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1. Case report: Identification of a novel variant p.Gly215Arg in the CHN1 gene causing Moebius syndrome

Author

Manso-Bazús, Carmen, primary, Spataro, Nino, additional, Gabau, Elisabeth, additional, Beltrán-Salazar, Viviana P., additional, Trujillo-Quintero, Juan Pablo, additional, Capdevila, Nuria, additional, Brunet-Vega, Anna, additional, Baena, Neus, additional, Jeyaprakash, A Arockia, additional, Martinez-Glez, Victor, additional, and Ruiz, Anna, additional

Published
2024
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2. Elimination of lipaemic interference by high-speed centrifugation

Author

Solé-Enrech, Gemma, Cano-Corres, Ruth, Aparicio-Calvente, Maria Isabel, Spataro, Nino, Solé-Enrech, Gemma, Cano-Corres, Ruth, Aparicio-Calvente, Maria Isabel, and Spataro, Nino

Abstract

IntroductionIn order to deliver high quality results, detection and elimination of possible analytical interferences, such as lipaemia, is crucial. The aim of this study is to evaluate the efficacy of high-speed centrifugation in eliminating lipaemic interference and to define own lipaemic index (LI) for the studied biochemical analytes. Materials and methodsEvaluated analytes were: albumin, alkaline phosphatase, alanine-aminotransferase (ALT), aspartate-aminotransferase (AST), calcium, creatinine, gamma-glutamyltransferase (GGT), glucose, phosphates, total proteins, urea and total bilirubin. Those analytes and LIs have been analysed in duplicate in the Roche Diagnostics-c8000 analyser in samples centrifuged at 3000 rpm/10 minutes in the SL16 (Thermo Scientific, Waltham, USA) centrifuge and according to an own high-speed centrifugation protocol (12,900 rpm/15 minutes) in the MicroCL17R (Thermo Scientific, Waltham, USA) centrifuge. Lipaemia has been measured in each sample. The efficiency of high-speed centrifugation is verified by the Wilcoxon test (P < 0.05). In cases where significant differences are observed, our own LI is calculated. For ALT and AST, it is verified by McNemar test (P < 0.05). For creatinine, both Wilcoxon and McNemar test were applied. ResultsThere were statistically significant differences in analyte concentration before and after high-speed centrifugation for: albumin, creatinine, GGT, glucose, phosphates, urea and total bilirrubin. Own LI is calculated. McNemar test shows statistically significant diferences in the proportion of delivered results before and after high-speed centrifugation in ALT, AST and creatinine. ConclusionsThis study confirms the efficacy of high-speed centrifugation protocol for all the considered analytes, excepting calcium, alkaline phosphatase and total proteins.

Published
2023

3. High Performance of a Dominant/X-Linked Gene Panel in Patients with Neurodevelopmental Disorders

Author

Spataro, Nino, primary, Trujillo-Quintero, Juan Pablo, additional, Manso, Carmen, additional, Gabau, Elisabeth, additional, Capdevila, Nuria, additional, Martinez-Glez, Victor, additional, Berenguer-Llergo, Antoni, additional, Reyes, Sara, additional, Brunet, Anna, additional, Baena, Neus, additional, Guitart, Miriam, additional, and Ruiz, Anna, additional

Published
2023
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4. Elimination of lipaemic interference by high-speed centrifugation

Author

Solé-Enrech, Gemma, Cano-Corres, Ruth, Aparicio-Calvente, Maria Isabel, and Spataro, Nino

Subjects
Biochemistry (medical), Clinical Biochemistry, lipaemia, high-speed centrifugation, lipaemic index
Abstract

IntroductionIn order to deliver high quality results, detection and elimination of possible analytical interferences, such as lipaemia, is crucial. The aim of this study is to evaluate the efficacy of high-speed centrifugation in eliminating lipaemic interference and to define own lipaemic index (LI) for the studied biochemical analytes. Materials and methodsEvaluated analytes were: albumin, alkaline phosphatase, alanine-aminotransferase (ALT), aspartate-aminotransferase (AST), calcium, creatinine, gamma-glutamyltransferase (GGT), glucose, phosphates, total proteins, urea and total bilirubin. Those analytes and LIs have been analysed in duplicate in the Roche Diagnostics-c8000 analyser in samples centrifuged at 3000 rpm/10 minutes in the SL16 (Thermo Scientific, Waltham, USA) centrifuge and according to an own high-speed centrifugation protocol (12,900 rpm/15 minutes) in the MicroCL17R (Thermo Scientific, Waltham, USA) centrifuge. Lipaemia has been measured in each sample. The efficiency of high-speed centrifugation is verified by the Wilcoxon test (P < 0.05). In cases where significant differences are observed, our own LI is calculated. For ALT and AST, it is verified by McNemar test (P < 0.05). For creatinine, both Wilcoxon and McNemar test were applied. ResultsThere were statistically significant differences in analyte concentration before and after high-speed centrifugation for: albumin, creatinine, GGT, glucose, phosphates, urea and total bilirrubin. Own LI is calculated. McNemar test shows statistically significant diferences in the proportion of delivered results before and after high-speed centrifugation in ALT, AST and creatinine. ConclusionsThis study confirms the efficacy of high-speed centrifugation protocol for all the considered analytes, excepting calcium, alkaline phosphatase and total proteins.

Published
2022
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6. De novo coding variants in the AGO1 gene cause a neurodevelopmental disorder with intellectual disability

