Developments In Genomic Research Research Articles

Basic principles of legal regulation in the field of human genomic information processing in the context of implementation of international legal norms to national legislation

The article focuses on the analysis of human rights factors that are formed within the framework of international legal relations. The development of genomic research and expanding their application in domestic jurisprudence is a fairly new area of research in the field of public administration. On the basis of the synthesis of general scientific and specialized legal methods of research, the principles of regulation of relations on the processing of genomic information for human registration in Ukraine are formulated and substantiated, taking into account the threats to the dignity and rights of the human personality, namely: priority of life and health of citizens over interests of science and society in conducting molecular genetic examinations (research); confidentiality or protection of the genetic information of each citizen as part of personal data; equality of citizens regardless of genetic characteristics; guarantees of personality of person when using genomic technologies; observance of human and citizen’s rights and freedoms in the exercise of the rights and freedoms of others; guarantees of a citizen’s accessibility to their own genetic information; preventive actions of the state to protect citizens from the risks of loss, damage, distortion, misuse, unauthorized access to genomic information; exchange of genomic information with other countries and international organizations. In the context of implementation of international legal norms, the proposed principles are of particular importance, since they allow to maintain the balance of legal regulation and serve as a guide for law enforcement. The proposal for the application of a number of principles of processing of human genome information must be enshrined in the Law of Ukraine «On State Registration of Genomic Information», which will facilitate the formation of legal bases into the national system of law.

Second law of information dynamics

One of the most powerful laws in physics is the second law of thermodynamics, which states that the entropy of any system remains constant or increases over time. In fact, the second law is applicable to the evolution of the entire universe and Clausius stated, “The entropy of the universe tends to a maximum.” Here, we examine the time evolution of information systems, defined as physical systems containing information states within Shannon’s information theory framework. Our observations allow the introduction of the second law of information dynamics (infodynamics). Using two different information systems, digital data storage and a biological RNA genome, we demonstrate that the second law of infodynamics requires the information entropy to remain constant or to decrease over time. This is exactly the opposite to the evolution of the physical entropy, as dictated by the second law of thermodynamics. The surprising result obtained here has massive implications for future developments in genomic research, evolutionary biology, computing, big data, physics, and cosmology.

Molecular Markers of Pediatric Solid Tumors-Diagnosis, Optimizing Treatments, and Determining Susceptibility: Current State and Future Directions.

Advances in molecular technologies, from genomics and transcriptomics to epigenetics, are providing unprecedented insight into the molecular landscape of pediatric tumors. Multi-omics approaches provide an opportunity to identify a wide spectrum of molecular alterations that account for the initiation of the neoplastic process in children, response to treatment and disease progression. The detection of molecular markers is crucial to assist clinicians in accurate tumor diagnosis, risk stratification, disease subtyping, prediction of treatment response, and surveillance, allowing also for personalized cancer management. This review summarizes the most recent developments in genomics research and their relevance to the field of pediatric oncology with the aim of generating an overview of the most important, from the clinical perspective, molecular markers for pediatric solid tumors. We present an overview of the molecular markers selected based on therapeutic protocols, guidelines from international committees and scientific societies, and published data.

Instruments for the protection of human rights violated during the study of human genome

The paper contains a comparative analysis of legal instruments used in the Russian legislation and in the legislation of other countries (Germany, Great Britain, USA, Japan) to protect (prevent violations, restore) human rights violated during the study of human genome. It was concluded that the existence of a comprehensive system of legal means for the protection and restoration of human rights violated during the study of human genome, is an incentive for the development of genomic research. In this regard, in Russia it is necessary to amend civil acts, Information, Criminal and Administrative Law in order to establish the peculiarities of the compensation for harm to human rights violations when studying human genome, special (different from the general) procedure for obtaining voluntary informed consent for genomic research, as well as special offences and administrative offenses committed during the study of the human genome.

A flow cytometry-based analysis to establish a cell cycle synchronization protocol for Saccharum spp.

