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Femina ; 49(8): 501-504, 20210831.
Article in Portuguese | LILACS | ID: biblio-1342421


A bexiga hiperativa caracteriza-se pela urgência miccional, geralmente acompa- nhada de noctúria e aumento da frequência urinária. Trata-se de afecção preva- lente, com enorme comprometimento da qualidade de vida, em todos os seus as- pectos. Diversos biomarcadores vêm sendo estudados para melhor caracterização dos diferentes fenótipos da afecção, entre eles as neurotrofinas urinárias, o ATP, a genômica e a microbiota urinária. Acredita-se que tal caracterização poderá ter implicações para prevenção, fisiopatologia e individualização do tratamento.(AU)

The overactive bladder is characterized by urinary urgency, usually accompanied by nocturia and increased urinary frequency. It is a prevalent condition, with enormous impairment of quality of life, in all its aspects. Several biomarkers have been studied to better characterize the different phenotypes of the condition, including urinary neurotrophins, ATP, genomics and urinary microbiota. It is believed that such charac- terization may have implications for prevention, pathophysiology and individualiza- tion of treatment.(AU)

Humans , Male , Female , Urinary Bladder, Overactive , Urinary Incontinence, Urge , Biomarkers , Adenosine Triphosphate , Genomics , Microbiota , Nerve Growth Factors
Guatemala; MSPAS; 29 ene. 2021. 6 p.
Non-conventional in Spanish | LILACS, LIGCSA | ID: biblio-1224473


En los antecedentes se presentan estadísticas del COVID-19 a la fecha en la que se elaboró el documento (enero 2021) y aborda las tres mutaciones del virus conocidas hasta la fecha del documento. "La caracterización genética de patógenos virales es la base para el desarrollo de protocolos de diagnóstico, vacunas y medicamentos antivirales. Esta estrategia también es una herramienta útil en salud pública para el seguimiento a brotes y control de enfermedades mediante estudios de epidemiología molecular." "…la secuenciación genómica del SARS-CoV-2 y la liberación oportuna de la información no solo permitió la caracterización del agente etiológico involucrado en el brote inicial, sino también el desarrollo oportuno de protocolos de diagnóstico y seguimiento a la evolución de la pandemia de COVID-19. Así, la secuenciación genómica se ha convertido en una herramienta esencial para generar datos virológicos de SARS-CoV-2, para impulsar la respuesta de laboratorio, y entender mejor los patrones de dispersión y evolución de SARS-CoV-2" De manera que el objetivo del documento es: "Generar información genética mediante la vigilancia genómica de casos confirmados de COVID-19 de pacientes que asisten a los servicios de salud públicos y privados del país, así como del Instituto Guatemalteco de Seguridad Social ­IGSS-."

Humans , Male , Female , Coronavirus Infections/diagnosis , Coronavirus Infections/prevention & control , Betacoronavirus , Laboratories/standards , Infection Control/standards , Safety Management/statistics & numerical data , Genomics/trends , Pandemics/prevention & control , Public Health Surveillance/methods
Article in Chinese | WPRIM | ID: wpr-879616


The use of whole exome sequencing (WES) for the detection of disease-causing variants of genetic diseases and for non-invasive prenatal screening (NIPS) of fetal aneuploidies are two major clinical applications of next generation sequencing (NGS). This article has summarized the official documents developed and updated by the American College of Medical Genetics and Genomics (ACMG) on governing WES and NIPS. These include the development of expert consensus policies and position statements on an ongoing basis to guide clinical application of NGS technology and variant analysis, establish evidence-based practical resources, as well as standards and guidelines to govern diagnosis and screening. These ACMG documents are valuable references to Chinese geneticists, but direct adoption of these standards and guidelines may not be practical due to the differences in disease-associated variant frequencies in Chinese population, socioeconomic status, and medical practice between the two countries. It is hoped that this review could facilitate the development of NGS and NIPS standards and guidelines that are consistent with international standards and concordant with medical genetics practice in China to provide high-quality, efficient and safe clinical services for patients and their families with genetic diseases.

