Hallazgos incidentales en medicina genómica / Incidental Findings in Genomic Medicine

Las técnicas de Biología Molecular de última generación, como es la secuenciación masiva en paralelo o NGS (Next Generation Sequencing), permite obtener gran cantidad de información genómica, la cual muchas veces va más allá de la detección de una variante patogénica en un gen que explique la patología (hallazgo primario). Es así como surgió desde hace años la discusión internacional respecto a la decisión a tomar frente a los hallazgos secundarios accionables, es decir, aquellos hallazgos de variantes clasificadas como patogénicas o probablemente patogénicas que no están relacionadas con el fenotipo del paciente, pero que tiene alguna medida preventiva o tratamiento posible y, por lo tanto, podría ser de utilidad para la salud del paciente. Luego de revisar la bibliografía internacional y debatir entre los expertos del Hospital de Pediatría Garrahan, se logró establecer una política institucional y reforzar el hecho de que se trata de una disciplina multidisciplinaria. Así, fue posible definir que solo se atenderá las cuestiones relacionadas con la edad pediátrica, dejando para un tratamiento posterior aquellas variantes detectadas en genes que sean accionables en edad adulta. En el Hospital Garrahan, ha sido posible definir claramente cómo proceder frente a los hallazgos secundarios, al adaptar el consentimiento informado a esta necesidad, definiendo cuándo serán informados, y sabiendo que serán buscados intencionalmente en los genes clínicamente accionables enlistados en la última publicación del American College of Medical Genetics and Genomics, siempre y cuando el paciente/padre/tutor lo consienta (AU)

The latest generation of molecular biology techniques, including massive parallel sequencing or NGS (Next Generation Sequencing), allows us to obtain a whealth of genomic information, which often goes beyond the detection of a pathogenic variant in a gene that explains the pathology (primary finding). As a result, an international discussion has arisen over the years regarding the decision-making concerning actionable secondary findings, it means, those findings of variants classified as pathogenic or probably pathogenic that are not related to the patient's phenotype, but which have some possible preventive measure or treatment and, therefore, could be useful for the patient's health. After reviewing the international literature and discussing among the experts of the Hospital de Pediatría Garrahan, an institutional policy was established and the concept that this is a multidisciplinary discipline was reinforced. Consequently, it has been defined that only issues related to children will be addressed, reserving those variants detected in genes that are actionable in adulthood for later treatment. At Garrahan Hospital, we were able to clearly define how to proceed with secondary findings by adapting the informed consent to this need, defining when they will be reported, and knowing that they will be intentionally searched for in the clinically actionable genes listed in the latest publication of the American College of Medical Genetics and Genomics, as long as the patient/parent/guardian consents (AU)

Standards for the interpretation of constitutional copy number gain: Recommendation from the American College of Medical Genetics and Genomics (ACMG) and Clinical Genome Resource (ClinGen) / 中华医学遗传学杂志

Copy number variants (CNVs) are common causes of human genetic diseases. CNVs detection has become a routine component of genetic testing, especially for pediatric neurodevelopmental disorders, multiple congenital abnormalities, prenatal evaluation of fetuses with structural anomalies detected by ultrasound. Although the technologies for CNVs detection are continuously improving, the interpretation is still challenging, with significant discordance across different laboratories. In 2020, the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen) developed a guideline for the interpreting and reporting of constitutional copy number variants, which introduced a quantitative, evidence-based scoring framework. Here, we detailed the key points of interpreting the copy number gain based on the guideline, used six examples of different categories to illuminate the scoring process and principles. We encourage a professional understanding and application of this guideline for the detected copy number gains in China in order to further improve the clinical evaluation accuracy and consistency across different laboratories.

CRISPR-Cas, el editor de genes / CRISPR, gene editor

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)

Genómica de los trastornos del desarrollo neurológico / Genomics of neurodevelopmental disorders

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)

Genoma humano: aspectos estructurales / Human genome: structural aspects / Genoma humano: aspectos estruturais

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.

