SeqBreed : a python tool to evaluate genomic prediction in complex scenarios

Background: Genomic prediction (GP) is a method whereby DNA polymorphism information is used to predict breeding values for complex traits. Although GP can significantly enhance predictive accuracy, it can be expensive and difficult to implement. To help design optimum breeding programs and experiments, including genome-wide association studies and genomic selection experiments, we have developed SeqBreed, a generic and flexible forward simulator programmed in python3. Results: SeqBreed accommodates sex and mitochondrion chromosomes as well as autopolyploidy. It can simulate any number of complex phenotypes that are determined by any number of causal loci. SeqBreed implements several GP methods, including genomic best linear unbiased prediction (GBLUP), single-step GBLUP, pedigree-based BLUP, and mass selection. We illustrate its functionality with Drosophila genome reference panel (DGRP) sequence data and with tetraploid potato genotype data. Conclusions: SeqBreed is a flexible and easy to use tool that can be used to optimize GP or genome-wide association studies. It incorporates some of the most popular GP methods and includes several visualization tools. Code is open and can be freely modified. Software, documentation, and examples are available at https://github.com/miguelperezenciso/SeqBreed

Seroepidemiology of infection with Toxoplasma gondii in healthy blood donors of Durango, Mexico

<p>Abstract</p> <p>Background</p> <p><it>Toxoplasma gondii </it>(<it>T. gondii</it>) infection in blood donors could represent a risk for transmission in blood recipients. There is scarce information about the epidemiology of <it>T. gondii </it>infection in blood donors in Mexico. Therefore, we sought to determine the prevalence of <it>T. gondii </it>infection and associated socio-demographic and behavioral characteristics in a population of healthy blood donors of Durango City, Mexico.</p> <p>Methods</p> <p>Four hundred and thirty two blood donors in two public blood banks of Durango City, Mexico were examined for <it>T. gondii </it>infection between August to September 2006. Blood donors were tested for anti-<it>T. gondii </it>IgG and IgM antibodies by using enzyme-linked immunoassays (Diagnostic Automation Inc., Calabasas, CA, USA). Socio-demographic and behavioral characteristics from each participant were also obtained.</p> <p>Results</p> <p>Thirty two (7.4%) of 432 blood donors had IgG anti-<it>T. gondii </it>antibodies. Eight (1.9%) of them had also IgM anti-<it>T. gondii </it>antibodies. Multivariate analysis using logic regression showed that <it>T. gondii </it>infection was associated with the presence of cats at home (adjusted OR = 3.81; 95% CI: 1.45–10.01). The age group of 45–60 years showed a significantly higher frequency of <it>T. gondii </it>infection than the group of 25–34 years (p = 0.02). Blood donors without education had a significantly higher frequency of infection (15.8%) than those with 13–19 years of education (4.5%) (p = 0.04). Other characteristics of blood donors including male gender, consumption of undercooked meat or blood transfusion did not show an association with infection.</p> <p>Conclusion</p> <p>The prevalence of <it>T. gondii </it>infection in healthy blood donors of Durango City, Mexico is lower than those reported in blood donors of south and central Mexico, and is one of the lowest reported in blood donors worldwide. <it>T. gondii </it>infection in our blood donors was most likely acquired by contact with cats. Prevalence of infection increased with age and decreased with educational level.</p

In vitro and in vivo anticancer effects of two quinoline–platinum(II) complexes on human osteosarcoma models