Modern sugarcane is an unusually complex heteroploid crop, and its genome comprises two or three subgenomes. To reduce the complexity of sugarcane genome research, the ploidy level and number of chromosomes can be reduced using flow chromosome sorting. However, a cell cycle synchronization (CCS) protocol for Saccharum spp. is needed that maximizes the accumulation of metaphase chromosomes. For flow cytometry analysis in this study, we optimized the lysis buffer, hydroxyurea(HU) concentration, HU treatment time and recovery time for sugarcane. We determined the mitotic index by microscopic observation and calculation. We found that WPB buffer was superior to other buffers for preparation of sugarcane nuclei suspensions. The optimal HU treatment was 2 mM for 18 h at 25 °C, 28 °C and 30 °C. Higher recovery treatment temperatures were associated with shorter recovery times (3.5 h, 2.5 h and 1.5 h at 25 °C, 28 °C and 30 °C, respectively). The optimal conditions for treatment with the inhibitor of microtubule polymerization, amiprophos-methyl (APM), were 2.5 μM for 3 h at 25 °C, 28 °C and 30 °C. Meanwhile, preliminary screening of CCS protocols for Badila were used for some main species of genus Saccharum at 25 °C, 28 °C and 30 °C, which showed that the average mitotic index decreased from 25 °C to 30 °C. The optimal sugarcane CCS protocol that yielded a mitotic index of >50% in sugarcane root tips was: 2 mM HU for 18 h, 0.1 X Hoagland’s Solution without HU for 3.5 h, and 2.5 μM APM for 3.0 h at 25 °C. The CCS protocol defined in this study should accelerate the development of genomic research and cytobiology research in sugarcane.

ФОРМИРОВАНИЕ СИСТЕМЫ САМОРЕГУЛИРОВАНИЯ ГЕНОМНЫХ ИССЛЕДОВАНИЙ В РОССИИ НА ОСНОВЕ МЕЖДУНАРОДНЫХ ЭТИЧЕСКИХ НОРМ И НАЦИОНАЛЬНОГО ЗАКОНОДАТЕЛЬСТВА

The development of genomic research as an applied field requires the determination of their legal status in the Russian Federation. One of the directions could be the use of self-regulation in this area. The article discusses the features of Russian legislation and the recognition of the status of medical intervention for genomic research. International ethical standards are considered as the basis for this approach.

Molecular characterization of Aedes, Culex, Anopheles, and Armigeres vector mosquitoes inferred by mitochondrial cytochrome oxidase I gene sequence analysis

The current epidemics of vector-borne diseases in tropical countries, especially in India, have extended the need for a comprehensive understanding of the distribution of epidemiologically important vector mosquitoes. The advanced developments in genomic research including phylogenetic studies will empower the molecular studies that are vital to determine the genetic divergence and evolutionary history of mosquito vectors. The use of the cytochrome oxidase c subunit I (COI) gene-based approaches to outline the interrelationship of vector mosquitoes from different genera could also elucidate the obscurity that has risen from improper taxonomical classification. The mosquitoes were collected from Nelliyampathy, Kerala, India and identified using systematic keys and catalogues. The genomic DNA of the mosquitoes was extracted using NucleoSpin® Tissue Kit and PCR amplification of the mitochondrial COI gene was accomplished by using the following primers: Forward 5′- GGTCAACAAATCATAAAGATATTGG-3′ and reverse 5′- TAAACTTCAGGGTGACCAAAAAATCA-3′. The genetic divergence was assessed by means of the NJ-K2P method. The neighbor-joining tree was constructed using the MEGA7 software. The diversity of mosquitoes was estimated using the Shannon index through SPSS and Venn diagram plotter. The COI gene-based mitochondrial DNA analysis revealed distinct clustering of individual mosquito species within every genus together with strong bootstrap support. In total, our investigation productively identified and confirmed the interrelationship between the COI gene sequences of ten epidemiologically important mosquito species. This study also discusses the substantial evidence of mosquito species complex formation. Our findings offer a base for future research which is essential for the better understanding of mosquito phylogeny and shed light upon, a novel vector control strategy.