China , Consensus , Female , Genomics , High-Throughput Nucleotide Sequencing , Humans , Pregnancy , Technology , United States
Article in Chinese | WPRIM | ID: wpr-879608


OBJECTIVE@#To explore the genetic basis for a girl featuring bone and tooth mineralization disorder, premature deciduous teeth, rickets and short stature.@*METHODS@#Genomic DNA was extracted and subjected to high-throughput whole exome sequencing. Suspected variants were confirmed by Sanger sequencing. Impact of potential variants was analyzed with bioinformatic software.@*RESULTS@#The child was found to carry compound heterozygous missense variants of the ALPL gene, including c.1130C>T (p.A377V), a known pathogenic mutation inherited from her father, and c.1300G>A (p.V434M) inherited from her mother, which was unreported previously and predicted to be likely pathogenic based on standards and guidelines from the American College of Medical Genetics and Genomics (PM2+PM5+PP3+PP4).@*CONCLUSION@#The compound heterozygous variants of c.1130C>T (p.Ala377Val) and c.1300G>A (p.Val434Met) of the ALPL gene probably underlay the disease in this child. Above finding has enriched the spectrum of ALPL gene variants.

Alkaline Phosphatase , Child , Female , Genomics , High-Throughput Nucleotide Sequencing , Humans , Hypophosphatasia/genetics , Mutation , Whole Exome Sequencing
Article in Chinese | WPRIM | ID: wpr-879545


OBJECTIVE@#To analyze the clinical features and genetic variants in two patients with Dravet syndrome (DS).@*METHODS@#Peripheral blood samples of the children and their parents were collected for the extraction of genomic DNA and high-throughput sequencing. Suspected variants were confirmed by Sanger sequencing.@*RESULTS@#By high-throughput sequencing, the two children were found to respectively harbor a c.2135delC frameshifting variant in exon 12 and a c.1522G>T nonsense variant in exon 10 of the SCN1A gene. Both variants were predicted to be pathogenic by bioinformatic analysis. Based on the American College of Medical Genetics and Genomics standards and guidelines, the c.2135delC and c.1522G>A variants of the SCN1A gene were predicted to be pathogenic (PVS1+ PS2+ PM2+ PP3).@*CONCLUSION@#The variants of the SCN1A gene probably underlay the DS in the patients. Above finding has enriched the variant spectrum and enabled genetic counseling for their families.

Epilepsies, Myoclonic/genetics , Genomics , Humans , Infant , Mutation , /genetics , Pedigree , Spasms, Infantile/genetics
Article in Chinese | WPRIM | ID: wpr-878704


Objective To analyze the research status,hotspots,and frontiers of atherosclerosis genomics from 2010 to 2019.Methods CiteSpace software was used to conduct data statistics and visual analysis on countries,institutions,authors,journals,co-cited papers,and keywords of the related papers published in the Web of Science from 2010 to 2019.Results A total of 1021 papers in English were included,and the annual number of publications generally showed an upward trend.The knowledge base in the research of atherosclerosis mostly focused on the genetic risk sites and biomarkers for coronary artery diseases such as coronary heart disease,myocardial infarction,and dyslipidemia.The related journals mainly involved the fields of molecular biology,biology,genetics,immunology,medicine,pharmacy,and clinical medicine.The latest research in atherosclerosis concentrated on genome-wide association study,DNA methylation,microRNA,messenger RNA and so on.The research frontiers involved long noncoding RNA,DNA methylation,and immune metabolism.Conclusion The studies in atherosclerotic genomics have gradually increased.

Atherosclerosis/genetics , Bibliometrics , Biomarkers , Genome-Wide Association Study , Genomics , Humans
Chinese Journal of Biotechnology ; (12): 331-341, 2021.
Article in Chinese | WPRIM | ID: wpr-878566


Genetic and epigenetic alterations accumulate in the process of hepatocellular carcinogenesis, but the role of genomic spatial organization in HCC is still unknown. Here, we performed in situ Hi-C in HCC cell line PLC/PRF/5 compared with normal liver cell line L02, together with RNA-seq and ChIP-seq of SMC3/CTCF/H3K27ac. The results indicate that there were significant compartment switching, TAD shifting and loop pattern altering in PLC/PRF/5. These spatial changes are correlated with abnormal gene expression and more opening promoter regions of the HCC cell line. Thus, the 3D genome organization alterations in PLC/PRF/5 are important in epigenetic mechanisms of HCC tumorigenesis.

