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Salgado Garrido, Josefa

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https://academica-e.unavarra.es/handle/2454/49949

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Salgado Garrido

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Josefa

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Ciencias de la Salud

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0000-0002-2764-8507

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750697

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812048

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2020 - 20245
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    PublicationOpen Access
    The Navarra 1000 Genomes Project (NAGEN 1000): benefits for predictive, preventive and personalized medicine
    (Springer, 2020) Pasalodos Sánchez, Sara; Salgado Garrido, Josefa; Miranda, María; Maíllo Ruiz de Infante, Alberto; Matalonga, L.; Beltrán, Sergi; Carmona, Rosario; Pérez-Florido, Javier; Etayo, G.; Lasheras, G.; Bernad, T.; Gómez-Cabrero, David; Ángel-González, L.; Brennan, P.; Gut, I.; Dopazo, Joaquín; Pinillos, I.; Lasa Uzcudun, Íñigo; Alonso Sánchez, Ángel Miguel; Ciencias de la Salud; Osasun Zientziak; Gobierno de Navarra / Nafarroako Gobernua
    In the past few years, extraordinary developments in the field of next generation sequencing (NGS) technologies, such as whole genome sequencing (WGS), have made it possible for clinicians to have access to a huge amount of biological information which could potentially explain complex genetic diagnoses, genetic predisposition to severe diseases, reproductive risks and inappropriate responses to certain medications. These advances herald a new era of predictive preventive personalized medicine (PPPM), although incorporation into clinical practice has proved to be challenging [1]. “NAGEN 1000” is a Spanish regional pilot study to implement recent advances of cutting edge genomic research technology into real clinical practice.
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    PublicationOpen Access
    Characterization of the common genetic variation in the spanish population of Navarre
    (MDPI, 2024) Maíllo Ruiz de Infante, Alberto; Huergo, Estefanía; Apellániz Ruiz, María Valvanera; Urrutia Lafuente, Edurne; Miranda, María; Salgado Garrido, Josefa; Pasalodos Sánchez, Sara; Delgado-Mora, Luna; Teijido Hermida, Óscar; Goicoechea, Ibai; Carmona, Rosario; Pérez-Florido, Javier; Aquino, Virginia; López-López, Daniel; Peña-Chilet, María; Beltrán, Sergi; Dopazo, Joaquín; Lasa Uzcudun, Íñigo; Beloqui, Juan José; NAGEN-Scheme; Alonso Sánchez, Ángel Miguel; Gómez-Cabrero, David; Ciencias de la Salud; Osasun Zientziak
    Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. To this end, we conducted a comprehensive characterization of exonic variants in the population of Navarre (Spain), utilizing whole genome sequencing data from 358 unrelated individuals of Spanish origin. Our analysis revealed 61,410 biallelic single nucleotide variants (SNV) within the Navarrese cohort, with 35% classified as common (MAF > 1%). By comparing allele frequency data from 1000 Genome Project (excluding the Iberian cohort of Spain, IBS), Genome Aggregation Database, and a Spanish cohort (including IBS individuals and data from Medical Genome Project), we identified 1069 SNVs common in Navarre but rare (MAF ≤ 1%) in all other populations. We further corroborated this observation with a second regional cohort of 239 unrelated exomes, which confirmed 676 of the 1069 SNVs as common in Navarre. In conclusion, this study highlights the importance of population-specific characterization of genetic variation to improve allele frequency filtering in sequencing data analysis to identify disease-causing variants.
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    PublicationOpen Access
    A crowdsourcing database for the copy-number variation of the Spanish population
    (BMC, 2023) López-López, Daniel; Roldán, Gema; Fernández-Rueda, José L.; Bostelmann, Gerrit; Carmona, Rosario; Aquino, Virginia; Pérez-Florido, Javier; Ortuño, Francisco; Pita, Guillermo; Núñez-Torres, Rocío; González Neira, Anna; Alonso Sánchez, Ángel Miguel; Salgado Garrido, Josefa; Pasalodos Sánchez, Sara; Ayuso, C.; Mínguez, P.; Ávila-Fernández, A.; Cortón, M.; Artuch, Rafael; Borrego, S.; Antiñolo, G.; Carracedo, A.; Amigo, J.; Castaño, L. A.; Tejada, I.; Delmiro, A.; Espinos, C.; Grinberg, D.; Guillén, E.; Lapunzin, A. P.; López-Escámez, J. A.; Gallego-Martínez, A.; Martí, R.; Rovira, E.; Millán, J. M.; Moreno, M. A.; Morin, M.; Moreno-Galdó, A.; Fernández-Cancio, M.; Morte, B.; Mulero, V.; García, D.; Nunes, V.; Palau, F.; Pérez, B.; Jurado, L. P.; Perona, R.; Pujol, A.; Ramos, F.; López, E.; Ribes, A.; Rosell, J.; Surrallés, J.; Peña-Chilet, María; Dopazo, Joaquín; Ciencias de la Salud; Osasun Zientziak
    Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.
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    PublicationOpen Access
    Genetic polymorphisms of CYP2C19 in Ecuadorian population: an interethnic approach
    (Elsevier, 2024) Alonso Llorente, Alba; Salgado Garrido, Josefa; Teijido Hermida, Óscar; González Andrade, Fabricio; Valiente Martín, Alberto; Fanlo Villacampa, Ana; Vicente Romero, Jorge; Ciencias de la Salud; Osasun Zientziak
    Introduction: CYP2C19 is a highly polymorphic gene responsible for metabolizing commonly used drugs. CYP2C192,3 (loss of activity alleles) and 17 (increased activity allele) are the principal alleles included in clinical guidelines, however their prevalence varies among different ethnicities. Ecuadorian population is formed by Mestizos, Afrodescendants and Native Americans and frequency of CYP2C19 alleles could be different among them. The objective of this study was to establish the frequency of these variants in the different populations of Ecuador and to compare them with other populations. Materials and methods: DNA from 105 Afrodescendants, 75 Native Americans of the Kichwa ethnicity, and 33 Mestizos Ecuadorians was analyzed by nested-PCR to identify CYP2C1917 carriers. CYP2C192 allele was analyzed in DNA from 78 Afrodescendants, 29 Native Americans of the Kichwa, and 16 Mestizos by TaqMan Allelic Discrimination Assay. CYP2C193 was analyzed in 33 Afrodescendants by nested-PCR. Results: The global frequencies of the alternate alleles were 14.22% (CYP2C192) and 2.10% (CYP2C1917). No differences (p > 0.05) were observed among the subgroups. No CYP2C193 carrier was identified. CYP2C192 frequencies in Ecuador were similar to the ones reported in Europe, Africa and Middle East countries and to some American populations. Low CYP2C1917 frequencies, like the ones in our population, were also observed in East and South Asia and in Native American groups. Discussion: Absence of differences in the ethnic groups in Ecuador for CYP2C192 and 17 could be due to either a bias in sample selection (ethnic group was assed by self-identification) or to a high interethnic admixture in the Ecuadorian population that would had diluted genetic differences. In addition, CYP2C192, *3, and *17 alleles frequencies in our study suggest that Ecuadorians ancestry is mostly of Native American origin.
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    PublicationOpen Access
    The correlation of two different real-time PCR devices for the analysis of CYP2C19 pharmacogenetic results
    (MDPI, 2023) Alonso Llorente, Alba; Salgado Garrido, Josefa; Teijido Hermida, Óscar; González Andrade, Fabricio; Valiente Martín, Alberto; Fanlo Villacampa, Ana; Vicente Romero, Jorge; Ciencias de la Salud; Osasun Zientziak
    CYP2C19 is a highly polymorphic gene responsible for the metabolism of commonly used drugs. CYP2C19*1, the wild-type allele, is associated with normal enzyme activity, whereas CYP2C19*2 and CYP2C19*17 lead to null and increased enzyme activity, respectively. The use of different instruments to perform the same pharmacogenetic tests should not affect the reliability of the results reported to clinicians, as required by the ISO 15189 standard. Genotyping assays allowed for the identification of gene variants corresponding to the CYP2C19*2 and CYP2C19*17 haplotypes in 44 selected samples. Each sample was analyzed in duplicate using the Thermo Fisher Taqman Drug Metabolism probes CYP2C19*2: c_25986767_70 (rs4244285) and CYP2C19*17: c_469857_10 (rs12248560). The experiments were performed on two widely used types of real-time PCR analyzers: ABI PRSIM™7500 and QuantStudioTM12KFlex (both from Applied Biosystems, Thermofisher). The data were analyzed in a Thermo Fisher Cloud facility. The analysis was performed independently by two qualified professionals. Both different instruments and analysts’ interpretations were consistent in identifying the native homozygous, heterozygous, and mutant homozygous variants for CYP2C19*2 and CYP2C19*17. The results provided by both the primary and backup analyzers showed a perfect correlation. This would allow for the use of the backup analyzer in case the main one is not available.