Genomics and Precision Medicine: Molecular Diagnostics Innovations Shaping the Future of Healthcare in Qatar

Unprecedented developments in genomics research and ancillary technologies are creating the potential for astonishing changes in both the healthcare field and the life sciences sector. The innovative genomics applications include the following: (1) embracing next generation sequencing (NGS) in clinical diagnostics setting (applying both whole genome and exome sequencing), (2) single cell sequencing studies, (3) quantifying gene expression changes (including whole transcriptome sequencing), (4) pharmacogenomics, and (5) cell-free DNA blood-based testing. This minireview describes the impact of clinical genomics disruptive innovations on the healthcare system in order to provide better diagnosis and treatment. The observed evolution is not limited to the point-of-care services. Genomics technological breakthroughs are pushing the healthcare environment towards personalized healthcare with the real potential to attain better wellbeing. In this article, we will briefly discuss the Gulf region population-based genome initiatives that intend to improve personalized healthcare by offering better prevention, diagnosis, and therapy for the individual (precision medicine). Qatar’s endeavor in genomics medicine will be underscored including the private Applied Biomedicine Initiative (ABI).

What will genomics mean for you?

In the next few years, probably sooner rather than later, there is going to be a major change in the conversations we have with the families with whom we work. The reason for this is the rapid developments in genomics research, says Crystal Oldman.

Evolution of bird genomes-a transposon's-eye view.

Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE "arms races" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.

Translating genetics beyond bench and bedside: A comparative perspective on health care infrastructures for ‘familial’ breast cancer

Developments in genomics research are considered to have great potential for improving health care – making genomics an urgent site for translational efforts. Yet while much emphasis is put on the technical challenges of translation, there is less scholarly attention for the social infrastructures through which novel medical interventions may be delivered to patient populations. Reflecting the idea that cancer is at the frontier of genomic applications in health care, this paper explores how the assessment of familial breast cancer risks was ‘translated’ into routine health care in Germany, the Netherlands and the United Kingdom. The paper identifies regulation, institutionalization and standardization as key mechanisms of translation that find distinct expression in particular sociocultural contexts and shape both the social and technical making of genomics into routine clinical practice. Translation is therefore an area of social as well as technical concern, and therefore requires collective decision-making.

A Strategy for Genomic Research on Common Cardiovascular Diseases Aiming at the Realization of Precision Medicine: Personal Insights and Perspectives.

Despite the development of genomic research on common cardiovascular diseases, genetic variants and/or loci shown to be disease associated have been seldom applied to risk prediction in a clinical setting, although they could provide us with novel mechanistic insights into the pathophysiology and potential therapeutic targets. Here, we discuss the significance and limitations of the up-to-date genomic studies on common diseases and propose what kind of genomic research should be prioritized in view of the realization of precision medicine. Many disease-associated loci have been identified using a genome-wide association study (GWAS) in a large-scale case–control design (more than several thousand cases and controls). A GWAS is an analytical method for the identification of disease-associated tag (lead) SNPs, which are indicators of disease-associated loci (linkage disequilibrium blocks) with a genome-wide significance ( P <5×10−8). Consequently, further analysis is required to identify the specific variants functioning as the most associated and/or risk variants1 within each disease-associated locus. Consistent with the genetic cause of monogenic diseases, novel biology on the risk genes and their regulatory pathways can be learned through detailed genetic and functional analysis after GWAS. Also, GWAS data on disease-associated pathways might be used in choosing drugs for treatment.2 We have experienced several successful stories. Single-nucleotide polymorphisms (SNPs) in PCSK9 , HMGCR , and NPC1L 1 were shown to be associated with hypercholesterolemia in GWAS on blood lipids.3 Although their effects shown in that GWAS were relatively weak (+2–3 mg/dL change in plasma cholesterol values), potent compounds targeting these gene-encoded proteins have been established as lipid-lowering agents (anti-PCSK9 antibody, statin, and ezetimibe, respectively). In this way, GWAS data can provide the scientific community with information about novel biology, mechanical pathways, and potential pharmaceutical drugs. Because current GWASs are usually performed with a case–control design, the results are …

Copy number variations and stroke.