Carcinoma, Hepatocellular/genetics , Cell Line , Cell Line, Tumor , Genomics , Humans , Liver Neoplasms/genetics
Braz. j. med. biol. res ; 54(3): e9571, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153526


Cancer cell lines are widely used as in vitro models of tumorigenesis, facilitating fundamental discoveries in cancer biology and translational medicine. Currently, there are few options for glioblastoma (GBM) treatment and limited in vitro models with accurate genomic and transcriptomic characterization. Here, a detailed characterization of a new GBM cell line, namely AHOL1, was conducted in order to fully characterize its molecular composition based on its karyotype, copy number alteration (CNA), and transcriptome profiling, followed by the validation of key elements associated with GBM tumorigenesis. Large numbers of CNAs and differentially expressed genes (DEGs) were identified. CNAs were distributed throughout the genome, including gains at Xq11.1-q28, Xp22.33-p11.1, Xq21.1-q21.33, 4p15.1-p14, 8q23.2-q23.3 and losses at Yq11.21-q12, Yp11.31-p11.2, and 15q11.1-q11.2 positions. Nine druggable genes were identified, including HCRTR2, ETV1, PTPRD, PRKX, STS, RPS6KA6, ZFY, USP9Y, and KDM5D. By integrating DEGs and CNAs, we identified 57 overlapping genes enriched in fourteen pathways. Altered expression of several cancer-related candidates found in the DEGs-CNA dataset was confirmed by RT-qPCR. Taken together, this first comprehensive genomic and transcriptomic landscape of AHOL1 provides unique resources for further studies and identifies several druggable targets that may be useful for therapeutics and biologic and molecular investigation of GBM.

Humans , Glioblastoma/genetics , Gene Expression Regulation, Neoplastic , Minor Histocompatibility Antigens , Genome , Genomics , Cell Line, Tumor , Histone Demethylases , Transcriptome
REME rev. min. enferm ; 25: e1380, 2021. tab
Article in English, Portuguese | LILACS, BDENF | ID: biblio-1340532


RESUMO Objetivo: identificar o conhecimento de enfermeiros em genética e genômica aplicado ao câncer de mama. Método: estudo transversal com a aplicação de um questionário desenvolvido pelos autores a enfermeiros assistenciais, maiores de 18 anos, atuantes na atenção secundária e terciária, no município de Belém do Pará, região Norte do Brasil. Realizada técnica de amostragem por conveniência em relação aos locais de coleta e amostragem aleatória simples para o número amostral mínimo de 71 participantes. Resultados: foram abordados 80 enfermeiros com idade média de 42 anos, sendo a maior parte de especialistas. Verificaram-se diferenças entre o nível da atenção em que os enfermeiros atuam e o primeiro contato com genética e/ou genômica (p<0,001); entre o conceito de DNA (p<0,0001); o conhecimento sobre o heredograma (p=0,004); conhecimento sobre a faixa etária do rastreamento mamográfico com risco familiar (p=0,027); o exame clínico realizado por um médico ou enfermeira treinados, anualmente, a partir de 40 anos (p=0,005). A maioria dos casos de CA de mama ocorre devido a alterações genéticas hereditárias (p=0,0004) e da menarca precoce, menopausa tardia, nuliparidade, alterações hormonais, sedentarismo, sobrepeso, tabagismo e terapia hormonal, que são os principais fatores de risco para o câncer de mama esporádico (p=0,0039). Conclusão: identificou-se uma lacuna de conhecimento sobre os conceitos de genética e genômica aplicados ao câncer de mama entre os dois grupos.

RESUMEN Objetivo: identificar los conocimientos de enfermeros en genética y genómica aplicadas al cáncer de mama. Método: estudio transversal con la aplicación de un cuestionario desarrollado por los autores a enfermeros asistenciales, mayores de 18 años, que trabajan en la atención secundaria y terciaria, en la ciudad de Belém do Pará, región norte de Brasil. Se realizó una técnica de muestreo por conveniencia con relación a los sitios de recolección y muestreo aleatorio simple para una muestra mínima de 71 participantes. Resultados: se abordó a 80 enfermeros con una edad promedio de 42 años, la mayoría especialistas. Hubo diferencias entre el nivel de atención en el que trabajan los enfermeros y el primer contacto con la genética y / o genómica (p <0,001); entre el concepto de ADN (p <0,0001); conocimiento sobre el árbol genealógica (p = 0,004); conocimiento sobre el grupo de edad de cribado mamográfico con riesgo familiar (p = 0,027); el examen clínico realizado por un médico o enfermero capacitado, anualmente, a partir de los 40 años (p = 0,005). La mayoría de los casos de CA de mama se producen por alteraciones genéticas hereditarias (p = 0,0004) y menarquia precoz, menopausia tardía, mujeres que nunca han parido, cambios hormonales, sedentarismo, sobrepeso, tabaquismo y terapia hormonal, que son los principales factores de riesgo de cáncer de mama esporádico (p = 0,0039). Conclusión: entre los dos grupos se identificó una brecha de conocimiento sobre los conceptos de genética y genómica aplicados al cáncer de mama.

