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1.
Rev. Hosp. Ital. B. Aires (2004) ; 41(1): 37-42, mar. 2021. ilus, tab
Article in Spanish | LILACS | ID: biblio-1178964

ABSTRACT

El término CRISPR, por su acrónimo en inglés refiere a Clustered Regularly Interspaced Short Palindromic Repeats, es decir, repeticiones palindrómicas cortas, agrupadas y regularmente esparcidas, por sus características en el genoma, pertenece naturalmente al sistema de defensa de bacterias y arqueas. Este ha sido adaptado biotecnológicamente para la edición del ADN de células eucariotas, incluso de células humanas. El sistema CRISPR-Cas para editar genes consta, en forma generalizada, de dos componentes: una proteína nucleasa (Cas) y un ARN guía (sgRNA). La simplicidad del complejo lo hace una herramienta molecular reprogramable capaz de ser dirigida y de editar cualquier sitio en un genoma conocido. Su principal foco son las terapias para enfermedades hereditarias monogénicas y para el cáncer. Sin embargo, además de editor de genes, la tecnología CRISPR se utiliza para edición epigenética, regulación de la expresión génica y método de diagnóstico molecular. Este artículo tiene por objetivo presentar una revisión de las aplicaciones de la herramienta molecular CRISPR-Cas, particularmente en el campo biomédico, posibles tratamientos y diagnósticos, y los avances en investigación clínica, utilizando terapia génica con CRISPR/Cas más relevantes hasta la fecha. (AU)


CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats, which naturally belong to the defense system of bacteria and archaea. It has been biotechnologically adapted for editing the DNA of eukaryotic cells, including human cells. The CRISPR-Cas system for editing genes generally consists of two components, a nuclease protein (Cas) and a guide RNA (sgRNA). The simplicity of the complex makes it a reprogrammable molecular tool capable of being targeted and editing any site in a known genome. Its main focus is therapies for monogenic inherited diseases and cancer. However, in addition to gene editor, CRISPR technology is used for epigenetic editing, regulation of gene expression, and molecular diagnostic methods. This article aims to present a review of the applications of the CRISPR-Cas molecular tool, particularly in the biomedical field, possible treatments and diagnoses, and the advances in clinical research, using the most relevant CRISPR-Cas gene therapy to date. (AU)


Subject(s)
Humans , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , CRISPR-Cas Systems/genetics , Biotechnology , Genetic Therapy/methods , Gene Expression , Genome, Human/genetics , Gene Expression Regulation , Epigenomics/trends , CRISPR-Associated Proteins/genetics , CRISPR-Associated Proteins/therapeutic use , Genetic Diseases, Inborn/therapy , Neoplasms/therapy
2.
Rev. colomb. psiquiatr ; 50(1): 57-63, Jan.-Mar. 2021. tab
Article in Spanish | LILACS, COLNAL | ID: biblio-1251635

ABSTRACT

RESUMEN El presente artículo es el resultado de una investigación, desde las perspectivas bioética y biojurídica, acerca de los lineamientos existentes en Colombia para el manejo de las pruebas farmacogenómicas y farmacogenéticas en los ensayos clínicos. La revisión de la legislación existente en nuestro medio se comparó con estándares internacionales y los propuestos por organismos supranacionales. Se encontró que en Colombia falta una regulación específica en esta área, lo que expone a una serie de riesgos bioéticos y jurídicos a los participantes e investigadores. No se deben subestimar estos riesgos, pues comprometen la viabilidad ética de la investigación clínica y básica en nuestro medio. Al final, desde la perspectiva de la ética de los principios, se proponen una serie de acciones para la creación y la promoción a escala nacional de lineamientos que sirvan para conformar una legislación aplicable a la protección de los datos genéticos y, por ende, los derechos de los sujetos que participan en esta clase de estudios de investigación en Colombia.


ABSTRACT This paper is the result of research, from the bioethics and bio-legal perspectives, on the existing guidelines in Colombia for the handling of pharmacogenomic and pharmacogenetic tests in clinical trials. Colombian legislation on this kind of research was reviewed and then compared with international and supranational standards. It was found that Colombia lacks specific legislation in this area, a situation that puts both participants and researchers at risk, from bioethical and legal perspectives. These risks should not be underestimated, as they compromise the ethical viability of clinical and basic research in our setting. In the end, a proposal, based on principles of ethics is made, proposing a series of actions for the creation and promotion nationwide of guidelines which can be used to shape legislation to be applied to protect the genetic data and the rights of subjects participating in these types of research studies in Colombia.


