Biome representational in silico karyotyping

Genome Research

Volumn 21, Issue 4, 2011, Pages 626-633

  Muthappan, Valliammai ^a,b   Lee, Aaron Y ^a   Lamprecht, Tamara L ^a,b   Akileswaran, Lakshmi ^b   Dintzis, Suzanne M ^c   Lee, Choli ^c   Magrini, Vincent ^a   Mardis, Elaine R ^a   Shendure, Jay ^c   Van Gelder, Russell N ^a,b,c  

^a WASHINGTON UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENOMIC DNA; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; BACTERIAL GENOME; BACTERIOPHAGE; BIOINFORMATICS; BIOME REPRESENTATIONAL IN SILICO KARYOTYPING; CHROMOSOME; CHROMOSOME WALKING; DNA SEQUENCE; EPSTEIN BARR VIRUS INFECTION; GENE SEQUENCE; HUMAN; HUMAN TISSUE; KARYOTYPING; METAGENOMICS; MICROORGANISM; MOUTH FLORA; MOUTH MUCOSA; NASOPHARYNX CARCINOMA; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

CARCINOMA; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KARYOTYPING; METAGENOME; METAGENOMICS; MOLECULAR SEQUENCE DATA; MOUTH MUCOSA;

HUMAN HERPESVIRUS 4;

EID: 79953331213     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.115758.110     Document Type: Article

References (37)