ABSTRACT Objective: to identify nurse's knowledge in genetics and genomics applied to breast cancer. Method: a cross-sectional study with the application of a questionnaire developed by the authors to clinical nurses, over 18 years old, working in secondary and tertiary care, in the city of Belém do Pará, the northern region of Brazil. Convenience sampling technique was performed in the collection places and simple random sampling for a minimum sample number of 71 participants. Results: Eighty nurses with an average age of 42 years old were approached, most of the experts. There were differences between the level of care in which nurses work and the first contact with genetics and/or genomics (p<0.001); between the concept of DNA (p<0.0001); knowledge about the genogram (p=0.004); knowledge about the age group of mammographic screening with familial risk (p=0.027); the clinical examination performed by a trained physician or nurse, annually, from 40 years old (p=0.005). Most cases of breast cancer occur due to hereditary genetic changes (p=0.0004) and early menarche, late menopause, nulliparity, hormonal changes, sedentary lifestyle, overweight, smoking, and hormonal therapy, which are the main risks factors for sporadic breast cancer (p=0.0039). Conclusion: a knowledge gap about the concepts of genetics and genomics applied to breast cancer was identified between the two groups.

Humans , Female , Adult , Middle Aged , Breast Neoplasms , Genomics , Genetics , Secondary Care , Tertiary Healthcare , Mass Screening , Risk Factors , Nurses
Mem. Inst. Oswaldo Cruz ; 116: e200634, 2021. graf
Article in English | LILACS | ID: biblio-1154876


The availability of Trypanosomatid genomic data in public databases has opened myriad experimental possibilities that have contributed to a more comprehensive understanding of the biology of these parasites and their interactions with hosts. In this review, after brief remarks on the history of the Trypanosoma cruzi and Leishmania genome initiatives, we present an overview of the relevant contributions of genomics, transcriptomics and functional genomics, discussing the primary obstacles, challenges, relevant achievements and future perspectives of these technologies.

Trypanosoma cruzi/genetics , Genome, Protozoan/genetics , Leishmania/genetics , Computational Biology , Genomics
Acta bioeth ; 26(2): 137-145, oct. 2020.
Article in Spanish | LILACS | ID: biblio-1141919


Resumen El presente artículo es una revisión de las reflexiones éticas sobre temas de genética y manipulación genética que se han publicado en 20 años de Acta Bioethica. Se identifican los siguientes temas relevantes en el diálogo bioético: evaluación de riesgos, inequidad, pérdida de la biodiversidad, eugenesia, definir los límites entre natural y artificial, diálogo entre detractores y promotores de la biotecnología, desafíos en el cuidado de la salud, manejo de la información y confidencialidad. Se concluye que la bioética puede actuar como intermediaria entre los diversos interlocutores ante los problemas que se suscitan al aplicar la tecnología a la vida, permitiendo reconocer y llegar a consensos para enfrentar con responsabilidad las diferencias en temas de equidad, autonomía y el balance entre riesgos y beneficios. Las reflexiones en Acta Bioethica sobre genómica son similares a las de otras revistas, solo que el énfasis es en la región latinoamericana. En veinte años de reflexión, los desafíos siguen siendo los mismos, aunque el énfasis está cambiando de la prevención y rechazo en cuanto a los riesgos de la modificación genética, a la regulación de la tecnología de ingeniería genética, que va perfeccionándose cada vez más. En cuanto a los beneficios, la medicina genómica siempre ha generado más expectativas que realidades, sin lograr demostrar eficacia en ensayos clínicos. Con las nuevas técnicas de edición genómica, se amplían aún más las expectativas de mejores intervenciones, pero aumenta la preocupación de que se realicen modificaciones genéticas sin finalidad terapéutica, afectando al equilibrio social y ecológico.

Abstract This article reviews ethical reflections about genetic research and genetic manipulation published in 20 years of Acta Bioethica. The following relevant topics are identified in bioethics dialogue: risks evaluation, inequity, loss of biodiversity, eugenics, definition of limits between artificial and natural, dialogue between detractors and promoters of biotechnology, challenges in health care, information and confidentiality management. Reflections consider that bioethics can act as mediator among diverse stakeholders affronting the problems that arise when applying technology to life, allowing to recognize and to reach consensus for solving differences in equity, autonomy and the balance of risks and benefices. The reflections in Acta Bioethica are similar to those of other journals, but with emphasis in the Latin American region. In twenty years of reflection, the challenges are similar, but the emphasis is changing from preventing to the avoidance of actual risks of genetic modifications, which demands regulation of genetic engineering, taking into account that it is more effective than before. Among the benefits, genomic medicine has always generated more expectations than actual therapy with problems in demonstrating efficacy in clinical trials. With the new technique of genomic edition, there are even more expectations for enhancing therapeutic approaches, but worries increase about using genetic modifications without therapeutic aim and interventions that affect the social and ecological equilibrium.