Subject(s)
Humans , Bioethics , Pharmacogenomic Testing , Psychiatry , Research , Social Control, Formal , Genome, Human , Colombia , Ethics, Research , Research Subjects
3.
Rev. cuba. pediatr ; 92(4): e918, oct.-dic. 2020. tab, graf
Article in English | LILACS, CUMED | ID: biblio-1144519

ABSTRACT

Introduction: Neurodevelopmental disorders (NDD) are featured by a delay in the acquisition of motor functions, cognitive abilities and speech, or combined deficits in these areas with the onset before the age of 5 years. Genetic causes account for approximately a half of all NDD cases. Objective: to describe alterations of the genome implied in neurodevelopmental disorders and some aspects of their genetic counseling. Methods: Bibliographic search in Medline, Pubmed, Scielo, LILACS and Cochrane, emphasizing in the last five years, the relationship between the various genetic factors that may be involved in neurodevelopmental disorders. Results: Multiple genetic factors are involved in neurodevelopmental disorders, from gross ones such as chromosomal aneuploidies to more subtle ones such as variations in the number of copies in the genome. Special emphasis is placed on microdeletion-micro duplication syndromes as a relatively frequent cause of NDDs and their probable mechanisms of formation are explained. Final Considerations: Genetic aberrations are found in at least 30-50 percent of children with NDD. Conventional karyotyping allows the detection of chromosomal aberrations encompassing more than 5-7 Mb, which represent 5-10 percent of causative genome rearrangements in NDD. Molecular karyotyping (e.g. SNP array/array CGH) can significantly improve the yield in patients with NDD and congenital malformations(AU)


Introducción: Los trastornos del neurodesarrollo están caracterizados por retardo en la adquisición de las funciones motoras, habilidades cognitivas para el habla o el déficit combinado en estas áreas; se presenta en niños menores de 5 años de edad. Las causas genéticas están implicadas en más de la mitad de los pacientes con estos trastornos Objetivo: Examinar las alteraciones del genoma implicados en los trastornos del neurodesarrollo y algunos aspectos de su asesoramiento genético. Métodos: Búsqueda bibliográfica en Medline, Pubmed, Scielo, LILACS y Cochrane con énfasis en los últimos cinco años, acerca de la relación entre los variados factores genéticos que pueden estar involucrados en los trastornos del neurodesarrollo. Resultados: Los factores genéticos involucrados pueden ser groseros como las aneuploidías cromosómicas hasta los más sutiles como las variaciones en el número de copias en el genoma. Se describen los síndromes de microdeleción-micro duplicación como una causa relativamente frecuente de los trastornos del neurodesarrollo y se explican sus probables mecanismos de formación. Se relacionan las aneuploidías cromosómicas y las variaciones en el número de copia como causas de estos trastornos. Consideraciones finales . Las aberraciones genéticas se encuentran en 30-50 por ciento de los niños con trastornos del neurodesarrollo. El cariotipo convencional permite la detección de aberraciones cromosómicas que abarcan más de 5-7 Mb, lo que representa 5-10 por ciento de los reordenamientos genómicos causales en estos trastornos. El cariotipo molecular (por ejemplo, una matriz de SNP/ CGH de matriz) puede mejorar significativamente la certeza del diagnóstico en pacientes con trastornos del neurodesarrollo y malformaciones congénitas(AU)


Subject(s)
Humans , Male , Female , Infant, Newborn , Infant , Child, Preschool , Chromosome Aberrations , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/epidemiology , Genome, Human/genetics
4.
Fractal rev. psicol ; 32(2): 111-119, maio-ago. 2020. tab
Article in Portuguese | LILACS, INDEXPSI | ID: biblio-1133939