1. Aas J, Paster B, Stokes L, Olsen I, Dewhirst F. 2005. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43: 5721-5732. (Pubitemid 41612354)
2. Bentley D, Balasubramanian S, Swerdlow H, Smith G, Milton J, Brown C, Hall K, Evers D, Barnes C, Bignell H, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
3. Bille E, Ure R, Gray S, Kaczmarski E, McCarthy N, Nassif X, Maiden M, Tinsley C. 2008. Association of a bacteriophage with meningococcal disease in young adults. PLoS ONE 3: e3885. doi: 10.1371/journal.pone.0003885.
4. Bredel M, Bredel C, Juric D, Kim Y, Vogel H, Harsh GR, Recht LD, Pollack JR, Sikic BI. 2005. Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA. J Mol Diagn 7: 171-182. (Pubitemid 40668299)
5. Costello E, Lauber C, Hamady M, Fierer N, Gordon J, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697.
6. Duncan C, Leary R, Lin J, Cummins J, Di C, Schaefer C, Wang T, Riggins G, Edwards J, Bigner D, et al. 2009. Identification of microbial DNA in human cancer. BMC Med Genomics 2: 22. doi: 10.1186/1755-8794-2-22.
7. Eckburg P, Bik E, Bernstein C, Purdom E, Dethlefsen L, Sargent M, Gill S, Nelson K, Relman D. 2005. Diversity of the human intestinal microbial flora. Science 308: 1635-1638. (Pubitemid 40807514)
8. Feng H, Shuda M, Chang Y, Moore P. 2008. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319: 1096-1100. (Pubitemid 351300792)
9. Fredricks D, Fiedler T, Thomas K, Mitchell C, Marrazzo J. 2009. Changes in vaginal bacterial concentrations with intravaginal metronidazole therapy for bacterial vaginosis as assessed by quantitative PCR. J Clin Microbiol 47: 721-726.
10. Graham J, Moore J, Jiru X, Goodall E, Dooley J, Hayes V, Dartt D, Downes C, Moore T. 2007. Ocular pathogen or commensal: A PCR-based study of surface bacterial flora in normal and dry eyes. Invest Ophthalmol Vis Sci 48: 5616-5623. (Pubitemid 351260863)
11. Grice E, Kong H, Conlan S, Deming C, Davis J, Young A, Bouffard G, Blakesley R, Murray P, Green E, et al. 2009. Topographical and temporal diversity of the human skin microbiome. Science 324: 1190-1192.
12. Hormozdiari F, Alkan C, Ventura M, Hajirasouliha I, Malig M, Hach F, Yorukoglu D, Dao P, Bakhshi M, Sahinalp SC, et al. 2011. Alu repeat discovery and characterization within human genomes. Genome Res (in press).
13. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. 2008. Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87: 1016-1020.
14. Ko W, David R, Akashi H. 2003. Molecular phylogeny of the Drosophila melanogaster species subgroup. J Mol Evol 57: 562-573. (Pubitemid 37339002)
15. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma V, Srivastava T, et al. 2007. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14: 169-181.
16. Lampe J. 2008. The Human Microbiome Project: Getting to the guts of the matter in cancer epidemiology. Cancer Epidemiol Biomarkers Prev 17: 2523-2524.
17. Leary R, Cummins J, Wang T, Velculescu V. 2007. Digital karyotyping. Nat Protoc 2: 1973-1986.
18. Leviel K, Olarte M, Sullivan PF. 2004. Genotyping accuracy for whole-genome amplification of DNA from buccal epithelial cells. Twin Res 7: 482-484. (Pubitemid 39403039)
19. Nasidze I, Li J, Quinque D, Tang K, Stoneking M. 2009a. Global diversity in the human salivary microbiome. Genome Res 19: 636-643.
20. Nasidze I, Quinque D, Li J, Li M, Tang K, Stoneking M. 2009b. Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches. Anal Biochem 391: 64-68.
21. Oakley B, Fiedler T, Marrazzo J, Fredricks D. 2008. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Appl Environ Microbiol 74: 4898-4909.
22. Palacios G, Quan P, Jabado O, Conlan S, Hirschberg D, Liu Y, Zhai J, Renwick N, Hui J, Hegyi H, et al. 2007. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis 13: 73-81. (Pubitemid 46057840)
23. Petrosino J, Highlander S, Luna R, Gibbs R, Versalovic J. 2009. Metagenomic pyrosequencing and microbial identification. Clin Chem 55: 856-866.
24. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
25. Tengs T, LaFramboise T, Den RB, Hayes DN, Zhang J, DebRoy S, Gentleman RC, O'Neill K, Birren B, Meyerson M. 2004. Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments. Nucleic Acids Res 32: e121. doi: 10.1093/nar/gnh120.
26. Thompson MP, Kurzrock R. 2004. Epstein-Barr virus and cancer. Clin Cancer Res 10: 803-821. (Pubitemid 38198878)
27. Tinsley C, Bille E, Nassif X. 2006. Bacteriophages and pathogenicity: More than just providing a toxin? Microbes Infect 8: 1365-1371.
28. Turnbaugh P, Ley R, Hamady M, Fraser-Liggett C, Knight R, Gordon J. 2007. The human microbiome project. Nature 449: 804-810. (Pubitemid 47598620)
29. Turnbaugh P, Hamady M, Yatsunenko T, Cantarel B, Duncan A, Ley R, Sogin M, Jones W, Roe B, Affourtit J, et al. 2009. A core gut microbiome in obese and lean twins. Nature 457: 480-484.
30. Venter J, Remington K, Heidelberg J, Halpern A, Rusch D, Eisen J, Wu D, Paulsen I, Nelson K, Nelson W, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74. (Pubitemid 38451457)
31. Verberkmoes N, Russell A, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud M, Apajalahti J, Tysk C, Hettich R, et al. 2009. Shotgun metaproteomics of the human distal gut microbiota. ISME J 3: 179-189.
32. Wang D, Coscoy L, Zylberberg M, Avila P, Boushey H, Ganem D, DeRisi J. 2002a. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci 99: 15687-15692. (Pubitemid 35403992)
33. Wang T, Maierhofer C, Speicher M, Lengauer C, Vogelstein B, Kinzler K, Velculescu V. 2002b. Digital karyotyping. Proc Natl Acad Sci 99: 16156-16161.
34. Wen L, Ley R, Volchkov P, Stranges P, Avanesyan L, Stonebraker A, Hu C, Wong F, Szot G, Bluestone J, et al. 2008. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455: 1109-1113.
35. Williamson S, Rusch D, Yooseph S, Halpern A, Heidelberg K, Glass J, Andrews-Pfannkoch C, Fadrosh D, Miller C, Sutton G, et al. 2008. The Sorcerer II Global Ocean Sampling Expedition: Metagenomic characterization of viruses within aquatic microbial samples. PLoS ONE 3: e1456. doi: 10.1371/journal.pone. 0001456.
36. Yujian L, Bo L. 2007. A normalized Levenshtein distance metric. IEEE Trans Pattern Anal Mach Intell 29: 1091-1095. (Pubitemid 46671075)
37. Zaura E, Keijser BJ, Huse SM, Crielaard W. 2009. Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol 9: 259. doi: 10.1186/1471-2180-9-259.