Author

Genetica Sectie Genoomdiagnostiek, Child Health, Schalk, Audrey, Cousin, Margot A, Dsouza, Nikita R, Challman, Thomas D, Wain, Karen E, Powis, Zoe, Minks, Kelly, Trimouille, Aurélien, Lasseaux, Eulalie, Lacombe, Didier, Angelini, Chloé, Michaud, Vincent, Van-Gils, Julien, Spataro, Nino, Ruiz, Anna, Gabau, Elizabeth, Stolerman, Elliot, Washington, Camerun, Louie, Ray, Lanpher, Brendan C, Kemppainen, Jennifer L, Innes, Micheil, Kooy, Frank, Meuwissen, Marije, Goldenberg, Alice, Lecoquierre, Francois, Vera, Gabriella, Diderich, Karin E M, Sheidley, Beth, El Achkar, Christelle Moufawad, Park, Meredith, Hamdan, Fadi F, Michaud, Jacques L, Lewis, Ann J, Zweier, Christiane, Reis, André, Wagner, Matias, Weigand, Heike, Journel, Hubert, Keren, Boris, Passemard, Sandrine, Mignot, Cyril, van Gassen, Koen, Brilstra, Eva H, Itzikowitz, Gina, O'Heir, Emily, Allen, Jake, Donald, Kirsten A, Korf, Bruce Richard, Skelton, Tammi, Thompson, Michelle, Robin, Nathaniel H, Rudy, Natasha L, Dobyns, William B, Foss, Kimberly, Zarate, Yuri Alexander, Bosanko, Katherine A, Alembik, Yves, Durand, Benjamin, Tran Mau-Them, Frederic, Ranza, Emmanuelle, Blanc, Xavier, Antonarakis, Stylianos E, McWalter, Kirsty, Torti, Erin, Millan, Francisca, Dameron, Amy, Tokita, Mari, Zimmermann, Michael T, Klee, Eric W, Piton, Amelie, Gerard, Benedicte, Genetica Sectie Genoomdiagnostiek, Child Health, Schalk, Audrey, Cousin, Margot A, Dsouza, Nikita R, Challman, Thomas D, Wain, Karen E, Powis, Zoe, Minks, Kelly, Trimouille, Aurélien, Lasseaux, Eulalie, Lacombe, Didier, Angelini, Chloé, Michaud, Vincent, Van-Gils, Julien, Spataro, Nino, Ruiz, Anna, Gabau, Elizabeth, Stolerman, Elliot, Washington, Camerun, Louie, Ray, Lanpher, Brendan C, Kemppainen, Jennifer L, Innes, Micheil, Kooy, Frank, Meuwissen, Marije, Goldenberg, Alice, Lecoquierre, Francois, Vera, Gabriella, Diderich, Karin E M, Sheidley, Beth, El Achkar, Christelle Moufawad, Park, Meredith, Hamdan, Fadi F, Michaud, Jacques L, Lewis, Ann J, Zweier, Christiane, Reis, André, Wagner, Matias, Weigand, Heike, Journel, Hubert, Keren, Boris, Passemard, Sandrine, Mignot, Cyril, van Gassen, Koen, Brilstra, Eva H, Itzikowitz, Gina, O'Heir, Emily, Allen, Jake, Donald, Kirsten A, Korf, Bruce Richard, Skelton, Tammi, Thompson, Michelle, Robin, Nathaniel H, Rudy, Natasha L, Dobyns, William B, Foss, Kimberly, Zarate, Yuri Alexander, Bosanko, Katherine A, Alembik, Yves, Durand, Benjamin, Tran Mau-Them, Frederic, Ranza, Emmanuelle, Blanc, Xavier, Antonarakis, Stylianos E, McWalter, Kirsty, Torti, Erin, Millan, Francisca, Dameron, Amy, Tokita, Mari, Zimmermann, Michael T, Klee, Eric W, Piton, Amelie, and Gerard, Benedicte

Published
2022

8. Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases

Author

Bullich, Gemma, primary, Matalonga, Leslie, additional, Pujadas, Montserrat, additional, Papakonstantinou, Anastasios, additional, Piscia, Davide, additional, Tonda, Raúl, additional, Artuch, Rafael, additional, Gallano, Pia, additional, Garrabou, Glòria, additional, González, Juan R., additional, Grinberg, Daniel, additional, Guitart, Míriam, additional, Laurie, Steven, additional, Lázaro, Conxi, additional, Luengo, Cristina, additional, Martí, Ramon, additional, Milà, Montserrat, additional, Ovelleiro, David, additional, Parra, Genís, additional, Pujol, Aurora, additional, Tizzano, Eduardo, additional, Macaya, Alfons, additional, Palau, Francesc, additional, Ribes, Antònia, additional, Pérez-Jurado, Luis A., additional, Beltran, Sergi, additional, Schlüter, Agatha, additional, Rodriguez-Palmero, Agustí, additional, Cáceres, Alejandro, additional, Nascimento, Andrés, additional, García-Cazorla, Àngels, additional, Cueto-González, Anna, additional, Marcé-Grau, Anna, additional, Nel.lo, Anna Ruiz, additional, Martínez-Monseny, Antonio, additional, Sànchez, Aurora, additional, García, Belén, additional, Pérez-Dueñas, Belén, additional, Gel, Bernat, additional, Fusté, Berta, additional, Hernández-Ferrer, Carles, additional, Casasnovas, Carlos, additional, Ortez, Carlos, additional, Arjona, César, additional, Hernando-Davalillo, Cristina, additional, de Benito, Daniel Natera, additional, Amador, Daniel Picó, additional, Gómez-Andrés, David, additional, Yubero, Dèlia, additional, Pelegrí-Sisó, Dolors, additional, Verdura, Edgard, additional, García-Arumí, Elena, additional, Castellanos, Elisabeth, additional, Gabau, Elisabeth, additional, Tobías, Ester, additional, López-Grondona, Fermina, additional, Cardellach, Francesc, additional, Garcia-Garcia, Francesc Josep, additional, Munell, Francina, additional, Tort, Frederic, additional, Aznar, Gemma, additional, Olivé-Cirera, Gemma, additional, Tell, Gemma, additional, Muñoz-Pujol, Gerard, additional, Paramonov, Ida, additional, Blanco, Ignacio, additional, Madrigal, Irene, additional, Valenzuela, Irene, additional, Gut, Ivo, additional, Cusco, Ivon, additional, Trotta, Jean-Rémi, additional, Cruz, Jordi, additional, Díaz-Manera, Jordi, additional, Milisenda, José César, additional, Ma Grau, Josep, additional, Garcia-Villoria, Judit, additional, Armstrong, Judith, additional, Cantó, Judith, additional, Sala-Coromina, Júlia, additional, Rodríguez-Revenga, Laia, additional, Alias, Laura, additional, Gort, Laura, additional, González-Quereda, Lídia, additional, Costa, Mar, additional, Fernández-Callejo, Marcos, additional, López-Sánchez, Marcos, additional, Álvarez-Mora, Maria Isabel, additional, Gut, Marta, additional, Serrano, Mercedes, additional, Raspall-Chaure, Miquel, additional, Toro, Mireia del, additional, Bayés, Mònica, additional, Díez, Neus Baena, additional, Spataro, Nino, additional, Capdevila, Núria, additional, Ugarteburu, Olatz, additional, Muñoz-Cabello, Patricia, additional, Duque, Penélope Romero, additional, Rabionet, Raquel, additional, Rojas-García, Ricard, additional, Calvo, Rosa, additional, Urreizti, Roser, additional, Bernal, Sara, additional, Boronat, Susana, additional, Balcells, Susanna, additional, and Vendrell, Teresa, additional