ABSTRACT

Este trabalho problematiza os pressupostos ontológicos assumidos no debate bioético sobre a seleção e edição do genoma humano. Com vistas ao manejo de desordens genéticas, diferentes terapêuticas têm sido empregadas clínica e experimentalmente, desde a década de 1990. Entre as estratégias de tratamento destacam-se a seleção de embriões (mediante diagnóstico genético pré-implantação) e a terapia gênica (mediante edição genética). O desenvolvimento destas técnicas suscita discussões acerca de suas implicações éticas. O presente artigo postula que distintas concepções de humanidade podem ser identificadas nas discussões, as quais fundamentam posicionamentos acerca de intervenções sobre o genoma da espécie. O artigo busca analisar essas concepções, percorrendo três passos. Primeiramente, apresenta-se o contexto biomédico de aplicação da seleção e edição do genoma humano. Em seguida, são evidenciadas discussões sobre os aspectos éticos de tais intervenções. Por fim, explicitam-se diferentes concepções de humanidade que fundamentam as referidas discussões, de maneira a problematizá-las, tendo em vista a noção de justiça distributiva.(AU)


This study discusses the ontological assumptions assumed in the bioethical debate about human genetic selection and gene editing. With a view to managing genetic disorders, different therapies have been employed clinically and experimentally, since the 1990s. Among the treatment strategies, we find embryo selection (by means of pre-implantation genetic diagnosis) and gene therapy (by means of gene editing). The development of these techniques raises discussions about their ethical implications. This article postulates that different conceptions of humanity can be identified in these discussions, grounding ethical positions regarding genome interventions. The article seeks to analyze these conceptions, following three steps. First, the biomedical context of genetic selection and gene editing is presented. Then, discussions on the ethical aspects of these interventions are highlighted. Finally, different conceptions of humanity grounding these discussions are identified and analyzed, considering the notion of distributive justice.(AU)


Subject(s)
Humans , Selection, Genetic , Genome, Human , Bioethical Issues
5.
Gac. méd. Méx ; 156(1): 53-59, ene.-feb. 2020.
Article in Spanish | LILACS | ID: biblio-1249870

ABSTRACT

Resumen En este ensayo se analizan las implicaciones bioéticas de la reciente manipulación genética en embriones humanos con CRISPR-Cas9 para eliminar el gen CCR5 y el nacimiento de dos gemelas discordantes. El experimento se divulgó en medios sociales. Los principales problemas bioéticos identificados son la justificación del modelo, el proceso de consentimiento informado y la falta de declaración de evidentes conflictos de interés. No se evaluaron apropiadamente las consecuencias del experimento sobre la vida de las gemelas nacidas como la afectación a su autonomía, los supuestos beneficios por recibir y los riesgos futuros de daño durante su vida. Habiendo manipulado la línea celular germinal, no se consideraron los efectos sobre su descendencia futura. Este tipo de acciones tiene un impacto negativo en la forma como la sociedad concibe la ciencia. La ingeniería genética debe reservarse al contexto experimental básico o bien como investigación cínica para la corrección de enfermedades conocidas graves de origen genético, bajo estricta supervisión regulatoria y bioética y de manera gradualista de acuerdo con el progreso de las técnicas de edición genética.


Abstract In this essay, the bioethical implications of the recent genetic manipulation in human embryos with CRISPR-Cas9 to eliminate the CCR5 gene and the birth of a pair of discordant twin girls are analyzed. The experiment was disseminated via social media. The main bioethical flaws identified include the justification of the model, the informed consent process and the lack of disclosure of evident conflicts of interest. The consequences of the experiment on the life of the twins that were born were not properly evaluated, such as the impact on their autonomy, the alleged benefits to be received and the future risks of harm during their lifetime. Having manipulated the germ cell line, the effects on their future offspring were not considered. This type of actions negatively affects the way society conceives science. Genetic engineering should be reserved to the basic experimental context or as clinical research for the correction of known serious diseases of genetic origin under strict regulatory and bioethical supervision and using a gradualist approach in accordance with the advances of gene editing techniques.