Platinum-based drugs, mainly cisplatin, are used for the treatment of several solid tumors such as OS. However, cisplatin treatment often results in the development of chemoresistance, leading therapeutic failure. We have previously reported that platinum complexes containing 8-hydroxyquinoline ligands have good antitumor activity against different cancer cell lines and with a different and better cytotoxic profile than cisplatin. Here, the anticancer properties of two different quinoline–platinum complexes [Pt(Cl)₂(quinoline)(dmso)] (1) [PtCl(8-O-quinoline)(dmso)] (2) on in vitro (2D and 3D) and in vivo models (xenograft tumor of human osteosarcoma in mice) are presented. In this order, [PtCl(8-O-quinoline)(dmso)] (2) impaired cell viability to have a more pronounced antitumor effect than cisplatin on MG-63 osteosarcoma cells (IC₅₀ 4 µM vs. 39 µM). Besides, [PtCl(8-O-quinoline)(dmso)] (2) increased ROS production in a dose-manner response and this compound induced early and late apoptotic fractions of human osteosarcoma cells. Finally, [PtCl(8-O-quinoline)(dmso)] (2) decreased the cell viability of multicellular spheroids and reduced the tumor volume on athymic nude mice N:NIH(S) Fox1nu without inducing side effects. In this way, [PtCl(8-O-quinoline)(dmso)] (2) did not alter the normal cytoarchitecture of liver and kidney and the blood biomarkers (GPT, GOT, uremia, and creatinine) did not suffer modifications. Taken together, our data indicate that these compounds showed a better anticancer performance than cisplatin on in vitro and in vivo studies. These results showed the importance of chelation in the antitumor properties, suggesting that the [PtCl(8-O-quinoline)(dmso)] (2) might be a promising agent for the treatment of human osteosarcoma tumors resistant to cisplatin.Facultad de Ciencias ExactasCentro de Química InorgánicaFacultad de Ciencias Veterinaria

Real-life disease monitoring in follicular lymphoma patients using liquid biopsy ultra-deep sequencing and PET/CT

In the present study, we screened 84 Follicular Lymphoma patients for somatic mutations suitable as liquid biopsy MRD biomarkers using a targeted next-generation sequencing (NGS) panel. We found trackable mutations in 95% of the lymph node samples and 80% of the liquid biopsy baseline samples. Then, we used an ultra-deep sequencing approach with 2 · 10−4 sensitivity (LiqBio-MRD) to track those mutations on 151 follow-up liquid biopsy samples from 54 treated patients. Positive LiqBio-MRD at first-line therapy correlated with a higher risk of progression both at the interim evaluation (HRINT 11.0, 95% CI 2.10–57.7, p = 0.005) and at the end of treatment (HREOT, HR 19.1, 95% CI 4.10–89.4, p < 0.001). Similar results were observed by PET/CT Deauville score, with a median PFS of 19 months vs. NR (p < 0.001) at the interim and 13 months vs. NR (p < 0.001) at EOT. LiqBio-MRD and PET/CT combined identified the patients that progressed in less than two years with 88% sensitivity and 100% specificity. Our results demonstrate that LiqBio-MRD is a robust and non-invasive approach, complementary to metabolic imaging, for identifying FL patients at high risk of failure during the treatment and should be considered in future response-adapted clinical trials.This study has been funded by Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union through the projects PI21/00314, PI19/01430, PI19/01518 and PI18/00295, PTQ2020-011372, CP19/00140, CP22/00082, Doctorado industrial CAM IND2020/TIC-17402 and CRIS cancer foundation

Mutational screening of newly diagnosed multiple myeloma patients by deep targeted sequencing

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Human Biogeography and Demographic Trend in Northpatagonic Monte: An Archaeological Approach from “El Corcovo” (SE of Mendoza)

