title: Development of genodynamic metrics for exploring the biophysics of DNA polymorphisms.
abstract: Single nucleotide polymorphisms (SNPs) represent an important type of dynamic sites within the human genome. These common variants often locally correlate within more complex multi-SNP haploblocks that are maintained throughout generations in a stable population. Information encoded in the structure of SNPs and SNP haploblock variation can be characterized through a normalized information content metric. Genodynamics is being developed as the analogous "thermodynamics" characterizing the state variables for genomic populations that are stable under stochastic environmental stresses. Since living systems have not been found to develop in the absence of environmental influences, this paper describes the analogous genomic free energy metrics in a given environment. SNP haploblocks were constructed by Haploview v4.2 for five chromosomes from phase III HapMap data, and the genomic state variables for each chromosome were calculated. Anin silicoanalysis was performed on SNP haploblocks with the lowest genomic energy measures. Highly favorable genomic energy measures were found to correlate with highly conserved SNP haploblocks. Moreover, the most conserved haploblocks were associated with an evolutionarily conserved regulatory element and domain.
authors: Computational Physics Laboratory, Department of Physics and Astronomy, Howard University, Washington, DC, 20059, U.S.
authors: James
authors: J
authors: Lindesay
authors: National Human Genome Center, Howard University, Washington, DC, 20060, U.S.
authors: Tshela E
authors: TE
authors: Mason
authors: Computational Physics Laboratory, Department of Physics and Astronomy, Howard University, Washington, DC, 20059, U.S.
authors: William
authors: W
authors: Hercules
authors: National Human Genome Center, Howard University, Washington, DC, 20060, U.S ; Department of Microbiology, Howard University, Washingto on, DC, 20059, U.S.
authors: Georgia M
authors: GM
authors: Dunston
keywords: Information theory; biological information; entropy; genodynamics; genomic variation
references: Science. 2002 Jun 21;296(5576):2225-9
references: 12029063
references: In Silico Biol. 2005;5(4):367-77
references: 16268781
references: Nat Genet. 2004 May;36(5):431-2
references: 15118671
references: Genomics. 2006 Jun;87(6):681-92
references: 16458478
references: Nat Rev Genet. 2004 Apr;5(4):316-23
references: 15131654
references: Nucleic Acids Res. 2008 Sep;36(15):4833-44
references: 18653530
references: BMC Genomics. 2007 Jan 18;8:20
references: 17233890
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52
references: 15215389
references: Gene. 2002 Oct 16;299(1-2):135-40
references: 12459261
references: Science. 1908 Jul 10;28(706):49-50
references: 17779291
references: Genome Biol. 2005;6(4):R30
references: 15833117
references: Trends Genet. 2006 Jan;22(1):1-5
references: 16290135
references: Biol Psychiatry. 1982 Apr;17(4):513-32
references: 7082716
references: EMBO J. 1989 Oct;8(10):2983-8
references: 2479540
references: Nucleic Acids Res. 2001 Jan 1;29(1):308-11
references: 11125122
references: Genome Biol. 2009;10(11):R130
references: 19919682
references: Nucleic Acids Res. 2006 Jul 18;34(12):3465-75
references: 16849434
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D820-4
references: 17986460
references: Genome Res. 2006 Jul;16(7):922-33
references: 16769979
references: J Inorg Biochem. 2012 Jun;111:104-9
references: 22855949
references: Chem Rev. 2009 Oct;109(10):4828-61
references: 19459624
references: Nutr Rev. 1998 Jan;56(1 Pt 1):27-8
references: 9481116
references: BMC Bioinformatics. 2006 Jan 13;7:18
references: 16409644
references: Aging (Milano). 1995 Apr;7(2):77-93
references: 7548268
references: Nucleic Acids Res. 2004 Sep 08;32(16):4812-20
references: 15356298
references: BMC Genomics. 2005 Jun 16;6:93
references: 15960846
references: Nutrition. 1995 Jan-Feb;11(1 Suppl):93-9
references: 7749260
references: Mol Cell Biol. 1990 Aug;10(8):4180-91
references: 1695323
references: Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10567-72
references: 20498051
references: Genome Res. 2012 Sep;22(9):1790-7
references: 22955989
references: J Clin Pharm Ther. 1992 Feb;17(1):51-4
references: 1548313
references: EMBO Rep. 2006 Dec;7(12):1216-22
references: 17139297
references: Genome Biol. 2005;6(6):R51
references: 15960803
references: J Lab Clin Med. 1994 Sep;124(3):322-7
references: 8083574
references: J Exp Biol. 2007 May;210(Pt 9):1526-47
references: 17449818
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jul;72(1 Pt 2):016123
references: 16090052
references: Bioinformatics. 2005 Jan 15;21(2):263-5
references: 15297300
references: Nat Biotechnol. 2003 Apr;21(4):379-86
references: 12640466
references: Genome Res. 2005 Apr;15(4):463-74
references: 15781571
references: J Comput Biol Bioinform Res. 2012 Feb;4(2):15-22
references: 24478921
references: Adv Biosci Biotechnol. 2014 Jun;5(7):623-626
references: 25635233
references: Genome Res. 2005 Nov;15(11):1592-3
references: 16251469
references: Front Genet. 2012 Oct 09;3:205
references: 23087702
references: Nat Genet. 1999 Apr;21(4):400-4
references: 10192391
references: Bioessays. 2007 Mar;29(3):288-99
references: 17295292
references: Synapse. 2009 Nov;63(11):1029-49
references: 19623531
references: Cancer Sci. 2008 Aug;99(8):1515-22
references: 18754861
references: Med Monatsschr Pharm. 2011 Mar;34(3):87-95
references: 21736013
references: J Biol Chem. 1991 Nov 25;266(33):22083-6
references: 1657988
references: Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
references: 16569694
references: Int J Mol Med. 2005 Feb;15(2):197-203
references: 15647831
references: Anim Genet. 2008 Jun;39(3):207-16
references: 18371128
references: Curr Opin Genet Dev. 2000 Apr;10(2):229-33
references: 10753780
references: Ann N Y Acad Sci. 1992 Oct 28;660:77-87
references: 1340159
references: Mol Biol (Mosk). 2000 Jul-Aug;34(4):572-83
references: 11042850
references: Genome Res. 2003 Jun;13(6B):1324-34
references: 12819130
references: Biochem Biophys Res Commun. 2004 Sep 17;322(2):593-600
references: 15325271
references: Proc Natl Acad Sci U S A. 1993 Apr 1;90(7):2715-8
references: 8464881
references: Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3542-7
references: 9108012