Subject(s)
Humans , Female , Receptors, CCR5/genetics , CRISPR-Cas Systems , Gene Editing/ethics , Publishing/ethics , Research Design , Twins, Dizygotic , Genetic Engineering/classification , Genetic Engineering/ethics , Genome, Human , HIV Infections/prevention & control , China , Conflict of Interest , Sperm Injections, Intracytoplasmic , Bioethical Issues , Therapeutic Human Experimentation/ethics , Informed Consent/ethics
6.
Rev. Investig. Salud. Univ. Boyacá (En línea) ; 7(2): 138-172, 2020. tab, ilust
Article in Spanish | LILACS, COLNAL | ID: biblio-1292512

ABSTRACT

Introducción: el objetivo de la secuenciación es determinar la composición de los nucleótidos presentes en el ADN o el ARN. Desde la finalización del proyecto genoma humano, surgieron diversas tecnologías de secuenciación rápida como Roche 454, SOLiD, Illumina, Ion Torrent, PacBio y Oxford Nanopore, más precisas y costoeficientes, que permiten desarrollar proyectos a gran escala y estudiar genes y genomas, la composición de microbiomas, enfermedades metabólicas y enfermedades genéticas que afectan a la población. Objetivo: describir los fundamentos de los métodos de secuenciación de ADN y sus aplicaciones en las ciencias biomédicas. Métodos: revisión descriptiva de las principales estrategias de secuenciación de ADN de primera, segunda y tercera generación y su aplicación en el entorno biomédico, a partir de la búsqueda de artículos en bases de datos electró-nicas especializadas en investigación científica. Se encontraron 118 documentos, de los cuales se excluyeron 6, por no cumplir con los criterios de inclusión, y se seleccionaron 112, por cumplir con todos los requisitos. Conclusiones:el surgimiento de los métodos de secuenciación de siguiente generación arroja una gran canti-dad de datos, incluidos genomas secuenciados completamente de varias especies, con un rendimiento extenso, tiempos reducidos y costoeficiencia, que lleva a la completa transformación de las ciencias de la vida y logra un progreso sin precedentes en el análisis de genomas, la evaluación de la ecología microbiana y el diagnóstico de enfermedades.


Introduction: The purpose of sequencing is to determine the composition of the nucleotides present in DNA or RNA. Since the completion of the human genome project, several sequencing technologies such as Roche 454, SOLiD, Illumina, Ion Torrent, PacBio and Oxford Nanopore have emerged as tools for rapid sequencing, with greater precision and cost-efficiency, allowing the development of lar-ge-scale projects and the study of genes and genomes, along with the composition of microbiomes and the study of metabolic and genetic diseases that affect the population. Objective: To describe the foundations of the methods of DNA sequencing and their applications in the biomedical sciences. Methods: Descriptive review of the main strategies of first, second and third generation DNA sequencing and their application in the biomedical environment. This review was carried out by searching articles in electronic databases specialized in scientific research. A total of 118 papers were found, of which 6 were excluded as they did not meet the inclusion criteria and 112 were selected as meeting all the requirements. Conclusions: The emergence of next-generation sequencing methods yielding a wealth of data, including fully sequenced genomes of various species, with extensive throughput, reduced time and cost-effec-tiveness that has led to the complete transformation of the life sciences, achieving unprecedented progress in genome analysis, assessment of microbial ecology and disease diagnosis


Introdução: o objetivo do sequenciamento é determinar a composição dos nucleotídeos presentes no DNA ou RNA. Desde a conclusão do projeto do genoma humano, surgiram diversas tecnologias de sequenciamento rápida como Roche 454, SOLiD, Illumina, Ion Torrent, PacBio e Oxford Nanopore, mais precisas e econômicas, que permitem o desenvolvimento de projetos de grande escala e estudo de genes e genomas, composição de microbiomas, doenças metabólicas e genéticas que afetam a popula-ção. Objetivo: descrever os fundamentos dos métodos de sequenciamento de DNA e suas aplicações nas ciências biomédicas. Métodos: revisão descritiva das principais estratégias de sequenciamento de DNA de primeira, segunda e terceira geração e sua aplicação no ambiente biomédico, a partir da busca de artigos em bases de dados eletrônicas especializadas em pesquisa científica. Foram encontrados 118 documen-tos, dos quais 6 foram excluídos por não atenderem aos critérios de inclusão e 112 fo-ram seleciona-dos por atenderem a todos os requerimentos. Conclusões: o surgimento de métodos de sequenciamento de próxima geração rende uma riqueza de dados, incluindo genomas totalmente se-quenciados de várias espécies, com produção extensa, tempos reduzidos e eficiência de custo, levando à transformação completa das ciências da vida e alcançando um progresso sem precedentes no genoma análise, avaliação de ecologia microbiana e diagnóstico de doenças.