El presente trabajo aporta al conocimiento de la biogeografía humana en ambientes áridos y las fases de poblamiento en relación a las trayectorias demográficas humanas. En ese marco, se presenta nueva información arqueológica del área El Corcovo, emplazada en el Monte surmendocino/nordpatagónico. Se detallan los trabajos de campo que contemplaron transectas, excavación arqueológica de un sitio y el relevamiento de arte rupestre de otros tres. Los resultados señalan el inicio de las ocupaciones en torno a 1900 años 14C AP y un cambio en el patrón de movilidad en torno a 600 años 14C AP. Ambas situaciones son consistentes con las estimaciones cronológicas relativas existentes para el arte rupestre del área. En base a un modelo demográfico regional del Monte, los resultados encuentran dos pulsos de incremento en la señal humana que se corresponden cronológicamente con la fecha inicial de ocupación estimada para el área y con la fecha obtenida para el cambio propuesto. Al asociarse estos pulsos con disminuciones significativas en el sector fitogeográfico de Patagonia se postulan explicaciones alternativas sobre la dinámica poblacional.The present paper attempt to improve the knowledge of human biogeography in arid environments and, understand the phases of settlement in relation to human demographic trajectories. In this framework, new archaeological information of the El Corcovo area is presented, located in Monte Surmendocino / Nordpatagónico. The field-works that contemplated transects, archaeological excavation of a site and the surveying of rock art of three others are detailed. The results indicate the beginning of occupations around 1900 years 14C AP and a change in the pattern of mobility around 600 years 14C AP. Both situations are consistent with the existing relative chronological estimates for the rock art of the area. Based on a regional demographic model for Monte area, the results show two pulses of increase in the human signal that correspond chronologically with the initial date of occupation estimated for the area and with the date obtained for the proposed change. By associating these pulses with significant falls in the phyto-geographic sector of Patagonia, alternative explanations on population dynamics are postulated.Fil: Gil, Adolfo Fabian. Universidad Tecnologica Nacional. Facultad Reg.san Rafael. Instituto de Evolucion, Ecologia Historica y Ambiente. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto de Evolucion, Ecologia Historica y Ambiente.; ArgentinaFil: Sugrañes, Nuria Andrea. Universidad Tecnologica Nacional. Facultad Reg.san Rafael. Instituto de Evolucion, Ecologia Historica y Ambiente. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto de Evolucion, Ecologia Historica y Ambiente.; ArgentinaFil: Acevedo, Agustín. Asociación de Investigaciones Antropológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Neme, Gustavo Adolfo. Universidad Tecnologica Nacional. Facultad Reg.san Rafael. Instituto de Evolucion, Ecologia Historica y Ambiente. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto de Evolucion, Ecologia Historica y Ambiente.; ArgentinaFil: Salgán, María Laura. Universidad Tecnologica Nacional. Facultad Reg.san Rafael. Instituto de Evolucion, Ecologia Historica y Ambiente. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto de Evolucion, Ecologia Historica y Ambiente.; Argentina. Comisión Nacional de Energía Atómica; ArgentinaFil: Giardina, Miguel Angel. Universidad Tecnologica Nacional. Facultad Reg.san Rafael. Instituto de Evolucion, Ecologia Historica y Ambiente. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto de Evolucion, Ecologia Historica y Ambiente.; ArgentinaFil: Tucker, Hugo. Centro Regional de Investigación y Desarrollo Cultural. Museo Regional Malargue; ArgentinaFil: Fiore, Danae. Asociación de Investigaciones Antropológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Seitz, Viviana Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaFil: Pompei, María de la Paz. Universidad Tecnologica Nacional. Facultad Reg.san Rafael. Instituto de Evolucion, Ecologia Historica y Ambiente. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto de Evolucion, Ecologia Historica y Ambiente.; ArgentinaFil: Ayala, Miriam I.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Museo de Historia Natural de San Rafael - Ianigla | Provincia de Mendoza. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Museo de Historia Natural de San Rafael - Ianigla | Universidad Nacional de Cuyo. Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales. Museo de Historia Natural de San Rafael - Ianigla; Argentin

Acceptance of living liver donation among medical students: A multicenter stratified study from Spain

AIM: To analyze the attitude of Spanish medical students toward living liver donation (LLD) and to establish which factors have an influence on this attitude. METHODS: STUDY TYPE: A sociological, interdisciplinary, multicenter and observational study. STUDY POPULATION: Medical students enrolled in Spain (n = 34000) in the university academic year 2010-2011. SAMPLE SIZE: A sample of 9598 students stratified by geographical area and academic year. Instrument used to measure attitude: A validated questionnaire (PCID-DVH RIOS) was self-administered and completed anonymously. Data collection procedure: Randomly selected medical schools. The questionnaire was applied to each academic year at compulsory sessions. STATISTICAL ANALYSIS: Student´s t test, ?(2) test and logistic regression analysis. RESULTS: The completion rate was 95.7% (n = 9275). 89% (n = 8258) were in favor of related LLD, and 32% (n = 2937) supported unrelated LLD. The following variables were associated with having a more favorable attitude: (1) age (P = 0.008); (2) sex (P < 0.001); (3) academic year (P < 0.001); (4) geographical area (P = 0.013); (5) believing in the possibility of needing a transplant oneself in the future (P < 0.001); (6) attitude toward deceased donation (P < 0.001); (7) attitude toward living kidney donation (P < 0.001); (8) acceptance of a donated liver segment from a family member if one were needed (P < 0.001); (9) having discussed the subject with one's family (P < 0.001) and friends (P < 0.001); (10) a partner's opinion about the subject (P < 0.001); (11) carrying out activities of an altruistic nature; and (12) fear of the possible mutilation of the body after donation (P < 0.001). CONCLUSION: Spanish medical students have a favorable attitude toward LLD