Joinville stroke biobank: study protocol and first year's results / Biobanco de acidente cerebrovascular de Joinville: protocolo de estudos e resultados dos primeiros anos

ABSTRACT Aiming to contribute to studies that use detailed clinical and genomic information of biobanks, we present the initial results of the first Latin American Stroke Biobank. Methods: Blood samples were collected from patients included in the Joinville Stroke Registry and four Brazilian cities. Demographic socio-economic data, cardiovascular risk factors, Causative Classification System for Ischemic Stroke, Trial of Org 10172 in Acute Stroke Treatment and National Institutes of Health scores, functional stroke status (modified Rankin) and brain images were recorded. Additionally, controls from both geographic regions were recruited. High-molecular-weight genomic DNA was obtained from all participants. Results: A total of 2,688 patients and 3,282 controls were included. Among the patients, 76% had ischemic stroke, 12% transient ischemic attacks, 9% hemorrhagic stroke and 3% subarachnoid hemorrhage. Patients with undetermined ischemic stroke were most common according the Trial of Org 10172 in Acute Stroke Treatment (40%) and Causative Classification System for Ischemic Stroke (47%) criteria. A quarter of the patients were under 55 years of age at the first-ever episode. Conclusions: We established the Joinville Stroke Biobank and discuss its potential for contributing to the understanding of the risk factors leading to stroke.

RESUMO Com o objetivo de contribuir para estudos que utilizam informações clínicas e genômicas de biobancos, apresentamos os resultados iniciais do primeiro Biobanco Latinoamericano em Acidente Vascular Cerebral (AVC). Métodos: Foram coletadas amostras de sangue de pacientes recrutados pelo Registro de AVC de Joinville e posteriormente de quatro cidades brasileiras. Foram registrados dados socioeconômicos demográficos, fatores de risco cardiovasculares, Causative Classification System (CCS), Trial of Org 10172 in Acute Stroke Treatment, National Institutes of Health, estado funcional (Rankin modificado) e imagens cerebrais. Adicionalmente, foram recrutados controles das regiões geográficas correspondentes. Obteve-se DNA genômico de todos participantes. Resultados: Foram incluídos 2688 pacientes e 3282 controles. Entre os pacientes, 76% tiveram AVC isquêmico, 12% ataques isquêmicos transitórios, 9% AVC hemorrágico e 3% hemorragia subaracnóidea. Os casos indeterminados foram os mais frequentes e classificados de acordo com TOAST (40%) e CCS (47%). Um quarto dos pacientes tinham menos de 55 anos no primeiro evento. Conclusões: Estabelecemos o Joinville Stroke Biobank, e discutimos aqui seu potencial na compreensão dos fatores de risco do AVC.

Pesquisa e propriedade intelectual envolvendo material humano: afinal,de quem são nossos genes? / /Research and intellectual property involving human material: after all,from whom are our genes? / /La investigación y la propiedad intelectual implicando material humano:¿al final, a quien pertenecen nuestros genes?

O presente artigo discute aspectos éticos, científicos e jurídicos sobre o patenteamento de genes humanos,partindo de um contexto histórico sobre propriedade intelectual de seres vivos e passando pela decisão da Suprema Corte dos EUA relativa ao caso Myriad Genetics, conflito em torno da patente dos genes BRCA1e BRCA2, relacionados ao câncer de mama e de ovário. Além disso, o artigo aborda diplomas normativos sobre o assunto, considerando tanto a legislação brasileira quanto a internacional. Por fim, contrapõe posições distintas sobre patente de genes humanos, adotando posicionamento crítico que o assunto merece...

This article discusses ethical, scientific and legal aspects of the patenting of human genes, startingfrom a historical context of intellectual property of living beings and passing through the decision ofthe US Supreme Court in Myriad Genetics case, conflict over patent of the genes BRCA1 and BRCA2,related to breast cancer and ovarian cancer. Moreover, the article discusses regulatory instrumentson the subject, considering both the Brazilian and international legislation. Finally, it contrastsdifferent positions on patent of human genes, adopting critical position that this matter deserves...

Este artículo aborda los aspectos éticos, científicos y legales de las patentes de genes humanos, a partir de uncontexto histórico de la propiedad intelectual de los seres vivos y pasando por la decisión de la Corte Suprema deEstados Unidos en el caso Myriad Genetics, el conflicto sobre patentes de los genes BRCA1 y BRCA2 relacionadoscon el cáncer de mama y cáncer de ovario. Además, el artículo analiza los instrumentos normativos sobre eltema, teniendo en cuenta tanto la legislación brasileña como internacional. Por último, contrasta diferentesposiciones sobre las patentes de los genes humanos, y adopta una posición crítica que este asunto merece...