Resumo O presente artigo é uma revisão das reflexões éticas sobre temas de genética e manipulação genética que foram publicadas em 20 anos de Acta Bioethica. Os seguintes temas de importância para o diálogo bioético foram identificados: avaliação de riscos, inequidade, perda da biodiversidade, eugenia, definir os limites entre natural e artificial, diálogo entre opositores e defensores da biotecnologia, desafios em cuidados à saúde, manejo da informação e confidencialidade. Concluiu-se que a bioética pode atuar como intermediaria entre os diversos interlocutores ante os problemas que aparecem ao aplicar a tecnologia à vida, permitindo reconhecer e alcançar consensos para enfrentar com responsabilidade as diferenças em temas de equidade e autonomia, e o equilíbrio entre riscos e benefícios. As reflexões na Acta Bioethica sobre genômica são similares às de outras revistas, mas com ênfase na região latino-americana. Em vinte anos de reflexão, os desafios seguem sendo os mesmos, ainda que a ênfase esteja mudando da prevenção e repúdio quanto aos riscos da modificação genética, à regulação da tecnologia de engenharia genética, que se aperfeiçoa cada vez mais. Quanto aos benefícios, a medicina genômica sempre gerou mais expectativas que realidades, sem conseguir demonstrar eficácia em ensaios clínicos. Com as novas técnicas de edição genômica, ampliam-se ainda mais as expectativas de melhores intervenções, mas aumenta a preocupação de que se realizem modificações genéticas sem finalidade terapêutica, afetando o equilíbrio social e ecológico.

Humans , Bioethics , Biotechnology , Genomics , Genetic Research , Ethics
Rev. MVZ Córdoba ; 25(1): 51-58, ene.-abr. 2020. tab
Article in Spanish | LILACS | ID: biblio-1279654


RESUMEN Objetivo. Estimar parámetros genéticos para peso a los ocho meses de edad (W8M), edad al primer parto (AFC) y primer intervalo entre partos (FCI) usando parentesco genómico y por pedigrí. Materiales y métodos. Se utilizaron 481, 3063 y 1098 registros fenotípicos para W8M, AFC y FCI, respectivamente. La información genómica estuvo compuesta por una población de 718 animales genotipados con un chip que incluyó 30106 marcadores genéticos tipo polimorfismo de nucleótido simple (SNP). Modelos univariado y bivariado fueron construidos bajo la metodología del mejor predictor lineal insesgado convencional (BLUP) y genómico en una etapa (ssGBLUP). Resultados. Las heredabilidades para W8M, AFC y FCI variaron desde 0.25 a 0.26, 0.20 a 0.22 y 0.04 a 0.08, respectivamente. Los modelos de AFC y FCI con la metodología ssGBLUP disminuyeron ligeramente el error y aumentaron la varianza genética aditiva, respectivamente. Conclusiones. La inclusión de información genómica mejora levemente la precisión de las estimaciones genéticas en esta población. Sin embargo, una población de animales genotipados más grande y con mayor conectividad genética por parentesco permitiría aumentar para los criadores el potencial de la metodología ssGBLUP en ganado Simmental de Colombia.

ABSTRACT Objective. To estimate genetic parameters for weight at eight months of age (W8M), age at first calving (AFC) and first calving interval (FCI) using pedigree and genomic relationship. Materials and methods. Phenotypic data on 481, 3063 and 1098 animals for W8M, AFC and FCI were used, respectively. The genomic information came from a population of 718 genotyped animals with a density chip of 30,106 single nucleotide polymorphism markers (SNP). Univariate and bivariate models were used under the conventional (BLUP) and single step genomic best linear unbiased predictor (ssGBLUP) methodologies. Results. The heritabilities for W8M, AFC and FCI ranged from 0.25 to 0.26, from 0.20 to 0.22 and from 0.04 to 0.08, respectively. The AFC and FCI models under ssGBLUP slightly decreased the error and increased the additive genetic variance, respectively. Conclusions. The inclusion of genomic information slightly increases the accuracy of the genetic estimates in this population. However, a larger amount of genotyped animals and with a higher genetic relationship connectivity would allow breeders to increase the potential of the ssGBLUP methodology in Colombian Simmental cattle.

