antonio Gómez-Tato | University of Santiago de Compostela (original) (raw)

Papers by antonio Gómez-Tato

Research paper thumbnail of Inference of Ancestry in Forensic Analysis II: Analysis of Genetic Data

Methods in molecular biology, 2016

Three approaches applicable to the analysis of forensic ancestry-informative marker data-STRUCTUR... more Three approaches applicable to the analysis of forensic ancestry-informative marker data-STRUCTURE, principal component analysis, and the Snipper Bayesian classification system-are reviewed. Detailed step-by-step guidance is provided for adjusting parameter settings in STRUCTURE with particular regard to their effect when differentiating populations. Several enhancements to the Snipper online forensic classification portal are described, highlighting the added functionality they bring to particular aspects of ancestry-informative SNP analysis in a forensic context.

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Research paper thumbnail of A common epigenetic clock from childhood to old age

Forensic Science International: Genetics

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Research paper thumbnail of Supplementary Table S4 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S4. List of proteins showing statistical differences between patients diagnos... more Supplementary Table S4. List of proteins showing statistical differences between patients diagnosed with endometrial hyperplasia (n=9) and the other non-EC controls (n=38) with adjusted p-value <0.05 and fold change > 2.

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Research paper thumbnail of Supplementary Table S2 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S2. List of precursors and related fragment ions extracted from PRM acquisition.

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Research paper thumbnail of Supplementary Table S5 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S5. Clinico-pathological characteristics of the 38 women from a previous stud... more Supplementary Table S5. Clinico-pathological characteristics of the 38 women from a previous study used to validate the robustness of the diagnostic panel.

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Research paper thumbnail of Supplementary Table S3 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S3. List of the Pearson correlation coefficients between the two peptides of ... more Supplementary Table S3. List of the Pearson correlation coefficients between the two peptides of each protein.

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Research paper thumbnail of Supplementary Table S1 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S1. Clinico-pathological characteristics of the 116 women enrolled in the study.

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Research paper thumbnail of Molecular Profiling of Circulating Tumour Cells Identifies Notch1 as a Principal Regulator in Advanced Non-Small Cell Lung Cancer

Scientific reports, Nov 30, 2016

Knowledge on the molecular mechanisms underlying metastasis colonization in Non-Small Cell Lung C... more Knowledge on the molecular mechanisms underlying metastasis colonization in Non-Small Cell Lung Cancer (NSCLC) remains incomplete. A complete overview integrating driver mutations, primary tumour heterogeneity and overt metastasis lacks the dynamic contribution of disseminating metastatic cells due to the inaccessibility to the molecular profiling of Circulating Tumour Cells (CTCs). By combining immunoisolation and whole genome amplification, we performed a global gene expression analysis of EpCAM positive CTCs from advanced NSCLC patients. We identified an EpCAM+ CTC-specific expression profile in NSCLC patients mostly associated with cellular movement, cell adhesion and cell-to-cell signalling mediated by PI3K/AKT, ERK1/2 and NF-kB pathways. NOTCH1 emerged as a driver connecting active signalling pathways, with a reduced number of related candidate genes (NOTCH1, PTP4A3, LGALS3 and ITGB3) being further validated by RT-qPCR on an independent cohort of NSCLC patients. In addition, t...

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Research paper thumbnail of Bioinformática (3 créditos)

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Research paper thumbnail of Pyrosequencing strategy to increase database resources in the turbot (Scophthalmus maximus) gonads

Genomics in Aquaculture International Symposium (GIA2011), 14-17 september 2011, HeraklionPeer Re... more Genomics in Aquaculture International Symposium (GIA2011), 14-17 september 2011, HeraklionPeer Reviewe

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Research paper thumbnail of The Lusternik-Schnirelmann category of 𝑆𝑝 (3)

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Research paper thumbnail of New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges

International Journal for Parasitology, 2020

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Research paper thumbnail of De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma

Journal of Invertebrate Pathology, 2016

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Research paper thumbnail of Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients

Molecular & Cellular Proteomics

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Research paper thumbnail of Targeted proteomics identifies proteomic signatures in liquid-biopsies of the endometrium to diagnose endometrial cancer and assist in the prediction of the optimal surgical treatment

Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 8, 2017

Endometrial cancer (EC) diagnosis relies on the observation of tumor cells in endometrial biopsie... more Endometrial cancer (EC) diagnosis relies on the observation of tumor cells in endometrial biopsies obtained by aspiration i.e., uterine aspirates), but it is associated with 22% undiagnosed patients and up to 50% of incorrectly assigned EC histotype and grade. We aimed to identify biomarker signatures in the fluid fraction of these biopsies to overcome these limitations. The levels of 52 proteins were measured in the fluid fraction of uterine aspirates from 116 patients by LC-PRM, the latest generation of targeted mass-spectrometry acquisition. A logistic regression model was used to assess the power of protein panels to differentiate between EC and non-EC patients and between EC histological subtypes. The robustness of the panels was assessed by the "leave-one-out" cross-validation procedure performed within the same cohort of patients and an independent cohort of 38 patients. The levels of 28 proteins were significantly higher in EC patients (n=69) compared to controls (...

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Research paper thumbnail of Genetic architecture of sex determination in turbot, Scophthalmus maximus

AQUA 2018, #WeRAquaculture we are the producers and investors, the scientists and technical advis... more AQUA 2018, #WeRAquaculture we are the producers and investors, the scientists and technical advisors, the legislators and educators, the students, civil society organizations and consumers of farmed aquatic products, 25-29 August 2018, Montpellier, France

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Research paper thumbnail of Las Matemáticas de la ancestralidad

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Research paper thumbnail of Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data

Frontiers in Genetics, 2020

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Research paper thumbnail of Global Gene Expression Characterization of Circulating Tumor Cells in Metastasic Castration-Resistant Prostate Cancer Patients

Journal of Clinical Medicine, 2020

Background: Current therapeutic options in the course of metastatic castration-resistant prostate... more Background: Current therapeutic options in the course of metastatic castration-resistant prostate cancers (mCRPC) reinforce the need for reliable tools to characterize the tumor in a dynamic way. Circulating tumor cells (CTCs) have emerged as a viable solution to the problem, whereby patients with a variety of solid tumors, including PC, often do not have recent tumor tissue available for analysis. The biomarker characterization in CTCs could provide insights into the current state of the disease and an overall picture of the intra-tumor heterogeneity. Methods: in the present study, we applied a global gene expression characterization of the CTC population from mCRPC (n = 9), with the goal to better understand the biology of these cells and identify the relevant molecules favoring this tumor progression. Results: This analysis allowed the identification of 50 genes specifically expressed in CTCs from patients. Six of these markers (HOXB13, QKI, MAOA, MOSPD1, SDK1, and FGD4), were va...

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Research paper thumbnail of Multiple evidences suggest sox2 as the main driver of a young and complex sex determining ZW/ZZ system in turbot (Scophthalmus maximus)

ABSTRACTA major challenge in evolutionary biology is to find an explanation for the variation in ... more ABSTRACTA major challenge in evolutionary biology is to find an explanation for the variation in sex-determining (SD) systems across taxa and to understand the mechanisms driving sex chromosome differentiation. We studied the turbot, holding a ZW/ZZ SD system and no sex chromosome heteromorphism, by combining classical genetics and genomics approaches to disentangle the genetic architecture of this trait. RAD-Seq was used to genotype 18,214 SNPs on 1,135 fish from 36 families and a genome wide association study (GWAS) identified a ∼ 6 Mb region on LG5 associated with sex (P < 0.05). The most significant associated markers were located close to sox2, dnajc19 and fxr1 genes. A segregation analysis enabled narrowing down the associated region and evidenced recombination suppression in a region overlapping the candidate genes. A Nanopore/Illumina assembly of the SD region using ZZ and WW individuals identified a single SNP fully associated with Z and W chromosomes. RNA-seq from 5-90 ...