Stroke is the third leading cause of death worldwide after heart disease and all forms of cancers. Monogenic disorders, genetic, and environmental risk factors contribute to damaging cerebral blood vessels and, consequently, cause stroke. Developments in genomic research led to the discovery of numerous copy number variants (CNVs) that have been recently identified as a new tool for understanding the genetic basis of many diseases. This review discusses the current understanding of the types of stroke, the existing knowledge on the involvement of specific CNVs in stroke as well as the limitations of the methods used for detecting CNVs like SNP-microarray. To confirm an unequivocally association between CNVs and stroke and extend the current findings, it would be desirable to use another methodology to detect smaller CNVs or CNVs in genomic regions poorly covered by this technique, for instance, CGH-array.

Mapping the Structure and Dynamics of Genomics-Related MeSH Terms Complex Networks

It has been proposed that the history and evolution of scientific ideas may reflect certain aspects of the underlying socio-cognitive frameworks in which science itself is developing. Systematic analyses of the development of scientific knowledge may help us to construct models of the collective dynamics of science. Aiming at scientific rigor, these models should be built upon solid empirical evidence, analyzed with formal tools leading to ever-improving results that support the related conclusions. Along these lines we studied the dynamics and structure of the development of research in genomics as represented by the entire collection of genomics-related scientific papers contained in the PubMed database. The analyzed corpus consisted in more than 49,000 articles published in the years 1987 (first appeareance of the term Genomics) to 2011, categorized by means of the Medical Subheadings (MeSH) content-descriptors. Complex networks were built where two MeSH terms were connected if they are descriptors of the same article(s). The analysis of such networks revealed a complex structure and dynamics that to certain extent resembled small-world networks. The evolution of such networks in time reflected interesting phenomena in the historical development of genomic research, including what seems to be a phase-transition in a period marked by the completion of the first draft of the Human Genome Project. We also found that different disciplinary areas have different dynamic evolution patterns in their MeSH connectivity networks. In the case of areas related to science, changes in topology were somewhat fast while retaining a certain core-stucture, whereas in the humanities, the evolution was pretty slow and the structure resulted highly redundant and in the case of technology related issues, the evolution was very fast and the structure remained tree-like with almost no overlapping terms.

A novel multi-stage feature selection method for microarray expression data analysis

With the development of genome research, finding method to classify cancer and detect biomarkers efficiently has become a challenging problem. In this paper, a novel multi-stage method for feature selection is proposed which considers all kinds of genes in the original gene set. The method eliminates the irrelevant, noisy and redundant genes and selects a subset of relevant genes at different stages. The proposed method is examined on microarray datasets of Leukemia, Prostate, Colon, Breast, Nervous and DLBCL by different classifiers and the best accuracies of the method in these datasets are 100%, 98.04%, 100%, 89.74%, 100% and 98.28%, respectively.

How Developments in Cryobiology, Reproductive Technologies and Conservation Genomics Could Shape Gene Banking Strategies for (Farm) Animals

Many local breeds are currently at risk because of replacement by a limited number of specialized commercial breeds. Concurrently, for many breeds, allelic diversity within breeds declines because of inbreeding. Gene banking of germplasm may serve to secure the breeds and the alleles for any future use, for instance to recover a lost breed, to address new breeding goals, to support breeding schemes in small populations to minimize inbreeding, and for conservation genetics and genomics research. Developments in cryobiology and reproductive technology have generated several possibilities for preserving germplasm in farm animals. Furthermore, in some mammalian and bird species, gene banking of material is difficult or impossible, requiring development of new alternative methods or improvement of existing methods. Depending on the species, there are interesting possibilities or research developments in the use of epididymal spermatozoa, oocytes and embryos, ovarian and testicular tissue, primordial germ cells, and somatic cells for the conservation of genetic diversity in farm- and other animal species. Rapid developments in genomics research also provide new opportunities to optimize conservation and sampling strategies and to characterize genome-wide genetic variation. With regard to gene banks for farm animals, collaboration between European countries is being developed through a number of organizations, aimed at sharing knowledge and expertise between national programmes. It would be useful to explore further collaboration between countries, within the framework of a European gene banking strategy that should minimize costs of conservation and maximize opportunities for exploitation and sustainable use of genetic diversity.