Published
2022
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9. De novo coding variants in the AGO1 gene cause a neurodevelopmental disorder with intellectual disability

Author

Schalk, Audrey, primary, Cousin, Margot A, additional, Dsouza, Nikita R, additional, Challman, Thomas D, additional, Wain, Karen E, additional, Powis, Zoe, additional, Minks, Kelly, additional, Trimouille, Aurélien, additional, Lasseaux, Eulalie, additional, Lacombe, Didier, additional, Angelini, Chloé, additional, Michaud, Vincent, additional, Van-Gils, Julien, additional, Spataro, Nino, additional, Ruiz, Anna, additional, Gabau, Elizabeth, additional, Stolerman, Elliot, additional, Washington, Camerun, additional, Louie, Ray, additional, Lanpher, Brendan C, additional, Kemppainen, Jennifer L, additional, Innes, Micheil, additional, Kooy, Frank, additional, Meuwissen, Marije, additional, Goldenberg, Alice, additional, Lecoquierre, Francois, additional, Vera, Gabriella, additional, Diderich, Karin E M, additional, Sheidley, Beth, additional, El Achkar, Christelle Moufawad, additional, Park, Meredith, additional, Hamdan, Fadi F, additional, Michaud, Jacques L, additional, Lewis, Ann J, additional, Zweier, Christiane, additional, Reis, André, additional, Wagner, Matias, additional, Weigand, Heike, additional, Journel, Hubert, additional, Keren, Boris, additional, Passemard, Sandrine, additional, Mignot, Cyril, additional, van Gassen, Koen, additional, Brilstra, Eva H, additional, Itzikowitz, Gina, additional, O'Heir, Emily, additional, Allen, Jake, additional, Donald, Kirsten A, additional, Korf, Bruce Richard, additional, Skelton, Tammi, additional, Thompson, Michelle, additional, Robin, Nathaniel H, additional, Rudy, Natasha L, additional, Dobyns, William B, additional, Foss, Kimberly, additional, Zarate, Yuri Alexander, additional, Bosanko, Katherine A, additional, Alembik, Yves, additional, Durand, Benjamin, additional, Tran Mau-them, Frederic, additional, Ranza, Emmanuelle, additional, Blanc, Xavier, additional, Antonarakis, Stylianos E, additional, McWalter, Kirsty, additional, Torti, Erin, additional, Millan, Francisca, additional, Dameron, Amy, additional, Tokita, Mari, additional, Zimmermann, Michael T, additional, Klee, Eric W, additional, Piton, Amelie, additional, and Gerard, Benedicte, additional

Published
2021
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10. New genes involved in Angelman syndrome-like: Expanding the genetic spectrum

Author

Aguilera, Cinthia, primary, Gabau, Elisabeth, additional, Ramirez-Mallafré, Ariadna, additional, Brun-Gasca, Carme, additional, Dominguez-Carral, Jana, additional, Delgadillo, Veronica, additional, Laurie, Steve, additional, Derdak, Sophia, additional, Padilla, Natàlia, additional, de la Cruz, Xavier, additional, Capdevila, Núria, additional, Spataro, Nino, additional, Baena, Neus, additional, Guitart, Miriam, additional, and Ruiz, Anna, additional

Published
2021
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12. De novo coding variants in the AGO1 gene cause a neurodevelopmental disorder with intellectual disability.

Author

Schalk, Audrey, Cousin, Margot A., Dsouza, Nikita R., Challman, Thomas D., Wain, Karen E., Powis, Zoe, Minks, Kelly, Trimouille, Aurélien, Lasseaux, Eulalie, Lacombe, Didier, Angelini, Chloé, Michaud, Vincent, Van-Gils, Julien, Spataro, Nino, Ruiz, Anna, Gabau, Elizabeth, Stolerman, Elliot, Washington, Camerun, Louie, Ray, and Lanpher, Brendan C.

Abstract

Background High-impact pathogenic variants in more than a thousand genes are involved in Mendelian forms of neurodevelopmental disorders (NDD). Methods This study describes the molecular and clinical characterisation of 28 probands with NDD harbouring heterozygous AGO1 coding variants, occurring de novo for all those whose transmission could have been verified (26/28). Results A total of 15 unique variants leading to amino acid changes or deletions were identified: 12 missense variants, two in- frame deletions of one codon, and one canonical splice variant leading to a deletion of two amino acid residues. Recurrently identified variants were present in several unrelated individuals: p.(Phe180del), p.(Leu190Pro), p.(Leu190Arg), p.(Gly199Ser), p.(Val254Ile) and p.(Glu376del). AGO1 encodes the Argonaute 1 protein, which functions in gene- silencing pathways mediated by small non- coding RNAs. Three- dimensional protein structure predictions suggest that these variants might alter the flexibility of the AGO1 linker domains, which likely would impair its function in mRNA processing. Affected individuals present with intellectual disability of varying severity, as well as speech and motor delay, autistic behaviour and additional behavioural manifestation Conclusion Our study establishes that de novo coding variants in AGO1 are involved in a novel monogenic form of NDD, highly similar to the recently reported AGO2-related NDD. [ABSTRACT FROM AUTHOR]

Published
2022
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13. Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence

Author

Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Generalitat de Catalunya, Instituto de Salud Carlos III, Instituto Nacional de Bioinformática (España), Red Española de Esclerosis Múltiple, Farré, Xavier, Spataro, Nino, Haziza, Frederic, Rambla, Jordi, Navarro, Arcadi, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, Generalitat de Catalunya, Instituto de Salud Carlos III, Instituto Nacional de Bioinformática (España), Red Española de Esclerosis Múltiple, Farré, Xavier, Spataro, Nino, Haziza, Frederic, Rambla, Jordi, and Navarro, Arcadi