Biological evolution: Some genetic considerations

The concept of biological evolution has long been accepted as a palatable theory aiming at explaining how life began and how creatures diverged so widely along the life span of the earth. Meticulous analysis and criticism of the different postulations of this concept, however, reveals that evolution is an illogic concept based on theoretical hypotheses that can never be tested. Creation, on the other hand, represents the other side of the coin, and up till now debates confronting creation versus evolution are still occupying much interest of atheist as well as of believer biologists. The motive for accepting the concept of evolution by most biologists, stems solely from their atheism and their saying that creation can neither be experimented nor validated, the same criticism directed against their assumptions regarding the basic aspects of evolution. This article, through analysis, criticism and reevaluation of some relevant genetic considerations that have long been traditionally considered as observations in support of the concept of evolution, viz. genetic memory and evolutionary variations, genomic adaptations to stress and evolution, comparative genomics and natural versus targeted selection, tries to elucidate and reveal some insensible assumptions embodied within the core ideas of evolution that stand in direct controversy with many well-known facts regarding the structure, function and behavior of living matter. Natural selection might be observed in nature but not in life. The concept of biological evolution is an illogic and insensible hypothesis since it stands in direct contradiction with our current knowledge regarding the behavior as well as the structural and functional characteristics of the human genome and human proteome. Additionally, almost all basic postulations of this concept can neither be tested nor imitated for experimentation, which is a prerequisite for acceptance and validation of any scientific hypotheses

Genomic sovereignty or the enemy within / Soberanía genómica o el enemigo interior / Soberania genômica ou o inimigo interior

Genomic sovereignty is a concept that has become very popular among developing countries such as India, China, South Africa and Mexico. This concept is a response to developed countries that have taken advantage of those countries and researchers who don't have the means for protecting their own biogenetic resources. In this article we argue that genomic sovereignty is not about the “others” extracting and exploiting local “human genetic resources”, but developing and implementing the ethical, legal and administrative tools, based on transparency, openness and equal access to biological material, in order to build up a robust research networks. Being biological samples a scarce and valuable good, we conclude that controlling the access to this resource by means of the law, without a well implemented biobanking system and a clear scientific policy may lead to a situation where asymmetric relations are generated among research groups of the very same developing country. We would advice to those countries pretending to protect their biological samples and data from the outside, before developing laws against possible “intrusions”, they need to design strategies to promote equal and fair access to both resources paramount to biomedical research.

“Soberanía genómica” es un concepto que se ha hecho muy popular entre los países en desarrollo, como India, China, Sudáfrica y México. Este concepto es una respuesta a los países desarrollados que han tomado ventaja, aprovechándose de aquellos países y de los investigadores que no tienen los medios para proteger sus propios recursos biogenéticos. En este artículo argumentamos que la soberanía genética no se trata de impedir que “otros” extraigan y exploten “los recursos genéticos humanos” locales, sino del desarrollo y de la aplicación de las herramientas éticas, jurídicas y administrativas basadas en la transparencia, la apertura e igualdad en el acceso al material biológico, con el fin de construir redes de investigación sólidas. Al ser las muestras biológicas un bien escaso y valioso, concluimos que el control del acceso a este recurso, por medio de la ley, sin un sistema de biobancos bien implementado y sin una política científica clara, puede llevar a una relación asimétrica entre los grupos de investigación del mismo país en desarrollo. Nos gustaría advertir a los países que pretenden proteger sus muestras biológicas y datos asociados que, antes que elaborar leyes contra posibles intrusiones, es necesario diseñar estrategias para promover el acceso justo y equitativo a los recursos primordiales para la investigación biomédica.

“Soberania genômica” é um conceito que se fez muito popular entre os países em desenvolvimento, como Índia, China, África do Sul e México. Este conceito é uma resposta aos países desenvolvidos que obtiveram vantagem, aproveitando-se daqueles países e dos investigadores que não têm meios para proteger os seus próprios recursos biogenéticos. Neste artigo argumentamos que a soberania genética não trata de impedir que “outros” extraiam e explorem “os recursos genéticos humanos” locais, senão do desenvolvimento e da aplicação das ferramentas éticas, jurídicas e administrativas baseadas na transparência, abertura e igualdade no acesso ao material biológico, com a finalidade de construir redes de investigação sólidas. Por serem as amostras biológicas um bem escasso e valioso, concluimos que o controle do acesso a este recurso, por meio da lei, sem um sistema de biobancos bem implementado e sem uma política científica clara, pode levar a uma relação assimétrica entre os grupos de investigação de um mesmo país em desenvolvimento. Gostaríamos advertir aos países que pretendem proteger suas amostras biológicas e dados associados que, antes de elaborar leis contra possíveis intromissões, é necessário projetar estratégias para promover o acesso justo e equitativo aos recursos primordiais para a investigação biomédica.

Promoters, toll like receptors and microRNAs: A strange association.

