About Author:
Robby Kumar*, Amar Nagesh Kumar*
*Department of Biochemistry,
SSR Medical College, Mauritius
ABSTRACT
Genomics is the study of an organism's genome and the use of the genes. It deals with the systematic use of genome information, associated with other data, to provide answers in biology, medicine, and industry.
Genomics has the potential of offering new therapeutic methods for the treatment of some diseases, as well as new diagnostic methods. Other applications are in the food and agriculture sectors. The major tools and methods related to genomics are bioinformatics, genetic analysis, measurement of gene expression, and determination of gene function.
REFERENCE ID: PHARMATUTOR-ART-1144
GENOMICS AND INFECTIOUS DISEASE: CURRENT STATUS
Infectious disease management is also transforming thanks to molecular technologies as seen in HIV (4,5), tuberculosis, malaria , and other neglected tropical diseases . Discovering novel pathogens and elucidating the implications of genetic variation among existing pathogens is critical for rapidly mitigating pandemic threats, as demonstrated recently with severe acute respiratory syndrome (SARS) and avian (H5N1) and pandemic H1N1 2009 influenza(3).
Genomics can be readily applied to follow outbreaks of infectious diseases. This is clearly illustrated during the severe acute respiratory syndrome (SARS) outbreak in 2002–2003 and the emergence and worldwide spread of the pandemic H1N1 2009 influenza virus this year. In both cases, genomics played a key role in the immediate response to the outbreak. Initially, very little was known about the virus responsible for the SARS outbreak. Pangenomic virus microarrays identified it as a coronavirus (6); however, it was only through detailed sequencing that the specific genotype of this virus could be determined (7). Comparative sequence analysis identified the SARS virus as distinct from other coronaviruses in terms of its encoded proteins responsible for antigen presentation. This finding ultimately lead to development of diagnostics (8) and potential therapeutics (9). This example of a sequencing approach as a rapid response to a virus outbreak demonstrates that genomics can be a useful and important, if not essential, epidemiological tool. In the ongoing H1N1 influenza outbreak, the National Center for Biotechnology Information (NCBI) established the Influenza Virus Resource, containing 462 complete viral genome sequences from worldwide viral samples. Some of the genomic data was completed, compared, and released to the public within two weeks of isolation of the DNA. The rapid generation of genome sequence data is providing a paradigm shift in the analysis of infectious disease outbreaks, from more classical methods of isolation to the rapid molecular examination of the pathogen in question.(9)
The fundamental idea that responses to environmental factors or treatments is to be found in our individual differences, the underlying concept of “genomic medicine”, is rooted in antiquity and based on millennia of simple observation. The objective of genomic medicine is to determine the genetic bases of those differences in response to environmental agents, including medications, and differences that may predispose to the development of common and potentially personally devastating and societally expensive disorders, and to use them in populations to thwart adverse response, increase the frequency of beneficial response, and intervene to prevent or delay onset of disease.(10) Approximately 1100 different genes have been shown to have at least one mutation in them that causes a disease. Total number of disease genes = approx. 1500 (11)
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The field of biodefense has thoroughly embraced genomics and made it a keystone for developing better identification technologies, diagnostic tools, and vaccines and improving our understanding of pathogen virulence and evolution. Enabling technologies and bioinformatics tools have shifted genomics from a separate research discipline to a tool so powerful that it can provide novel insights that were not imaginable a few years ago, including for example redefining the notion of strains or cultures in the context of biopreparedness or microbial forensics. Challenges remain, though, mostly in the form of large amounts of data that are being generated, and will continue to be generated in the future, and are becoming difficult to manage. The need for better bioinformatic algorithms, access to faster computing capabilities, larger or novel and more efficient data storage devices, and better training in genomics are all in critical demand, and will be required to fully embrace the genomic revolution.(9) There are several areas of new knowledge that will have to be developed to create a reality of genomic medicine. These include the characterization of genomic variation among individuals in the target populations (and each separate population will probably have to be studied anew), the identification of the clinically significant variants in each group, the assessment of the extent to which intervention could change predicted outcome–taking into account other changes in environmental exposure and behaviors, and the development of an understanding of the costs of these processes for the society and weighing them against other societal needs.(10) Selecting strategies for monitoring the DNA variations associated with human disease requires careful consideration and new innovative methodologies. First, the cost of detecting DNA variations is still too high to enable screening for tens of thousands of SNPs in massive epidemiological study samples. Second, the annotation and cataloging of variations and their frequencies in various populations is not systematically organized. Third, the selection of relevant variants for epidemiological and functional studies is still a guessing game. We know amazingly little about the relative importance of variations in the regulatory and intronic sequences of human genes and how they differ between populations. Fourth, quantitative analyses of the effects of thousands of DNA variations and the "genome-wide" variant profiles that predispose individuals to complex diseases are still in their infancy. All of these issues require methodological developments, coordinated efforts, and better solutions than those currently available to genetic epidemiologists.(11) We are rapidly advancing upon the postgenomic era in which genetic information will have to be examined in multiple health care situations throughout the lives of individuals. Currently, newborn babies can be screened for treatable genetic diseases such as phenylketonuria. Perhaps in the not-so-distant future, children at high risk for coronary artery disease will be identified and treated to prevent changes in their vascular walls during adulthood. Parents will have the option to be told their carrier status for many recessive diseases before they decide to start a family. For middle-aged and older populations, we will be able to determine risk profiles for numerous late-onset diseases, preferably before the appearance of symptoms, which at least could be partly prevented through dietary or pharmaceutical interventions.
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10. Peter Byers, The role of genomics in medicine?past, present and future, J Zhejiang Univ Sci B. 2006 February; 7(2): 159–160. Peltonen and McKusick, Science 291: 1224-29 (2001).
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