Abstract

[Motivation] Association studies based on SNP arrays and Next Generation Sequencing technologies have enabled the discovery of thousands of genetic loci related to human diseases. Nevertheless, their biological interpretation is still elusive, and their medical applications limited. Recently, various tools have been developed to help bridging the gap between genomes and phenomes. To our knowledge, however none of these tools allows users to retrieve the phenotype-wide list of genetic variants that may be linked to a given disease or to visually explore the joint genetic architecture of different pathologies., [Results] We present the Genome-Phenome Explorer (GePhEx), a web-tool easing the visual exploration of phenotypic relationships supported by genetic evidences. GePhEx is primarily based on the thorough analysis of linkage disequilibrium between disease-associated variants and also considers relationships based on genes, pathways or drug-targets, leveraging on publicly available variant-disease associations to detect potential relationships between diseases. We demonstrate that GePhEx does retrieve well-known relationships as well as novel ones, and that, thus, it might help shedding light on the patho-physiological mechanisms underlying complex diseases. To this end, we investigate the potential relationship between schizophrenia and lung cancer, first detected using GePhEx and provide further evidence supporting a functional link between them.

Published
2020

14. A new risk variant for multiple sclerosis at 11q23.3 locus is associated with expansion of CXCR5+ circulating regulatory T cells

Author

European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), Gil-Varea, Elia, Fedetz, María, Eixarch, Herena, Spataro, Nino, Villar, Luisa María, Urcelay, Elena, Sáiz, Albert, Fernández, Óscar, Leyva, Laura, Ramió-Torrentà, Lluís, Vandenbroeck, Koen, Otaegui, David, Castillo-Triviño, Tamara, Izquierdo, Guillermo, Malhotra, Sunny, Bosch, Elena, Navarro, Arcadi, Alcina, Antonio, Montalbán, Xavier, Matesanz, F., Comabella, Manuel, European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Ministerio de Economía y Competitividad (España), Gil-Varea, Elia, Fedetz, María, Eixarch, Herena, Spataro, Nino, Villar, Luisa María, Urcelay, Elena, Sáiz, Albert, Fernández, Óscar, Leyva, Laura, Ramió-Torrentà, Lluís, Vandenbroeck, Koen, Otaegui, David, Castillo-Triviño, Tamara, Izquierdo, Guillermo, Malhotra, Sunny, Bosch, Elena, Navarro, Arcadi, Alcina, Antonio, Montalbán, Xavier, Matesanz, F., and Comabella, Manuel

Abstract

Genome-wide association studies and meta-analysis have contributed to the identification of more than 200 loci associated with multiple sclerosis (MS). However, a proportion of MS heritability remains unknown. We aimed to uncover new genetic variants associated with MS and determine their functional effects. For this, we resequenced the exons and regulatory sequences of 14 MS risk genes in a cohort of MS patients and healthy individuals (n = 1070) and attempted to validate a selection of signals through genotyping in an independent cohort (n = 5138). We identified three new MS-associated variants at C-X-C motif chemokine receptor 5 (CXCR5), Ts translation elongation factor, mitochondrial (TSFM) and cytochrome P450 family 24 subfamily A member 1 (CYP24A1). Rs10892307 resulted in a new signal at the CXCR5 region that explains one of the associations with MS within the locus. This polymorphism and three others in high linkage disequilibrium mapped within regulatory regions. Of them, rs11602393 showed allele-dependent enhancer activity in the forward orientation as determined by luciferase reporter assays. Immunophenotyping using peripheral blood mononuclear cells from MS patients associated the minor allele of rs10892307 with increased percentage of regulatory T cells expressing CXCR5. This work reports a new signal for the CXCR5 MS risk locus and points to rs11602393 as the causal variant. The expansion of CXCR5+ circulating regulatory T cells induced by this variant could cause its MS association.

Published
2020

15. FBXO28 causes developmental and epileptic encephalopathy with profound intellectual disability

Author

Schneider, Amy L., primary, Myers, Candace T., additional, Muir, Alison M., additional, Calvert, Sophie, additional, Basinger, Alice, additional, Perry, M. Scott, additional, Rodan, Lance, additional, Helbig, Katherine L., additional, Chambers, Chelsea, additional, Gorman, Kathleen M., additional, King, Mary D., additional, Donkervoort, Sandra, additional, Soldatos, Ariane, additional, Bönnemann, Carsten G., additional, Spataro, Nino, additional, Gabau, Elisabeth, additional, Arellano, Montserrat, additional, Cappuccio, Gerarda, additional, Brunetti‐Pierri, Nicola, additional, Rossignol, Elsa, additional, Hamdan, Fadi F., additional, Michaud, Jacques L., additional, Balak, Christopher, additional, Mefford, Heather C., additional, and Scheffer, Ingrid E., additional

Published
2020
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17. A New Risk Variant for Multiple Sclerosis at 11q23.3 Locus Is Associated with Expansion of CXCR5+ Circulating Regulatory T Cells

Author

Gil-Varea, Elia, primary, Fedetz, Maria, additional, Eixarch, Herena, additional, Spataro, Nino, additional, Villar, Luisa María, additional, Urcelay, Elena, additional, Saiz, Albert, additional, Fernández, Óscar, additional, Leyva, Laura, additional, Ramió-Torrentà, Lluís, additional, Vandenbroeck, Koen, additional, Otaegui, David, additional, Castillo-Triviño, Tamara, additional, Izquierdo, Guillermo, additional, Malhotra, Sunny, additional, Bosch, Elena, additional, Navarro, Arcadi, additional, Alcina, Antonio, additional, Montalban, Xavier, additional, Matesanz, Fuencisla, additional, and Comabella, Manuel, additional

Published
2020
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18. Reply to: Retesting the influences of mutation accumulation and antagonistic pleiotropy on human senescence and disease

Author

Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Rodríguez, Juan Antonio, Farré, Xavier, Muntané, Gerard, Marigorta, Urko M., Hughes, David A., Spataro, Nino, Bosch, Elena, Navarro, Arcadi, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Generalitat de Catalunya, Rodríguez, Juan Antonio, Farré, Xavier, Muntané, Gerard, Marigorta, Urko M., Hughes, David A., Spataro, Nino, Bosch, Elena, and Navarro, Arcadi

Abstract

Long and Zhang1 present empirical and conceptual objections to our results2. Concerning data, they observe that a single disease provides nearly all the support for mutation accumulation (MA). On a more theoretical note, they find no evidence for a putative prediction of antagonistic pleiotropy (AP): that at ‘each’ antagonistic pleiotropic single nucleotide polymorphism (SNP), the risk allele frequencies (RAFs) should be lower for early-onset rather than late-onset diseases.