Toll-like receptors (TLRs) are proteins that play key role in the innate immune system. In the present study, ~1000 base pairs upstream are taken from the transcription start site of the various TLR genes (10 known) in human. About 40 microRNAs have been identified that share 12-19 nucleotide sequence similarity with the promoter regions of 10 TLRs. It is proposed that the microRNA performs potential role in identification of promoter sequence and initiation of transcription.

Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology

Vaccine development faces major difficulties partly because of genetic variation in both infectious organisms and humans. This causes antigenic variation in infectious agents and a high interindividual variability in the human response to the vaccine. The exponential growth of genome sequence information has induced a shift from conventional culture-based to genome-based vaccinology, and allows the tackling of challenges in vaccine development due to pathogen genetic variability. Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. Accumulating results provide evidence for the existence of a number of genes involved in protective immune responses that are induced either by natural infections or vaccines. Variation in immune responses could be viewed as the result of a perturbation of gene networks; this should help in understanding how a particular polymorphism or a combination thereof could affect protective immune responses. Here we will present: i) the first genome-based vaccines that served as proof of concept, and that provided new critical insights into vaccine development strategies; ii) an overview of genetic predisposition in infectious diseases and genetic control in responses to vaccines; iii) population genetic differences that are a rationale behind group-targeted vaccines; iv) an outlook for genetic control in infectious diseases, with special emphasis on the concept of molecular networks that will provide a structure to the huge amount of genomic data.

Effect of gene polymorphisms on periodontal diseases.

Periodontal diseases are inflammatory diseases of supporting structures of the tooth. It results in the destruction of the supporting structures and most of the destructive processes involved are host derived. The processes leading to destruction and regeneration of the destroyed tissues are of great interest to both researchers and clinicians. The selective susceptibility of subjects for periodontitis has remained an enigma and wide varieties of risk factors have been implicated for the manifestation and progression of periodontitis. Genetic factors have been a new addition to the list of risk factors for periodontal diseases. With the availability of human genome sequence and the knowledge of the complement of the genes, it should be possible to identify the metabolic pathways involved in periodontal destruction and regeneration. Most forms of periodontitis represent a life-long account of interactions between the genome, behaviour, and environment. The current practical utility of genetic knowledge in periodontitis is limited. The information contained within the human genome can potentially lead to a better understanding of the control mechanisms modulating the production of inflammatory mediators as well as provides potential therapeutic targets for periodontal disease. Allelic variants at multiple gene loci probably influence periodontitis susceptibility.

Differences of DNA methylation profiles in monozygotic twins' blood samples / 法医学杂志

OBJECTIVE@#To evaluate the potential usefulness of DNA methylation in individual discrimination of monozygotic twins by investigating the differences of DNA methylation profiles in monozygotic twins' blood samples.@*METHODS@#Blood samples from 22 pairs of monozygotic twins were obtained with informed consent. Genomic DNA extracts were bisulfite treated followed by detection with Infinium HumanMethylation27 BeadChip Assays(Illumina, USA). Epigenetic distances between each pair of monozygotic twins and each pair of unrelated individuals of same gender were calculated with Euclidean distance algorithms. Distribution of epigenetic distance in monozygotic twin group was statistically compared with that in unrelated individuals.@*RESULTS@#Difference of epigenetic distance between male and female pairs was not statistically significant in unrelated individual group or in monozygotic twin group (P = 0.0695 and 0.4825, respectively). Epigenetic distance of monozygotic twins was significantly lower than that of unrelated individual pair of same gender (Median: 6.02 vs 7.20, P = 0.0002). However, all the epigenetic distance in monozygotic twin group or in unrelated individuals were significantly higher than 4.00 (P < 0.000 1).@*CONCLUSION@#DNA methylation profiles of monozygotic twin's blood samples were significantly different with each other, which was similar to that in unrelated individuals of same gender. These results indicated that DNA methylation was a useful biomarker in individual discrimination of monozygotic twins.

