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Research Article

Identifying Selected Regions from Heterozygosity and Divergence Using a Light-Coverage Genomic Dataset from Two Human Populations

  • Taras K. Oleksyk mail,

    *E-mail: oleksyk@ncifcrf.gov

    Affiliations: Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America, Basic Research Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America

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  • Kai Zhao,

    Affiliation: Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America

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  • Francisco M. De La Vega,

    Affiliation: Applied Biosystems, Foster City, California, United States of America

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  • Dennis A. Gilbert,

    Affiliation: Applied Biosystems, Foster City, California, United States of America

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  • Stephen J. O'Brien,

    Affiliation: Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America

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  • Michael W. Smith

    Affiliations: Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America, Basic Research Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America

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  • Published: March 05, 2008
  • DOI: 10.1371/journal.pone.0001712

Reader Comments (16)

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possible applications in radiobiology

Posted by gaschak on 14 Apr 2008 at 15:37 GMT

The approaches suggested by authors seem intriguing enough since they promise to reveal some hidden mechanisms which allow non-human biota to survive successfully in conditions of long-term and extremely high
radioactive contamination of environment. During last 20 years many researchers (myself included) tried to study radiation genetic effects in populations of wild and lab organisms in Chernobyl. Unfortunately, results have been rather disappointing, since they provided a lot of contradictory information. Some studies exhibited elevated level of gene diversity in the most contaminated sites vs. the less polluted areas. Others reported generic identity of haplotype and nucleotide diversity and their variation
throughout the vast region with no correlation to the levels of radioactivity. However, some researchers found out low heterozygosity as effect of radiation impact. Undoubtedly, high radiation causes destabilization of genomes. But what does it reflect? My opinion, everything looks like different sides of the same adaptation mechanism: a response of
biota to selective pressures. So far, there are no evidences that radioactive contamination caused by Chernobyl led to appearance of new beneficial mutations. At least vertebrates permanently inhabited the most radioactive areas around Chernobyl NPP appear to be genetically same as distant reference populations. However, there are also signs of adaptation. Unfortunately, there are few data what describe the mechanism of this adaptation. Mostly the studies focus on different biological systems that provide compensative and reparative reactions, and maintain the necessary level reproduction. However, there is very little information about selection of carriers which have genes of 'radioresistance' or vice versa 'radiosensitivity'. If the methods that Oleksyk et al suggested are really capable to reveal DNA regions with radiation related SNP, it would be very useful to look into the problem. Indeed, resident wild animals of Chernobyl area (those that were genetically studied and those that weren't) could serve as a very appropriate model for validation of the method, since for
tens generations they suffered from very strong selective pressures in the adverse environment, and very likely might have a 'radiation signatures' in their genomes compared to the reference populations.


RE: possible applications in radiobiology

oleksyk replied to gaschak on 16 Apr 2008 at 23:56 GMT

Thank you for your comment, it definitely adds a different twist to the problem. As you know, I was thinking precisely of those kinds of populations you have mentioned. It would be interesting to apply this or any other genome selection search methods to the data you have probably already collected in Chernobyl.