Published
2019

20. De novocoding variants in the AGO1gene cause a neurodevelopmental disorder with intellectual disability

Author

Schalk, Audrey, Cousin, Margot A, Dsouza, Nikita R, Challman, Thomas D, Wain, Karen E, Powis, Zoe, Minks, Kelly, Trimouille, Aurélien, Lasseaux, Eulalie, Lacombe, Didier, Angelini, Chloé, Michaud, Vincent, Van-Gils, Julien, Spataro, Nino, Ruiz, Anna, Gabau, Elizabeth, Stolerman, Elliot, Washington, Camerun, Louie, Ray, Lanpher, Brendan C, Kemppainen, Jennifer L, Innes, Micheil, Kooy, Frank, Meuwissen, Marije, Goldenberg, Alice, Lecoquierre, Francois, Vera, Gabriella, Diderich, Karin E M, Sheidley, Beth, El Achkar, Christelle Moufawad, Park, Meredith, Hamdan, Fadi F, Michaud, Jacques L, Lewis, Ann J, Zweier, Christiane, Reis, André, Wagner, Matias, Weigand, Heike, Journel, Hubert, Keren, Boris, Passemard, Sandrine, Mignot, Cyril, van Gassen, Koen, Brilstra, Eva H, Itzikowitz, Gina, O'Heir, Emily, Allen, Jake, Donald, Kirsten A, Korf, Bruce Richard, Skelton, Tammi, Thompson, Michelle, Robin, Nathaniel H, Rudy, Natasha L, Dobyns, William B, Foss, Kimberly, Zarate, Yuri Alexander, Bosanko, Katherine A, Alembik, Yves, Durand, Benjamin, Tran Mau-them, Frederic, Ranza, Emmanuelle, Blanc, Xavier, Antonarakis, Stylianos E, McWalter, Kirsty, Torti, Erin, Millan, Francisca, Dameron, Amy, Tokita, Mari, Zimmermann, Michael T, Klee, Eric W, Piton, Amelie, and Gerard, Benedicte

Abstract

BackgroundHigh-impact pathogenic variants in more than a thousand genes are involved in Mendelian forms of neurodevelopmental disorders (NDD).MethodsThis study describes the molecular and clinical characterisation of 28 probands with NDD harbouring heterozygous AGO1coding variants, occurring de novo for all those whose transmission could have been verified (26/28).ResultsA total of 15 unique variants leading to amino acid changes or deletions were identified: 12 missense variants, two in-frame deletions of one codon, and one canonical splice variant leading to a deletion of two amino acid residues. Recurrently identified variants were present in several unrelated individuals: p.(Phe180del), p.(Leu190Pro), p.(Leu190Arg), p.(Gly199Ser), p.(Val254Ile) and p.(Glu376del). AGO1encodes the Argonaute 1 protein, which functions in gene-silencing pathways mediated by small non-coding RNAs. Three-dimensional protein structure predictions suggest that these variants might alter the flexibility of the AGO1 linker domains, which likely would impair its function in mRNA processing. Affected individuals present with intellectual disability of varying severity, as well as speech and motor delay, autistic behaviour and additional behavioural manifestations.ConclusionOur study establishes that de novo coding variants in AGO1are involved in a novel monogenic form of NDD, highly similar to the recently reported AGO2-related NDD.

Published
2022
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21. Functional relevance for CXCR5 variants associated with multiple sclerosis

Author

Gil-Varea, Elia, Fedetz, María, Spataro, Nino, Fernández, Óscar, Sáiz, Albert, Ramió-Torrentà, Lluís, Izquierdo, Guillermo, Malhotra, Sunny, Navarro, Arcadi, Bosch, Elena, Alcina, Antonio, Montalbán, Xavier, Matesanz, F., Comabella, Manuel, Gil-Varea, Elia, Fedetz, María, Spataro, Nino, Fernández, Óscar, Sáiz, Albert, Ramió-Torrentà, Lluís, Izquierdo, Guillermo, Malhotra, Sunny, Navarro, Arcadi, Bosch, Elena, Alcina, Antonio, Montalbán, Xavier, Matesanz, F., and Comabella, Manuel

Published
2018

22. The MS risk variant rs2762943 of the CYP24A1 gene is associated with decreased serum levels of the active form of vitamin D

Author

Gil-Varea, Elia, Matesanz, F., Ferrer, R., Spataro, Nino, Fernández, O., Sáiz, Albert, Ramió-Torrentà, Lluís, Izquierdo, Guillermo, Malhotra, Sunny, Navarro, Arcadi, Bosch, Elena, Alcina, Antonio, Montalbán, Xavier, Comabella, Manuel, Gil-Varea, Elia, Matesanz, F., Ferrer, R., Spataro, Nino, Fernández, O., Sáiz, Albert, Ramió-Torrentà, Lluís, Izquierdo, Guillermo, Malhotra, Sunny, Navarro, Arcadi, Bosch, Elena, Alcina, Antonio, Montalbán, Xavier, and Comabella, Manuel

Published
2018

23. FBXO28 causes developmental and epileptic encephalopathy with profound intellectual disability.

Author

Schneider, Amy L., Myers, Candace T., Muir, Alison M., Calvert, Sophie, Basinger, Alice, Perry, M. Scott, Rodan, Lance, Helbig, Katherine L., Chambers, Chelsea, Gorman, Kathleen M., King, Mary D., Donkervoort, Sandra, Soldatos, Ariane, Bönnemann, Carsten G., Spataro, Nino, Gabau, Elisabeth, Arellano, Montserrat, Cappuccio, Gerarda, Brunetti‐Pierri, Nicola, and Rossignol, Elsa

Subjects
INTELLECTUAL disabilities, CHILDREN with epilepsy, MOVEMENT disorders, LENNOX-Gastaut syndrome, INFANTILE spasms, 22Q11 deletion syndrome, AGE of onset, PEOPLE with epilepsy
Abstract