Subject(s)
High-Throughput Nucleotide Sequencing , DNA , Genome, Human , Genetic Techniques , Sequence Analysis
7.
Article in Chinese | WPRIM | ID: wpr-827181

ABSTRACT

OBJECTIVE@#To analyze the genome-wide DNA methylation differences in umbilical cord blood nucleated red blood cells (NRBCs) between term and preterm infants by using the methylation gene chip technology, and to screen the genes of differential methylation and biological signaling pathways which may be related to the expression of γ-globin gene (HBG).@*METHODS@#Umbilical cord bloods of eight term infants and eight preterm infants were collected, and NRBCs of each sample was isolated, then genome DNA was extracted and bisulfite conversion was performed. The DNA methylation sites were detected by using the Illumina 850K BeadChip. Differential DNA methylation sites were screened, and the function of genes with differential methylation was analyzed by using GO and KEGG enrichment analysis.@*RESULTS@#Compared with the preterm group, 4749 differential DNA methylation sites of term group were screened out, including 4359 hypomethylation sites and 390 hypermethylation sites. GO and KEGG analysis indicated that the function of genes with differential methylation mainly involved in the hemopoietic system, growth and development process, Wnt and Notch signal pathways.@*CONCLUSION@#The differentical methylation sites at genome-wide level in umbilicar cord blood NRBC of term and preterm infants have been obtained, and the signal pathway and genes which possibily related with swiching the expression of γ-globin gene to β-globin gene have been screened-out. This study provide the new targets for studing the mechamism regulating expression of HBG gene.


Subject(s)
DNA , DNA Methylation , Epigenesis, Genetic , Fetal Blood , Genome, Human , Humans , Infant, Newborn , Infant, Premature
9.
Rev. MED ; 27(2): 7-9, jul.-dic. 2019.
Article in Spanish | LILACS | ID: biblio-1115224
10.
Gac. méd. Méx ; 155(5): 463-470, Sep.-Oct. 2019. tab, graf
Article in English | LILACS | ID: biblio-1286544

ABSTRACT

The first draft of the human genome sequencing published in 2001 reported a large number of single nucleotide polymorphisms (SNPs). Given that these polymorphisms could practically represent all the variability involved in the susceptibility, protection, severity, among other aspects, of various common diseases, as well as in their response to medications, it was thought that they might be “the biomarkers of choice” in personalized genomic medicine. With the new information obtained from the sequencing of a larger number of genomes, we have understood that SNPs are only an important part of the genetic markers involved in these traits. In addition to SNPs, other variants have been identified, such as insertions/deletions (INDELs) and copy number variants (CNVs), which – in addition to classic variable number tandem repeats (VNTRs) and short tandem repeats (STRs) – originate or contribute to the development of diseases. The use of these markers has served to identify regions of the genome involved in Mendelian diseases (one gene-one disease) or genes directly associated with multifactorial diseases. This review has the purpose to describe the role of STRs, VNTRs, SNPs, CNVs and INDELs in linkage and association studies and their role in Mendelian and multifactorial diseases.


Subject(s)
Humans , Genetic Variation/physiology , Disease/genetics , Polymorphism, Single Nucleotide , Genetic Markers , Genome, Human , Mutagenesis, Insertional , Gene Deletion , Tandem Repeat Sequences , Lod Score , Mutation
12.
Article in English | WPRIM | ID: wpr-785801