NGS-Based Molecular Karyotyping of Multiple Myeloma: Results from the GEM12 Clinical Trial

Simple Summary Multiple Myeloma (MM) is considered an incurable chronic disease, which prognosis depends on the presence of different genomic alterations. To accomplish a complete molecular diagnosis in a single essay, we have designed and validated a capture-based NGS approach to reliably identify pathogenic mutations (SNVs and indels), genomic alterations (CNVs and chromosomic translocations), and IGH rearrangements. We have observed a good correlation of the results obtained using our capture panel with data obtained by both FISH and WES techniques. In this study, the molecular classification performed using our approach was significantly associated with the stratification and outcome of MM patients. Additionally, this panel has been proven to detect specific IGH rearrangements that could be used as biomarkers in patient follow-ups through minimal residual disease (MRD) assays. In conclusion, we think that MM patients could benefit from the use of this capture-based NGS approach with a more accurate, single-essay molecular diagnosis. Next-generation sequencing (NGS) has greatly improved our ability to detect the genomic aberrations occurring in multiple myeloma (MM); however, its transfer to routine clinical labs and its validation in clinical trials remains to be established. We designed a capture-based NGS targeted panel to identify, in a single assay, known genetic alterations for the prognostic stratification of MM. The NGS panel was designed for the simultaneous study of single nucleotide and copy number variations, insertions and deletions, chromosomal translocations and V(D)J rearrangements. The panel was validated using a cohort of 149 MM patients enrolled in the GEM2012MENOS65 clinical trial. The results showed great global accuracy, with positive and negative predictive values close to 90% when compared with available data from fluorescence in situ hybridization and whole-exome sequencing. While the treatments used in the clinical trial showed high efficacy, patients defined as high-risk by the panel had shorter progression-free survival (p = 0.0015). As expected, the mutational status of TP53 was significant in predicting patient outcomes (p = 0.021). The NGS panel also efficiently detected clonal IGH rearrangements in 81% of patients. In conclusion, molecular karyotyping using a targeted NGS panel can identify relevant prognostic chromosomal abnormalities and translocations for the clinical management of MM patients

Genetic landscape of 6089 inherited retinal dystrophies affected cases in Spain and their therapeutic and extended epidemiological implications

Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.This work was supported by the Instituto de Salud Carlos III (ISCIII) of the Spanish Ministry of Health (FIS; PI16/00425 and PI19/00321), Centro de Investigación Biomédica en Red Enfermedades Raras (CIBERER, 06/07/0036), IIS-FJD BioBank (PT13/0010/0012), Comunidad de Madrid (CAM, RAREGenomics Project, B2017/BMD-3721), European Regional Development Fund (FEDER), the Organización Nacional de Ciegos Españoles (ONCE), Fundación Ramón Areces, Fundación Conchita Rábago and the University Chair UAM-IIS-FJD of Genomic Medicine. Irene Perea-Romero is supported by a PhD fellowship from the predoctoral Program from ISCIII (FI17/00192). Ionut F. Iancu is supported by a grant from the Comunidad de Madrid (CAM, PEJ-2017-AI/BMD7256). Marta del Pozo-Valero is supported by a PhD grant from the Fundación Conchita Rábago. Berta Almoguera is supported by a Juan Rodes program from ISCIII (JR17/00020). Pablo Minguez is supported by a Miguel Servet program from ISCIII (CP16/00116). Marta Corton is supported by a Miguel Servet program from ISCIII (CPII17/00006). The funders played no role in study design, data collection, data analysis, manuscript preparation and/or publication decisions