Animals , Livestock , Reproduction , Genomics
Article in Chinese | WPRIM | ID: wpr-829041


OBJECTIVE@#To investigate the gene mutation occurved in AML patients with 29 kinds of fusion genes and 51 kinds of tumor gene.@*METHODS@#Next-generation sequencing (NGS) was used to detected the 49 kinds of targeted gene. FLT3 internal tandem duplication (FLT3-ITD), CALR, NPM1 and CEBPA mutation were detected by DNA-based PCR and Sanger sequencing. Twenty-nine kinds of fusion genes were dected by multiplex nested RT-PCR.@*RESULTS@#The total gene mutation rate was 91% (109/121) in all the 121 patients. On average, 2.1 mutated genes per patient were identified, among these 121 patients, coexistence of ≥ 3 mutations was frequent (34.7%). The most commonly mutated genes were NRAS (23.96%, n=29), followed by NPM1 (14.04%, n=17), CEBPA double mutations (14.04%, n=17), KRAS (11.57%, n=14),FLT3-ITD (10.74%, n=13), CSF3R (10.74%, n=13), TET2 (9.92%, n=12) and IDH1 (9.1%, n=11). Overall, fusion genes were detected in 47 (37.3%) patients, including AML/ETO (n=12), CBFβ/MYH11 (n=11), PML/RARa (n=12), MLL rearranagement realated mutation MLL-X (n=10). TLS/ERG (n=1) and DEK/CAN (n=1) in an order of decreasing frequency. Patients with normal karyotype (NK)- AML exhibited more mutations in CEBPA, NPM1, TET2, RUNX1 and IDH1, comparing with abnormal karyotype patients. KRAS mutation in abnormal kayotype patients was significantly higher than that in normal kayotype patients (P=0.014). TP53 mutations were predominantly associated with complex cytogenetics (P=0.199). KRAS mutations were more frequent in core binding factor (CBF) acute myeloid leukemia (AML) and 11q23/MLL rearrangement leukemia, compared with NK-AML (P=0.006 and 0.003, respectively). KIT mutations predominated in CBF-AML (P=0.006). JAK2V617F mutations were detected in two patients and co-occurred with AML-ETO fusions.@*CONCLUSION@#At least one mutation is observed in more than 90% patients. On average, more than 2 mutated genes per patient are identified. Some gene mutations are associated with gene rearrangement.

Chromosomal Proteins, Non-Histone , Genomics , High-Throughput Nucleotide Sequencing , Humans , Leukemia, Myeloid, Acute , Mutation , Oncogene Proteins , Poly-ADP-Ribose Binding Proteins , Prognosis
Article in English | WPRIM | ID: wpr-880488


Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13-15 million years ago (MYA) and another about 125-142 MYA, during the evolution of the genome of Selaginella moellendorffii, a model lycophyte. In addition, comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleo-polyploidization events than seed plants. Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages-lycophytes and seed plants-of vascular plants.

Evolution, Molecular , Genome, Plant , Genomics , Phylogeny , Polyploidy , Selaginellaceae/genetics
Article in English | WPRIM | ID: wpr-880484


The dynamic activity of transposable elements (TEs) contributes to the vast diversity of genome size and architecture among plants. Here, we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons (LTR-RTs) in Arabidopsis thaliana (Ath) and three of its relatives, Arabidopsis lyrata (Aly), Eutrema salsugineum (Esa), and Schrenkiella parvula (Spa), in Brassicaceae. Our analyses revealed the distinct evolutionary dynamics of Gypsyretrotransposons, which reflects the different patterns of genome size changes of the four species over the past million years. The rate of Gypsy transposition in Aly is approximately five times more rapid than that of Ath and Esa, suggesting an expanding Aly genome. Gypsy insertions in Esa are strictly confined to pericentromeric heterochromatin and associated with dramatic centromere expansion. In contrast, Gypsy insertions in Spa have been largely suppressed over the last million years, likely as a result of a combination of an inherent molecular mechanism of preferential DNA removal and purifying selection at Gypsy elements. Additionally, species-specific clades of Gypsy elements shaped the distinct genome architectures of Aly and Esa.

