PerspectivesAre you interested in submitting a Perspective Article? Be sure to read The Science Advisory Board's Editorial Guides for Perspective Articles. Click here. Pick of Recent Times: A Review of a Seminal Genomics Paper by Chetan Datta Poduri, Ph.D. Occasionally, a few publications in science literature may not make any impact on the scientific community initially. But, over-a-period, realization dawns on the researchers, making them look back to those publications, essentially to re-look/re-think what actually did those original researchers meant. In this process of looking back, research in one particular direction comes to a stand still. And then the popular collective thinking takes up an entirely new course, previously unimagined. Classic example among others includes Mendel’s publications. Among the publications in recent times, I should like to pick: the Weber et al., publication in Nature Genetics (1) [the associated news & views in the same issue by Relman DA (2) makes for a compelling reading], that will fit the above description and is bound to exert its influence on our thinking in genomics in future. Weber’s publication in Nature Genetics describes, in part, the sequence similarity of human express sequence tags (ESTs) with a number of viral sequences. While the sequence similarity could not be explained, completely or properly, what is noteworthy in their study is that these ESTs are from tissues, which the viruses target. For example, Hepatitis B virus (HBV), a hepatotropic virus, shows similarities with ESTs from hepatic samples. Further investigations in this direction with regard to specific viruses such as Hepatitis C virus (HCV), uncover interesting sequence similarities with more number of human ESTs [approximately fifty-one EST sequences, from humans, and plants, show similarities of about 90-100% over small/short stretches with HCV when I last did a similarity search in 2003 (Poduri CD, unpublished data)] and other organism ESTs. Here I am talking about one virus. There are many other phylogenetically unrelated organisms that show similarities. Such similarities can be between animal-animal or animal-plant or plant-plant. Weber et al., themselves have reported one phylogenetically unrelated similarity: human brain ESTs with Caenorhabditis elegans. If these sequence similarities are genuine, then: i. The similarities may reveal useful insights into the life cycles of many of the viruses (all types of animal, plant, etc.); ii. They may also represent something akin to mapping of mutant fungus Aspergillus with the long arm of chromosome 3 in humans (3, 4); and iii. Contaminations of the original sources from where these ESTs and/or viral sequences were generated (here contamination also represents infection of the original sample with various pathogens) ˆ for delineation of the same, necessary investigations were not performed at the time of submission or reporting of these sequences. [Mind you, if this is the case, going-back and redoing of all the experiments, might in all likelihood make the researchers involved mental wrecks]. In addition to the above, many of the sequences being partial and incomplete, impedes a thorough investigation in any of the above-mentioned directions. This also calls for a better control/regulation in submission of partial and/or incomplete sequences to public databases. Whatever might be the case, one must realize that the sequence similarities between evolutionarily unrelated organisms are much more than what is reported by Weber et al., and here. Definitely Weber et al., gave a new direction to genomics. Pop comes to mind the question “Why do phylogenetically unrelated organisms show genomic or EST sequence similarity?” Answering this question might make the scientific community rewrite some concepts, if not textbooks. Needless-to-say, the report of Weber et al., is just a tip of the iceberg. References: 1. Weber et al. Nature Genetics, 2002; 30 (2): 141 ˆ 142. 2. Relman DA. Nature Genetics, 2002; 30 (2): 131 ˆ 133. 3. Scazzocchio C. Trends in Genetics, 1997; 13: 125 ˆ 127. 4. Fernandez-canon & Penalva. Proc Natl Acad Sci, USA, 1995; 92: 9132 ˆ 6. ### << Previous Next >> [ View All Perspectives ] |
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