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Research paper thumbnail of Inference of Ancestry in Forensic Analysis II: Analysis of Genetic Data

Methods in molecular biology, 2016

Three approaches applicable to the analysis of forensic ancestry-informative marker data-STRUCTUR... more Three approaches applicable to the analysis of forensic ancestry-informative marker data-STRUCTURE, principal component analysis, and the Snipper Bayesian classification system-are reviewed. Detailed step-by-step guidance is provided for adjusting parameter settings in STRUCTURE with particular regard to their effect when differentiating populations. Several enhancements to the Snipper online forensic classification portal are described, highlighting the added functionality they bring to particular aspects of ancestry-informative SNP analysis in a forensic context.

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Research paper thumbnail of A common epigenetic clock from childhood to old age

Forensic Science International: Genetics

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Research paper thumbnail of Supplementary Table S4 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S4. List of proteins showing statistical differences between patients diagnos... more Supplementary Table S4. List of proteins showing statistical differences between patients diagnosed with endometrial hyperplasia (n=9) and the other non-EC controls (n=38) with adjusted p-value <0.05 and fold change > 2.

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Research paper thumbnail of Supplementary Table S2 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S2. List of precursors and related fragment ions extracted from PRM acquisition.

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Research paper thumbnail of Supplementary Table S5 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S5. Clinico-pathological characteristics of the 38 women from a previous stud... more Supplementary Table S5. Clinico-pathological characteristics of the 38 women from a previous study used to validate the robustness of the diagnostic panel.

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Research paper thumbnail of Supplementary Table S3 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S3. List of the Pearson correlation coefficients between the two peptides of ... more Supplementary Table S3. List of the Pearson correlation coefficients between the two peptides of each protein.

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Research paper thumbnail of Supplementary Table S1 from Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment

Supplementary Table S1. Clinico-pathological characteristics of the 116 women enrolled in the study.

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Research paper thumbnail of Molecular Profiling of Circulating Tumour Cells Identifies Notch1 as a Principal Regulator in Advanced Non-Small Cell Lung Cancer

Scientific reports, Nov 30, 2016

Knowledge on the molecular mechanisms underlying metastasis colonization in Non-Small Cell Lung C... more Knowledge on the molecular mechanisms underlying metastasis colonization in Non-Small Cell Lung Cancer (NSCLC) remains incomplete. A complete overview integrating driver mutations, primary tumour heterogeneity and overt metastasis lacks the dynamic contribution of disseminating metastatic cells due to the inaccessibility to the molecular profiling of Circulating Tumour Cells (CTCs). By combining immunoisolation and whole genome amplification, we performed a global gene expression analysis of EpCAM positive CTCs from advanced NSCLC patients. We identified an EpCAM+ CTC-specific expression profile in NSCLC patients mostly associated with cellular movement, cell adhesion and cell-to-cell signalling mediated by PI3K/AKT, ERK1/2 and NF-kB pathways. NOTCH1 emerged as a driver connecting active signalling pathways, with a reduced number of related candidate genes (NOTCH1, PTP4A3, LGALS3 and ITGB3) being further validated by RT-qPCR on an independent cohort of NSCLC patients. In addition, t...

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Research paper thumbnail of Bioinformática (3 créditos)

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Research paper thumbnail of Pyrosequencing strategy to increase database resources in the turbot (Scophthalmus maximus) gonads

Genomics in Aquaculture International Symposium (GIA2011), 14-17 september 2011, HeraklionPeer Re... more Genomics in Aquaculture International Symposium (GIA2011), 14-17 september 2011, HeraklionPeer Reviewe

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Research paper thumbnail of The Lusternik-Schnirelmann category of 𝑆𝑝 (3)

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Research paper thumbnail of New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges

International Journal for Parasitology, 2020

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Research paper thumbnail of De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma

Journal of Invertebrate Pathology, 2016

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Research paper thumbnail of Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients

Molecular & Cellular Proteomics

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Research paper thumbnail of Targeted proteomics identifies proteomic signatures in liquid-biopsies of the endometrium to diagnose endometrial cancer and assist in the prediction of the optimal surgical treatment

Clinical cancer research : an official journal of the American Association for Cancer Research, Jan 8, 2017

Endometrial cancer (EC) diagnosis relies on the observation of tumor cells in endometrial biopsie... more Endometrial cancer (EC) diagnosis relies on the observation of tumor cells in endometrial biopsies obtained by aspiration i.e., uterine aspirates), but it is associated with 22% undiagnosed patients and up to 50% of incorrectly assigned EC histotype and grade. We aimed to identify biomarker signatures in the fluid fraction of these biopsies to overcome these limitations. The levels of 52 proteins were measured in the fluid fraction of uterine aspirates from 116 patients by LC-PRM, the latest generation of targeted mass-spectrometry acquisition. A logistic regression model was used to assess the power of protein panels to differentiate between EC and non-EC patients and between EC histological subtypes. The robustness of the panels was assessed by the "leave-one-out" cross-validation procedure performed within the same cohort of patients and an independent cohort of 38 patients. The levels of 28 proteins were significantly higher in EC patients (n=69) compared to controls (...

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Research paper thumbnail of Genetic architecture of sex determination in turbot, Scophthalmus maximus

AQUA 2018, #WeRAquaculture we are the producers and investors, the scientists and technical advis... more AQUA 2018, #WeRAquaculture we are the producers and investors, the scientists and technical advisors, the legislators and educators, the students, civil society organizations and consumers of farmed aquatic products, 25-29 August 2018, Montpellier, France

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Research paper thumbnail of Las Matemáticas de la ancestralidad

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Research paper thumbnail of Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data

Frontiers in Genetics, 2020

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Research paper thumbnail of Global Gene Expression Characterization of Circulating Tumor Cells in Metastasic Castration-Resistant Prostate Cancer Patients

Journal of Clinical Medicine, 2020

Background: Current therapeutic options in the course of metastatic castration-resistant prostate... more Background: Current therapeutic options in the course of metastatic castration-resistant prostate cancers (mCRPC) reinforce the need for reliable tools to characterize the tumor in a dynamic way. Circulating tumor cells (CTCs) have emerged as a viable solution to the problem, whereby patients with a variety of solid tumors, including PC, often do not have recent tumor tissue available for analysis. The biomarker characterization in CTCs could provide insights into the current state of the disease and an overall picture of the intra-tumor heterogeneity. Methods: in the present study, we applied a global gene expression characterization of the CTC population from mCRPC (n = 9), with the goal to better understand the biology of these cells and identify the relevant molecules favoring this tumor progression. Results: This analysis allowed the identification of 50 genes specifically expressed in CTCs from patients. Six of these markers (HOXB13, QKI, MAOA, MOSPD1, SDK1, and FGD4), were va...

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Research paper thumbnail of Multiple evidences suggest sox2 as the main driver of a young and complex sex determining ZW/ZZ system in turbot (Scophthalmus maximus)

ABSTRACTA major challenge in evolutionary biology is to find an explanation for the variation in ... more ABSTRACTA major challenge in evolutionary biology is to find an explanation for the variation in sex-determining (SD) systems across taxa and to understand the mechanisms driving sex chromosome differentiation. We studied the turbot, holding a ZW/ZZ SD system and no sex chromosome heteromorphism, by combining classical genetics and genomics approaches to disentangle the genetic architecture of this trait. RAD-Seq was used to genotype 18,214 SNPs on 1,135 fish from 36 families and a genome wide association study (GWAS) identified a ∼ 6 Mb region on LG5 associated with sex (P < 0.05). The most significant associated markers were located close to sox2, dnajc19 and fxr1 genes. A segregation analysis enabled narrowing down the associated region and evidenced recombination suppression in a region overlapping the candidate genes. A Nanopore/Illumina assembly of the SD region using ZZ and WW individuals identified a single SNP fully associated with Z and W chromosomes. RNA-seq from 5-90 ...

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