Brassicaceae/genetics , Evolution, Molecular , Genome Size , Genome, Plant , Genomics , Phylogeny , Retroelements , Species Specificity
Article in Chinese | WPRIM | ID: wpr-826364


To investigate the relationship of both DNA methylation level and methylenetrahydrofolate reductase(MTHFR)gene polymorphism with ankylosing spondylitis(AS). Totally 200 Chinese AS patients with HLA-B27(+)and 120 healthy controls were included from Hunan Province.All the cases were diagnosed according to the 1984 modified New York criteria for AS.The DNA methylation was examined by cytosine extension method,while the MTHFR gene C677T polymorphism was analyzed by the polymerase chain reaction(PCR)and restriction fragment length polymorphism(RFLP).The plasma homocysteine(Hcy)level was examined by enzyme-linked immunosorbent assay(ELISA),while the red blood folate level was analyzed by the specific immunoassays. The ratio of the T/T genotype mutation in the AS group was significantly higher than in the control group(17.0% 5.0%;=9.874, =0.002).The plasma homocysteine concentration of AS group was(18.71 ± 2.42)μmol/L,which was significantly higher than that in normal control group [(10.97 ± 2.93)μmol/L](=24.402, <0.001).The plasma Hcy concentration of the T/T genotype [(21.70±1.80)μmol/L] was significantly higher than that of the C/C genotype[(18.31±1.94)μmol/L](=12.088, =0.01)and the C/T genotype [(17.80±2.18)μmol/L](=6.496, =0.01)in the AS group.The DNA methylation level of the T/T genotype in AS group was significantly lower than that in normal control group(=5.655, <0.001)and also significantly lower than those of the C/C genotype(=11.514, <0.001)and the C/T genotype in AS group(=10.287, <0.001). In the Han population in Hunan Province,the C677T polymorphism of the MTHFR gene is associated with the onset of AS.The T/T mutation at position 677 of the MTHFR gene is an important influencing factor for hyperhcyemia in the AS patients.The T/T mutation at position 677 of the MTHFR gene is associated with genomic DNA hypomethylation.Thus,hypomethylation of DNA may be one of the pathogenic mechanisms of AS.

DNA , DNA Methylation , Genomics , Genotype , Humans , Methylenetetrahydrofolate Reductase (NADPH2) , Polymorphism, Genetic , Spondylitis, Ankylosing
Article in Chinese | WPRIM | ID: wpr-878817


Unraveling the genetic basis of medicinal plant metabolism and developmental traits is a long-standing goal for pharmacologists and plant biologists. This paper discusses the definition of molecular genetics of medicinal plants, which is an integrative discipline with medicinal plants as the research object. This discipline focuses on the heredity and variation of medicinal plants, and elucidates the relationship between the key traits of medicinal plants(active compounds, yield, resistance, etc.) and genotype, studies the structure and function, heredity and variation of medicinal plant genes mainly at molecular level, so as to reveal the molecular mechanisms of transmission, expression and regulation of genetic information of medicinal plants. Specifically, we emphasize on three major aspects of this discipline.(1)Individual and population genetics of medicinal plants, this part mainly highlights the genetic mechanism of the domestication, the individual genomics at the species level, and the formation of genetic diversity of medicinal plants.(2)Elucidation of biosynthetic pathways of active compounds and their evolutionary significance. This part summarizes the biosynthesis, diversity and molecular evolution of active compounds in medicinal plants.(3) Molecular mechanisms that shaping the key agronomic traits by internal and external factors. This part focuses on the accumulation and distribution of active compounds within plants and the regulation of metabolic network by environmental factors. Finally, we prospect the future direction of molecular genetics of medicinal plants based on the rapid development of multi-omics technology, as well as the application of molecular genetics in the future strategies to achieve conservation and breeding of medicinal plants and efficient biosynthesis of active compounds.

Biosynthetic Pathways , Genomics , Molecular Biology , Plant Breeding , Plants, Medicinal
Chinese Journal of Biotechnology ; (12): 2791-2812, 2020.
Article in Chinese | WPRIM | ID: wpr-878530


Three-dimensional (3D) genomics is an emerging discipline that studies the 3D spatial structure and function of genomes, focusing on the 3D spatial conformation of genome sequences in the nucleus and its biological effects on biological processes such as DNA replication, DNA recombination and gene expression regulation. The invention of chromosome conformation capture (3C) technology speeds up the research on 3D genomics and its related fields. Furthermore, the development of 3C-based technologies, such as the genome-wide chromosome conformation capture (Hi-C) and chromatin interaction analysis using paired-end tag sequencing (ChIA-PET), help scientists get insight into the 3D genomes of various species. Aims of 3D genomics are to reveal the spatial genome organization, chromosomal interaction patterns, mechanisms underlying the transcriptional regulation and formation of biological traits of microorganism, plant, animal. Additionally, the identification of key genes and signaling pathways associated with biological processes and disease via chromosome 3C technology boosts the rapid development of agricultural science, life science and medical science. This paper reviews the research progress of 3D genomics, mainly in the concept of 3D genomics, the development of chromosome 3C technologies and their applications in agricultural science, life science and medical science, specifically in the field of tumor.