Integrative epigenomic and genomic analysis of malignant pheochromocytoma

Epigenomic and genomic changes affect gene expression and contribute to tumor development. The histone modifications trimethylated histone H3 lysine 4 (H3K4me3) and lysine 27 (H3K27me3) are epigenetic regulators associated to active and silenced genes, respectively and alterations of these modifications have been observed in cancer. Furthermore, genomic aberrations such as DNA copy number changes are common events in tumors. Pheochromocytoma is a rare endocrine tumor of the adrenal gland that mostly occurs sporadic with unknown epigenetic/genetic cause. The majority of cases are benign. Here we aimed to combine the genome-wide profiling of H3K4me3 and H3K27me3, obtained by the ChIP-chip methodology, and DNA copy number data with global gene expression examination in a malignant pheochromocytoma sample. The integrated analysis of the tumor expression levels, in relation to normal adrenal medulla, indicated that either histone modifications or chromosomal alterations, or both, have great impact on the expression of a substantial fraction of the genes in the investigated sample. Candidate tumor suppressor genes identified with decreased expression, a H3K27me3 mark and/or in regions of deletion were for instance TGIF1, DSC3, TNFRSF10B, RASSF2, HOXA9, PTPRE and CDH11. More genes were found with increased expression, a H3K4me3 mark, and/or in regions of gain. Potential oncogenes detected among those were GNAS, INSM1, DOK5, ETV1, RET, NTRK1, IGF2, and the H3K27 trimethylase gene EZH2. Our approach to associate histone methylations and DNA copy number changes to gene expression revealed apparent impact on global gene transcription, and enabled the identification of candidate tumor genes for further exploration.

DNA tests probe the genomic ancestry of Brazilians

We review studies from our laboratories using different molecular tools to characterize the ancestry of Brazilians in reference to their Amerindian, European and African roots. Initially we used uniparental DNA markers to investigate the contribution of distinct Y chromosome and mitochondrial DNA lineages to present-day populations. High levels of genetic admixture and strong directional mating between European males and Amerindian and African females were unraveled. We next analyzed different types of biparental autosomal polymorphisms. Especially useful was a set of 40 insertion-deletion polymorphisms (indels) that when studied worldwide proved exquisitely sensitive in discriminating between Amerindians, Europeans and Sub-Saharan Africans. When applied to the study of Brazilians these markers confirmed extensive genomic admixture, but also demonstrated a strong imprint of the massive European immigration wave in the 19th and 20th centuries. The high individual ancestral variability observed suggests that each Brazilian has a singular proportion of Amerindian, European and African ancestries in his mosaic genome. In Brazil, one cannot predict the color of persons from their genomic ancestry nor the opposite. Brazilians should be assessed on a personal basis, as 190 million human beings, and not as members of color groups.

Comparison of allele frequency for HLA-DR and HLA-DQ between patients with ECC and caries-free children.

BACKGROUND: Early childhood caries (ECC) is one of the most common diseases of childhood. The etiology of ECC is multifactorial and both genetic and environmental factors play important roles in the pathogenesis of the disease. Genetic variations in the hosts may contribute to changes in the risk for dental caries. Genetic factors such as human leukocyte antigen (HLA) have recently been suggested as a predisposing factor. AIM: The aim of this study was to look for an association between HLA-DRB1 and HLA-DQB1 with ECC for developing new strategies for the diagnosis as well as the prevention of the disease. DESIGN: In this study, we extracted the genomic DNAs from whole blood samples of 44 patients with ECC and 35 caries-free children by the salting-out method. We amplified the genomic DNA by PCR-SSP and then HLA-typing was performed for all alleles. RESULTS: The results revealed a significant increase in the frequency of HLA-DRB1*04 in the patient group (P=0.019). The odds ratio for this allele was detected to be 10. The frequency of HLA-DQB1 alleles was not significantly different between the two groups. CONCLUSION: The above results suggest that HLA-DRB1*04 is associated with the susceptibility to ECC. Thus HLA-DRB1*04 detection as a molecular marker for early diagnosis of ECC may be recommended.

Heritability and linkage study on heart rates in a Mongolian population

Elevated heart rate has been proposed as an independent risk factor for cardiovascular diseases, but their interrelationships are not well understood. In this study, we performed a genome-wide linkage scan in 1,026 individuals (mean age 30.6 years, 54.5% women) from 73 extended families of Mongolia and determined quantitative trait loci that influence heart rate. The DNA samples were genotyped using deCODE 1,039 microsatellite markers for 3 cM density genome-wide linkage scan. Correlation analysis was carried out to evaluate the correlation of the covariates and the heart rate. T-tests of the heart rate were also performed on sex, smoking and alcohol intake. Consequently, this model was used in a nonparametric genome-wide linkage analysis using variance component model to create a multipoint logarithm of odds (LOD) score and a corresponding P value. In the adjusted model, the heritability of heart rate was estimated as 0.32 (P<.0001) and a maximum multipoint LOD score of 2.03 was observed in 77 cM region at chromosome 18. The second largest LOD score of 1.52 was seen on chromosome 5 at 216 cM. Genes located on the specified locations in chromosomes 5 and 18 may be involved in the regulation of heart rate.