Chromosome 1q41‐q42 deletion syndrome is a rare cause of intellectual disability, seizures, dysmorphology, and multiple anomalies. Two genes in the 1q41‐q42 microdeletion, WDR26 and FBXO28, have been implicated in monogenic disease. Patients with WDR26 encephalopathy overlap clinically with those with 1q41‐q42 deletion syndrome, whereas only one patient with FBXO28 encephalopathy has been described. Seizures are a prominent feature of 1q41‐q42 deletion syndrome; therefore, we hypothesized that pathogenic FBXO28 variants cause developmental and epileptic encephalopathies (DEEs). We describe nine new patients with FBXO28 pathogenic variants (four missense, including one recurrent, three nonsense, and one frameshift) and analyze all 10 known cases to delineate the phenotypic spectrum. All patients had epilepsy and 9 of 10 had DEE, including infantile spasms (3) and a progressive myoclonic epilepsy (1). Median age at seizure onset was 22.5 months (range 8 months to 5 years). Nine of 10 patients had intellectual disability, which was profound in six of nine and severe in three of nine. Movement disorders occurred in eight of 10 patients, six of 10 had hypotonia, four of 10 had acquired microcephaly, and five of 10 had dysmorphic features, albeit different to those typically seen in 1q41‐q42 deletion syndrome and WDR26 encephalopathy. We distinguish FBXO28 encephalopathy from both of these disorders with more severe intellectual impairment, drug‐resistant epilepsy, and hyperkinetic movement disorders. [ABSTRACT FROM AUTHOR]

Published
2021
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24. Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence.

Author

Farré, Xavier, Spataro, Nino, Haziza, Frederic, Rambla, Jordi, and Navarro, Arcadi

Subjects
*PHENOTYPES, *LUNG cancer, *SCHIZOPHRENIA, *LINKAGE disequilibrium, *DATA mining
Abstract

Motivation Association studies based on SNP arrays and Next Generation Sequencing technologies have enabled the discovery of thousands of genetic loci related to human diseases. Nevertheless, their biological interpretation is still elusive, and their medical applications limited. Recently, various tools have been developed to help bridging the gap between genomes and phenomes. To our knowledge, however none of these tools allows users to retrieve the phenotype-wide list of genetic variants that may be linked to a given disease or to visually explore the joint genetic architecture of different pathologies. Results We present the Genome-Phenome Explorer (GePhEx), a web-tool easing the visual exploration of phenotypic relationships supported by genetic evidences. GePhEx is primarily based on the thorough analysis of linkage disequilibrium between disease-associated variants and also considers relationships based on genes, pathways or drug-targets, leveraging on publicly available variant-disease associations to detect potential relationships between diseases. We demonstrate that GePhEx does retrieve well-known relationships as well as novel ones, and that, thus, it might help shedding light on the patho-physiological mechanisms underlying complex diseases. To this end, we investigate the potential relationship between schizophrenia and lung cancer, first detected using GePhEx and provide further evidence supporting a functional link between them. Availability and implementation GePhEx is available at: https://gephex.ega-archive.org/. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2020
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25. Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients

Author

Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Spataro, Nino, Roca-Umbert, Ana, Valles, Mònica, Bosch, Elena, Ministerio de Ciencia e Innovación (España), Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Spataro, Nino, Roca-Umbert, Ana, Valles, Mònica, and Bosch, Elena

Abstract

[Background] The analysis of coverage depth in next-generation sequencing data allows the detection of gene dose alterations. We explore the frequency of such structural events in a Spanish cohort of sporadic PD cases., [Methods] Gene dose alterations were detected with the eXome-Hidden Markov Model (XHMM) software from depth of coverage in resequencing data available for 38 Mendelian and other risk PD loci in 394 individuals (249 cases and 145 controls) and subsequently validated by quantitative PCR., [Results] We identified 10 PD patients with exon dosage alterations in PARK2, GBA-GBAP1, and DJ1. Additional functional variants, including 2 novel nonsense mutations (p.Arg1552Ter in LRRK2 and p.Trp90Ter in PINK1), were confirmed by Sanger sequencing. This combined approach disclosed the genetic cause of 12 PD cases., [Conclusions] Gene dose alterations related to PD can be correctly identified from targeting resequencing data. This approach substantially improves the detection rate of cases with causal genetic alterations. © 2016 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.

Published
2017

26. Human genetic disorders: Mendelian and complex diseases

Author

Spataro, Nino, 1984, Bosch Fusté, Elena, and Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut

Subjects
Mendelian disorders, Parkinson's disease, Malaltia de Parkinson, Mètodes de col.lapse, Copy number variation (CNVs), Collapsing methods, Malalties mendelianes, Complex diseases, Malalties complexes, Variació en el número de còpies
Abstract

From Darwin’s “On the Origin of Species”, many years elapsed before human diseases were considered in an evolutionary framework. Besides theoretical and empirical advances, we are far from the complete understanding of disease aetiology. Highly penetrant disorders with Mendelian inheritance are mostly explained by the mutation-selection balance model, which is insufficient to describe the selective pressures acting on the full set of alleles related to diseases. We show in the first two papers that Next Generation Sequencing (NGS) technologies provide a unique opportunity to investigate variation and contribute to the understanding of the genetic architecture of disease. Besides exploring the role of rare and copy number variants in Parkinson’s disease (PD), we demonstrate the functional relation between Mendelian and idiopathic PD. In the last paper, we report that variation in genes previously related to Mendelian disorders has a more important role in driving complex disease susceptibility than genes associated only to complex diseases., Des de l'Origen de les Espècies de Darwin van passar molts anys abans que les malalties humanes fossin considerades sota un marc evolutiu. Tanmateix, tot i els darrers avenços teòrics i empírics, estem molt lluny de tenir una comprensió completa de l'etiologia de les malalties humanes. Mentre els trastorns altament penetrants amb herència mendeliana poden explicar-se sota un model d’equilibri mutació-selecció, aquest és insuficient per descriure les pressions selectives que actuen sobre tot el conjunt d'al·lels associats a malalties. Mostrem en els dos primers treballs que les noves tecnologies de seqüenciació proporcionen una oportunitat única per investigar la variació i contribuir a la comprensió de l'arquitectura genètica de la malaltia. A més d'explorar el paper de les variants rares i en el nombre de còpies en la malaltia de Parkinson (PD), demostrem la relació funcional entre les formes mendelianes i idiopàtiques d’aquesta malaltia. En el darrer treball, mostrem sota una perspectiva evolutiva i funcional que, en comparació amb la variació genètica en gens associats només a malalties complexes, la variació en gens prèviament relacionats amb trastorns Mendelians sembla tenir un paper clarament més important en la susceptibilitat a la malaltia complexa.