ABSTRACT

While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate. For the last 10 years, the availability of long read data of human genomes from PacBio or Nanopore platforms has increased, which makes it easier to detect long insertions/deletions. However, because long read data have a critical disadvantage due to their relatively high cost, many next generation sequencing data are produced mainly by short read sequencing machines. Here, we constructed programs to detect so-called unmapped regions (UMRs, where no reads are mapped on the reference genome), scanned 40 Korean genomes to select UMR long deletion candidates, and compared the candidates with the long deletion break points within the genomes available from the 1000 Genomes Project (1KGP). An average of about 36,000 UMRs were found in the 40 Korean genomes tested, 284 UMRs were common across the 40 genomes, and a total of 37,943 UMRs were found. Compared with the 74,045 break points provided by the 1KGP, 30,698 UMRs overlapped. As the number of compared samples increased from 1 to 40, the number of UMRs that overlapped with the break points also increased. This eventually reached a peak of 80.9% of the total UMRs found in this study. As the total number of overlapped UMRs could probably grow to encompass 74,045 break points with the inclusion of more Korean genomes, this approach could be practically useful for studies on long deletions utilizing short read data.


Subject(s)
Genome , Genome, Human , Humans , Nanopores , Polymorphism, Single Nucleotide
13.
Chinese Journal of Biotechnology ; (12): 1295-1306, 2019.
Article in Chinese | WPRIM | ID: wpr-771799

ABSTRACT

Tumor-specific gene mutations might generate suitable neoepitopes for cancer immunotherapy that are highly immunogenic and absent in normal tissues. The high heterogeneity of the tumor genome poses a big challenge for precision cancer immunotherapy. Mutations characteristic of each tumor can help to distinguish it from other tumors. Based on these mutations' characteristic, it is possible to develop immunotherapeutic strategies for specific tumors. In this study, a tumor neoantigen prediction scheme was proposed, in which both the intracellular antigen presentation process and the ability to bind with extracellular MHC molecule were taken into consideration. The overall design is meritorious and may help reduce the cost for validation experiments compared with conventional methods. This strategy was tested with several cancer genome datasets in the TCGA database, and a number of potential tumor neoantigens were predicted for each dataset. These predicted neoantigens showed tumor type specificity and were found in 20% to 70% of cancer patients. This scheme might prove useful clinically in future.


Subject(s)
Antigens, Neoplasm , Computational Biology , Genome, Human , Humans , Immunotherapy , Mutation , Neoplasms
14.
Article in English | WPRIM | ID: wpr-772957

ABSTRACT

As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits, a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data, sample quality issues, such as gender mismatch, abnormal inbreeding coefficient, cryptic relatedness, and population outliers, can also have fundamental impact on downstream analysis. However, there is a lack of tools specialized in identifying problematic samples from NGS data, often due to the limitation of sample size and variant counts. We developed SeqSQC, a Bioconductor package, to automate and accelerate sample cleaning in NGS data of any scale. SeqSQC is designed for efficient data storage and access, and equipped with interactive plots for intuitive data visualization to expedite the identification of problematic samples. SeqSQC is available at http://bioconductor.org/packages/SeqSQC.


Subject(s)
Breast Neoplasms , Genetics , Cohort Studies , Continental Population Groups , Genetics , Female , Genome, Human , High-Throughput Nucleotide Sequencing , Methods , Reference Standards , Humans , Software , Whole Exome Sequencing
15.
An. Facultad Med. (Univ. Repúb. Urug., En línea) ; 5(2): 12-28, dic. 2018. tab, graf
Article in Spanish | LILACS, BNUY, UY-BNMED | ID: biblio-1088677

ABSTRACT

El genoma humano, como el de todos los mamíferos y aves, es un mosaico de isocoros, los que son regiones muy largas de ADN (>>100 kb) que son homogéneas en cuanto a su composición de bases. Los isocoros pueden ser divididos en un pequeño número de familias que cubren un amplio rango de niveles de GC (GC es la relación molar de guanina+citosina en el ADN). En el genoma humano encontramos cinco familias, que (yendo de valores bajos a altos de GC) son L1, L2, H1, H2 y H3. Este tipo de organización tiene importantes consecuencias funcionales, tales como la diferente concentración de genes, su regulación, niveles de transcripción, tasas de recombinación, tiempo de replicación, etc. Además, la existencia de los isocoros lleva a las llamadas "correlaciones composicionales", lo que significa que en la medida en que diferentes secuencias están localizadas en diferentes isocoros, todas sus regiones (exones y sus tres posiciones de los codones, intrones, etc.) cambian su contenido en GC, y como consecuencia, cambian tanto el uso de aminoácidos como de codones sinónimos en cada familia de isocoros. Finalmente, discutimos el origen de estas estructuras en un marco evolutivo.