The Impact of Genomics on Pediatric Research and Medicine

In this review, we discuss some of the most recent developments in genomics research and their relevance to the field of pediatrics. In particular, we examine 3 major approaches that are being used to identify genetic correlates of disease: genome-wide association studies, copy number variation studies, and next-generation sequencing. In the past few years, these approaches have yielded major insights into the causes and pathophysiology of a wide range of diseases but are also constrained by certain limitations. This review provides an overview of the genomic landscape in complex pediatric disorders and sets the stage for translating new discoveries into clinical practice, the future of genomic medicine.

Recent application developments in genomic research using the AdvanCE™ FS capillary electrophoresis platform

Central to genomic research is the analysis of nucleic acids, which requires versatile, sensitive and high throughput technologies that can deliver accurate results in a short time. Reported herein are recent developments for sizing and/or quantifying nucleic acids (dsDNA and RNA) on a parallel capillary electrophoresis platform with LED-based fluorescence detection (AdvanCE™ FS system). This flexible multi-capillary platform has been employed for applications such as SSR, gDNA analysis, RNA analysis, quantification of next generation sequencing (NGS) libraries, and the separation and sizing of large cDNA from Populus spp,This poster will discuss recent validation of the platform for a subset of these applications in detail. The AdvanCE™ FS system successfully scored all SSR samples with resolution as low as 2 bp. Assessment of the quality/concentration of gDNA is also demonstrated with a new separation matrix, for separation of large DNA fragments. Separation and sizing of large cDNA was also demonstrated with good resolution and accuracy. A method for rapid and sensitive detection of total RNA concentration and quality will be discussed, as well as the sizing and quantification of NGS libraries.The AdvanCE™ FS platform offers rapid separation and ample resolution with excellent sensitivity and dynamic range, to benefit a variety of applications in genomic research.

What is a meaningful result? Disclosing the results of genomic research in autism to research participants

Developments in genomics research have been accompanied by a controversial ethical injunction: that researchers disclose individually relevant research results to research participants. With the explosion of genomic research on complex psychiatric conditions such as autism, researchers must increasingly contend with whether--and which results--to report. We conducted a qualitative study with researchers and participants involved in autism genomics research, including 4 focus groups and 23 interviews with parents of autistic children, and 23 interviews with researchers. Respondents considered genomic research results 'reportable' when results were perceived to explain cause, and answer the question 'why;' that is, respondents set a standard for reporting individually relevant genetic research results to individual participants that is specific to autism, reflecting the metaphysical value that genetic information is seen to offer in this context. In addition to this standard of meaning, respondents required that results be deemed 'true.' Here, respondents referenced standards of validity that were context nonspecific. Yet in practice, what qualified as 'true' depended on evidentiary standards within specific research disciplines as well as fundamental, and contested, theories about how autism is 'genetic.' For research ethics, these finding suggest that uniform and context-free obligations regarding result disclosure cannot readily be specified. For researchers, they suggest that result disclosure to individuals should be justified not only by perceived meaning but also by clarity regarding appropriate evidentiary standards, and attention to the status of epistemological debates regarding the nature and cause of disorders.

Construction of an Escherichia coli to Bacillus thuringiensis shuttle vector for large DNA fragments

Shuttle vectors for Bacillus thuringiensis or Bacillus cereus usually cannot hold fragments larger than 20 kb. With the development of genome research, shuttle vectors with higher loading capacity are necessary. We constructed an Escherichia coli to B. thuringiensis shuttle vector, pEMB0557, with a large loading capacity. This vector incorporated the ori60 replicon from B. thuringiensis subsp. kurstaki YBT-1520, erythromycin resistance (B. thuringiensis), and chloromycetin resistance (E. coli) genes. A bacterial artificial chromosome library of B. thuringiensis strain CT-43 was constructed and pEMB0557 was able to accommodate at least a 70-kb DNA fragment. Simultaneously, the cry1B gene on a 40-kb fragment could express a 140-kDa protein in plasmid-cured B. thuringiensis BMB171. Due to its high capacity and utility in expressing exogenous genes, pEMB0557 will be useful in cloning (especially silencing genes) and expressing large DNA fragments (e.g., gene clusters) in B. thuringiensis. Plasmid pEMB0557 provides a new tool for B. thuringiensis genome or B. cereus group research.