Animals , Cell Nucleus , Chromatin/genetics , Chromosomes/genetics , Genome , Genomics
Brasília; IPEA; 2020. 59 p. ilus.(Texto para Discussão / IPEA, 2557).
Monography in Portuguese | LILACS, ECOS | ID: biblio-1100676


A medicina de precisão, ou medicina personalizada, é a customização de tratamento médico com base na capacidade de classificar indivíduos em subpopulações que diferem na susceptibilidade a uma determinada doença ou na resposta a um tratamento específico. Essa nova percepção sobre a forma de diagnóstico e tratamento vem ganhando espaço, dado o envelhecimento da população e a consequente transição epidemiológica, com ganho de evidência para as doenças crônico-degenerativas. As principais tecnologias incorporadas pela literatura no conceito de medicina de precisão são testes genéticos (diagnóstico); biossensores e wearables (monitoramento); e terapias celulares e gênicas (tratamento), sendo a maioria de recente implementação ou ainda em desenvolvimento. Os benefícios individuais do uso dessas tecnologias são claros, mas ainda há desafios para seu uso coletivo, tendo em vista, principalmente, seus custos. Este texto apresenta as tecnologias de medicina de precisão já existentes e discute sua eficácia e eficiência, bem como seus impactos nos custos e nos sistemas de saúde de forma geral. Além disso, são avaliados os desafios para o seu desenvolvimento e em que medida países como o Brasil podem atuar como usuários ou produtores dessas tecnologias.

Precision medicine or personalized medicine refers to the customization of medical treatment based on the ability to classify individuals into subpopulations that differ in susceptibility to a particular disease or in response to a specific treatment. This new perception about diagnosis and treatment is growing throughout the world, given the aging of the population and the consequent epidemiological transition, with gain of evidence for chronic-degenerative diseases. The main technologies incorporated by the literature in the concept of precision medicine are genetic tests (diagnosis), biosensors and wearables (monitoring), cellular and gene therapies (treatment), most of which have been recently implemented or are still under development. Individual benefits of precision medicine are clear, but there are still challenges for their collective use, given mainly its costs. This text presents the existing technologies and discusses their effectiveness and efficiency as well as their costs and impacts on the health system. In addition, we also discuss challenges to its development and to how countries such as Brazil could play a role as users or producers of these technologies.

Genetic Testing , Health , Genomics , Precision Medicine
Clinics ; 75: e1913, 2020. tab, graf
Article in English | LILACS | ID: biblio-1133412


OBJECTIVES: High-throughput sequencing of genomes, exomes, and disease-focused gene panels is becoming increasingly common for molecular diagnostics. However, identifying a single clinically relevant pathogenic variant among thousands of genetic polymorphisms is a challenging task. Publicly available genomic databases are useful resources to filter out common genetic variants present in the population and enable the identification of each disease-causing variant. Based on our experience applying these technologies at Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo, Brazil, we recognized that the Brazilian population is not adequately represented in widely available genomic databases. METHODS: Here, we took advantage of our 5-year experience as a high-throughput sequencing core facility focused on individuals with putative genetic disorders to build a genomic database that may serve as a more accurate reference for our patient population: SELAdb. RESULTS/CONCLUSIONS: Currently, our database comprises a final cohort of 523 unrelated individuals, including patients or family members managed by different clinics of HCFMUSP. We compared SELAdb with other publicly available genomic databases and demonstrated that this population is very heterogeneous, largely resembling Latin American individuals of mixed origin, rather than individuals of pure European ancestry. Interestingly, exclusively through SELAdb, we identified a spectrum of known and potentially novel pathogenic variants in genes associated with highly penetrant Mendelian disorders, illustrating that pathogenic variants circulating in the Brazilian population that is treated in our clinics are underrepresented in other population databases. SELAdb is freely available for public consultation at:

Humans , Genomics , Databases, Genetic , Brazil , Cohort Studies , High-Throughput Nucleotide Sequencing