The human genome, as the genome of all mammals and birds, are mosaic of isochores, which are very long streches (>> 100 kb) of DNA that are homogeneous in base composition. Isochores can be divided in a small number of families that cover a broad range of GC levels (GC is the molar ratio of guanine+cytosine in DNA). In the human genome, we find five families, which are (going from GC- poor to GC- rich) L1, L2, H1, H2 and H3. This organization has important consequences, as is the case of the concentration of genes, their regulation, transcription levels, rate of recombination, time of replication, etc. Furthermore, the existence of isochores has as a consequence the so called "compositional correlations", which means that as long as sequences are placed in different families of isochores, all of their regions (exons and their three codon positions, introns, etc.) change their GC content, and as a consequence, both codon and amino acids usage change in each isochore family. Finally, we discuss the origin of isochores within an evolutioary framework.


O genoma humano, como todos os mamíferos e aves, é um mosaico de isocóricas, que são muito longas regiões de ADN (>> 100 kb) que são homogéneos na sua composição de base. Isóquos podem ser divididos em um pequeno número de famílias que cobrem uma ampla gama de níveis de GC (GC é a razão molar de guanina + citosina no DNA). No genoma humano, encontramos cinco famílias, que (variando de valores baixos a altos de GC) são L1, L2, H1, H2 e H3. Este tipo de organização tem importantes conseqüências funcionais, como a diferente concentração de genes, sua regulação, níveis de transcrição, taxas de recombinação, tempo de replicação, etc. Além disso, a existência de isocóricas portada chamado "correlações de composição", o que significa que, na medida em que diferentes sequências estão localizados em diferentes isocóricas, todas as regiões (exs e três posições de codões, intrs, etc.) mudam seu conteúdo em GC e, como consequência, alteram tanto o uso de aminoácidos quanto de códons sinônimos em cada família de isócoros. Finalmente, discutimos a origem dessas estruturas em uma estrutura evolucionária.


Subject(s)
Humans , Genome, Human/genetics , Isochores/genetics , Base Composition , Introns/genetics
16.
Medicina (Bogotá) ; 40(2(121)): 226-227, Abr-Jun, 2018.
Article in Spanish | LILACS | ID: biblio-910452

ABSTRACT

Hace 60 años Julian Huxley (1887­1975), el gran biólogo evolucionista británico, propul-sor de la eugenesia entendida como la dis-ciplina que busca el perfeccionamiento de la especie humana mediante la aplicación de las leyes de la he-rencia, escribió: "Hasta ahora la vida humana ha sido, en general, como Hobbes la describió, «desagradable, brutal y corta¼; la gran mayoría de los seres humanos (si aún no han muerto jóvenes) han sido afectados con la miseria... podemos sostener justificadamente la creencia de que existen estas tierras de posibilidad, y que las actuales limitaciones y frustraciones misera-bles de nuestra existencia podrían ser en gran medida sobrellevadas... La especie humana puede, si lo desea, trascenderse a sí misma - y no sólo de forma esporá-dica, un individuo aquí de una manera, un individuo no de otra manera, sino en su totalidad, como huma-nidad. "La especie humana puede, si así lo desea, trascen-der -no esporádicamente, un individuo de una manera aquí, otro individuo de otra forma allá, sino en su tota-lidad, como humanidad. Se requiere un término para significar ello. Tal vez Transhumanismo puede servir: el ser humano sigue siendo ser humano, pero trascien-de, dándose cuenta de las nuevas posibilidades de y para su naturaleza humana. Una vez que haya un nú-mero suficiente de personas que de verdad sean cons-cientes de que la especie humana está al borde de una nueva forma de existencia, tan diferente de la nuestra como lo es el Hombre de Pekín


Subject(s)
Humans , Biological Evolution , Genome, Human
17.
Article in English | WPRIM | ID: wpr-714226