Published
2016

27. Signatures of human adaptation in quantitative trait loci influencing micronutrient homeostasis in liver

Author

Engelken, Johannes, Scherr, Anna-Lena, Jiménez-Álvarez, Victoria, Codina-Solà, Marta, Medina-Stacey, Daniel, Spataro, Nino, Calafell, Francesc, and Bosch, Elena

Abstract

Engelken, Johannes.-- Trabajo presentado en el V Congreso de la Sociedad Española de Biología Evolutiva (SESBE 2016), celebrado en Murcia del 18 al 21 de enero de 2016., Micronutrients possess vital functions at molecular, cellular and physiological levels, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 human liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 SNPs in the same sample set. We detected significant associations between SNP genotypes and eight protein abundances (pQTLs), 10 mRNA levels (eQTLs) and 15 micronutrient concentrations (nutriQTLs). Six of these survived the false discovery rate (FDR) cutoff: i) one pQTL for GPX2 (rs10133290); ii) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and iii) three nutriQTLs: the pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1 GPX3, SLC30A9 and SLC39A8, which are related to zinc and selenium. Overall, this multilayered, integrative study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients.

Published
2016

28. Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients

Author

Spataro, Nino, Roca-Umbert, Ana, Cervera Carles, Laura, Vallès, Mònica, Anglada, Roger, Pagonabarraga, Javier, Pascual-Sedano, Berta, Campolongo, Antonia, Kulisevsky, Jaime, Casals, Ferran, Clarimón, Jordi, Bosch, Elena, and Universitat Autònoma de Barcelona

Subjects
Parkinson's disease, Next generation sequencing, Structural variants, XHMM software
Abstract

The analysis of coverage depth in next-generation sequencing data allows the detection of gene dose alterations. We explore the frequency of such structural events in a Spanish cohort of sporadic PD cases. Gene dose alterations were detected with the eXome-Hidden Markov Model (XHMM) software from depth of coverage in resequencing data available for 38 Mendelian and other risk PD loci in 394 individuals (249 cases and 145 controls) and subsequently validated by quantitative PCR. We identified 10 PD patients with exon dosage alterations in PARK2, GBA-GBAP1, and DJ1. Additional functional variants, including 2 novel nonsense mutations (p.Arg1552Ter in LRRK2 and p.Trp90Ter in PINK1), were confirmed by Sanger sequencing. This combined approach disclosed the genetic cause of 12 PD cases. Gene dose alterations related to PD can be correctly identified from targeting resequencing data. This approach substantially improves the detection rate of cases with causal genetic alterations. © 2016 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.

Published
2016

29. Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver

Author

Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, Instituto de Salud Carlos III, Volkswagen Foundation, Engelken, Johannes, Scherr, Anna-Lena, Jiménez-Álvarez, Victoria, Codina-Solà, Marta, Medina-Stacey, Daniel, Spataro, Nino, Calafell, Francesc, Bosch, Elena, Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, Instituto de Salud Carlos III, Volkswagen Foundation, Engelken, Johannes, Scherr, Anna-Lena, Jiménez-Álvarez, Victoria, Codina-Solà, Marta, Medina-Stacey, Daniel, Spataro, Nino, Calafell, Francesc, and Bosch, Elena

Abstract

Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs10133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients.

Published
2016

30. Disease genes and evolution: a complex issue

Author

Spataro, Nino, Rodríguez-Pérez, Juan Antonio, Navarro, Arcadi, and Bosch, Elena

Abstract

Trabajo presentado en la 4th Meeting of the Spanish Society of the Evolutionary Biology (SESBE 2013) celebrada en Barcelona del 27 al 29 de noviembre de 2013.

Published
2013

31. Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver

Author

Engelken, Johannes, primary, Espadas, Guadalupe, additional, Mancuso, Francesco M., additional, Bonet, Nuria, additional, Scherr, Anna-Lena, additional, Jímenez-Álvarez, Victoria, additional, Codina-Solà, Marta, additional, Medina-Stacey, Daniel, additional, Spataro, Nino, additional, Stoneking, Mark, additional, Calafell, Francesc, additional, Sabidó, Eduard, additional, and Bosch, Elena, additional

Published
2015
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32. Mendelian genes for Parkinson's disease contribute to the sporadic forms of the disease†

Author

Spataro, Nino, primary, Calafell, Francesc, additional, Cervera-Carles, Laura, additional, Casals, Ferran, additional, Pagonabarraga, Javier, additional, Pascual-Sedano, Berta, additional, Campolongo, Antònia, additional, Kulisevsky, Jaime, additional, Lleó, Alberto, additional, Navarro, Arcadi, additional, Clarimón, Jordi, additional, and Bosch, Elena, additional

Published
2014
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33. Draft Genome Sequence of the Aeromonas diversa Type Strain

Author

Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, Universidad de Barcelona, Farfán, Maribel, Spataro, Nino, Sanglas Baulenas, Ariadna, Albarral, Vicenta, Lorén, J. G., Bosch, Elena, Fusté, M. C., Ministerio de Ciencia e Innovación (España), Generalitat de Catalunya, Universidad de Barcelona, Farfán, Maribel, Spataro, Nino, Sanglas Baulenas, Ariadna, Albarral, Vicenta, Lorén, J. G., Bosch, Elena, and Fusté, M. C.

Abstract

We present here the first genome sequence of the Aeromonas diversa type strain (CECT 4254T). This strain was isolated from the leg wound of a patient in New Orleans (Louisiana) and was originally described as enteric group 501 and distinguished from A. schubertii by DNA-DNA hybridization and phenotypical characterization.

Published
2013

36. Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver.

