical diagnosis and has improved genetic counselling and patient management. &lt;/p&gt;</style></abstract><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27032803?dopt=Abstract</style></custom1></record></records></xml>