ABSTRACT

PURPOSE: We aimed to develop molecular classifier that can predict lymphatic invasion and their clinical significance in epithelial ovarian cancer (EOC) patients. MATERIALS AND METHODS: We analyzed gene expression (mRNA, methylated DNA) in data from The Cancer Genome Atlas. To identify molecular signatures for lymphatic invasion, we found differentially expressed genes. The performance of classifier was validated by receiver operating characteristics analysis, logistic regression, linear discriminant analysis (LDA), and support vector machine (SVM). We assessed prognostic role of classifier using random survival forest (RSF) model and pathway deregulation score (PDS). For external validation, we analyzed microarray data from 26 EOC samples of Samsung Medical Center and curatedOvarianData database. RESULTS: We identified 21 mRNAs, and seven methylated DNAs from primary EOC tissues that predicted lymphatic invasion and created prognostic models. The classifier predicted lymphatic invasion well, which was validated by logistic regression, LDA, and SVM algorithm (C-index of 0.90, 0.71, and 0.74 for mRNA and C-index of 0.64, 0.68, and 0.69 for DNA methylation). Using RSF model, incorporating molecular data with clinical variables improved prediction of progression-free survival compared with using only clinical variables (p < 0.001 and p=0.008). Similarly, PDS enabled us to classify patients into high-risk and low-risk group, which resulted in survival difference in mRNA profiles (log-rank p-value=0.011). In external validation, gene signature was well correlated with prediction of lymphatic invasion and patients' survival. CONCLUSION: Molecular signature model predicting lymphatic invasion was well performed and also associated with survival of EOC patients.


Subject(s)
Disease-Free Survival , DNA , Forests , Gene Expression , Genome , Genome, Human , Humans , Logistic Models , Lymphatic Metastasis , Ovarian Neoplasms , RNA, Messenger , ROC Curve , Support Vector Machine , Transcriptome
18.
Intestinal Research ; : 327-337, 2018.
Article in English | WPRIM | ID: wpr-715888

ABSTRACT

Colorectal cancer (CRC) arise from multi-step carcinogenesis due to genetic mutations and epigenetic modifications of human genome. Genetic mutations and epigenetic modifications were originally established as 2 independent mechanisms contributing to colorectal carcinogenesis. However, recent evidences demonstrate that there are interactions between these 2 mechanisms. Genetic mutations enable disruption of epigenetic controls while epigenetic modifications can initiate genomic instability and carcinogenesis. This review summarized genetic mutations and epigenetic modifications in colorectal carcinogenesis and molecular classification of CRC subtype based on genetic or epigenetic biomarkers for treatment response and prognosis. Molecular subtypes of CRC will permit the implementation of precision medicine with better outcome of management for CRC.


Subject(s)
Biomarkers , Carcinogenesis , Classification , Colorectal Neoplasms , Epigenesis, Genetic , Epigenomics , Genome, Human , Genomic Instability , Humans , Precision Medicine , Prognosis
19.
Article in Chinese | WPRIM | ID: wpr-775272

ABSTRACT

OBJECTIVE@#To screening coagulation and anticoagulation genes and mutations in Chinese patients with venous thromboembolism suspected of inhered thrombophilia.@*METHODS@#Patients with venous thromboembolism caused by inherited thrombophilia were collected from the second Affiliated Hospital, Zhejiang University School of Medicine during June 2015 and December 2017. Gene sequencing was conducted to screen the anticoagulant-related genes and coagulation-related genes . The thousands of human genome database, ESP6500 database, Genoma database, HGMD mutation database were used to compare the mutation sites, and the pathogenic mutation sites were predicted according to SIFT, Polyphen, MutationTaster and CADD databases.@*RESULTS@#Among 25 patients screened, eight patients with mutations, two patients with mutations, three patients with mutations; one patient with mutation, one patient with mutation, one patient with mutation, two patient with mutations, and one patient with mutation.@*CONCLUSIONS@#The second generation gene sequencing helps to diagnose inherited thrombophilia and guide the decision of anticoagulation duration.


Subject(s)
Blood Proteins , Genetics , China , Genome, Human , Genetics , Humans , Mutation , Thrombophilia , Diagnosis , Genetics
20.
Article in English | WPRIM | ID: wpr-773007

ABSTRACT

The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects.


Subject(s)
Animals , CRISPR-Cas Systems , Gene Editing , Methods , Genetic Engineering , Methods , Genome, Human , High-Throughput Nucleotide Sequencing , Humans
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