Author

Engelken, Johannes, Espadas, Guadalupe, Mancuso, Francesco M., Bonet, Nuria, Scherr, Anna-Lena, Jímenez-Álvarez, Victoria, Codina-Solà, Marta, Medina-Stacey, Daniel, Spataro, Nino, Stoneking, Mark, Calafell, Francesc, Sabidó, Eduard, and Bosch, Elena

Abstract

Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs1 0133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients. [ABSTRACT FROM AUTHOR]

Published
2016
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37. Draft genome sequence of Aeromonas molluscorum strain 848TT, isolated from bivalve molluscs

Author

Spataro, Nino, Farfán Sellarés, Maribel, Albarral Ávila, Vicenta, Sanglas Baulenas, Ariadna, Lorén Egea, José Gaspar, Fusté Munné, M. Carme, Bosch, Elena, and Universitat de Barcelona

Subjects
Genètica bacteriana, Pathogenic bacteria, Bacterial genetics, Bacteris patògens, health care economics and organizations
Abstract

We report here the draft genome sequence of Aeromonas molluscorum 848T, the type strain of this Aeromonas species, which was isolated from wedge shells (Donax trunculus) obtained from a retail market in Barcelona, Spain, in 1997.

38. Draft genome sequence of aeromonas molluscorum strain 848TT, isolated from bivalve molluscs

Author

Spataro, Nino, 1984, Farfán, Maribel, Albarral, Vicenta, Sanglas, Ariadna, Lorén, J. Gaspar, Fusté, Mª Carme, and Bosch Fusté, Elena

Subjects
Genòmica, Bivalves, Aeromonas
Abstract

We report here the draft genome sequence of Aeromonas molluscorum 848T, the type strain of this Aeromonas species, which was isolated from wedge shells (Donax trunculus) obtained from a retail market in Barcelona, Spain, in 1997. This work was partially funded by grant SAF2011-29239; from the Ministerio de Ciencia e Innovación, Spanish Government; grant 2009SGR-1101 from Direcció General de Recerca, Generalitat de Catalunya; and grant ARZ00F01 from the University of Barcelona

39. SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population.

Author

Moreno-Cabrera JM, Feliubadaló L, Pineda M, Prada-Dacasa P, Ramos-Muntada M, Del Valle J, Brunet J, Gel B, Currás-Freixes M, Calsina B, Salazar-Hidalgo ME, Rodríguez-Balada M, Roig B, Fernández-Castillejo S, Durán Domínguez M, Arranz Ledo M, Infante Sanz M, Castillejo A, Dámaso E, Soto JL, de Miguel M, Hidalgo Calero B, Sánchez-Zapardiel JM, Ramon Y Cajal T, Lasa A, Gisbert-Beamud A, López-Novo A, Ruiz-Ponte C, Potrony M, Álvarez-Mora MI, Osorio A, Lorda-Sánchez I, Robledo M, Cascón A, Ruiz A, Spataro N, Hernan I, Borràs E, Moles-Fernández A, Earl J, Cadiñanos J, Sánchez-Heras AB, Bigas A, Capellá G, and Lázaro C

Subjects
Humans, Spain, Genetic Variation, Neoplasms genetics, Genes, Neoplasm, Genetic Predisposition to Disease, Databases, Genetic
Abstract

Accurate classification of genetic variants is crucial for clinical decision-making in hereditary cancer. In Spain, genetic diagnostic laboratories have traditionally approached this task independently due to the lack of a dedicated resource. Here we present SpadaHC, a web-based database for sharing variants in hereditary cancer genes in the Spanish population. SpadaHC is implemented using a three-tier architecture consisting of a relational database, a web tool and a bioinformatics pipeline. Contributing laboratories can share variant classifications and variants from individuals in Variant Calling Format (VCF) format. The platform supports open and restricted access, flexible dataset submissions, automatic pseudo-anonymization, VCF quality control, variant normalization and liftover between genome builds. Users can flexibly explore and search data, receive automatic discrepancy notifications and access SpadaHC population frequencies based on many criteria. In February 2024, SpadaHC included 18 laboratory members, storing 1.17 million variants from 4306 patients and 16 343 laboratory classifications. In the first analysis of the shared data, we identified 84 genetic variants with clinically relevant discrepancies in their classifications and addressed them through a three-phase resolution strategy. This work highlights the importance of data sharing to promote consistency in variant classifications among laboratories, so patients and family members can benefit from more accurate clinical management. Database URL: https://spadahc.ciberisciii.es/., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
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40. Elimination of lipaemic interference by high-speed centrifugation.

Author

Solé-Enrech G, Cano-Corres R, Aparicio-Calvente MI, and Spataro N

Subjects
Humans, Creatinine, Alkaline Phosphatase, Centrifugation, Glucose, Alanine Transaminase, Albumins, Phosphates, Calcium, Hyperlipidemias
Abstract

Introduction: In order to deliver high quality results, detection and elimination of possible analytical interferences, such as lipaemia, is crucial. The aim of this study is to evaluate the efficacy of high-speed centrifugation in eliminating lipaemic interference and to define own lipaemic index (LI) for the studied biochemical analytes., Materials and Methods: Evaluated analytes were: albumin, alkaline phosphatase, alanine-aminotransferase (ALT), aspartate-aminotransferase (AST), calcium, creatinine, gamma-glutamyltransferase (GGT), glucose, phosphates, total proteins, urea and total bilirubin. Those analytes and LIs have been analysed in duplicate in the Roche Diagnostics-c8000 analyser in samples centrifuged at 3000 rpm/10 minutes in the SL16 (Thermo Scientific, Waltham, USA) centrifuge and according to an own high-speed centrifugation protocol (12,900 rpm/15 minutes) in the MicroCL17R (Thermo Scientific, Waltham, USA) centrifuge. Lipaemia has been measured in each sample. The efficiency of high-speed centrifugation is verified by the Wilcoxon test (P < 0.05). In cases where significant differences are observed, our own LI is calculated. For ALT and AST, it is verified by McNemar test (P < 0.05 ) . For creatinine, both Wilcoxon and McNemar test were applied., Results: There were statistically significant differences in analyte concentration before and after high-speed centrifugation for: albumin, creatinine, GGT, glucose, phosphates, urea and total bilirrubin. Own LI is calculated. McNemar test shows statistically significant diferences in the proportion of delivered results before and after high-speed centrifugation in ALT, AST and creatinine., Conclusions: This study confirms the efficacy of high-speed centrifugation protocol for all the considered analytes, excepting calcium, alkaline phosphatase and total proteins., Competing Interests: Potential conflict of interest None declared., (Croatian Society of Medical Biochemistry and Laboratory Medicine.)

Published
2023
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