Biome representational in silico karyotyping
- Valliammai Muthappan1,2,7,
- Aaron Y. Lee1,7,
- Tamara L. Lamprecht1,2,
- Lakshmi Akileswaran2,
- Suzanne M. Dintzis3,
- Choli Lee4,
- Vincent Magrini5,
- Elaine R. Mardis5,
- Jay Shendure4 and
- Russell N. Van Gelder1,2,6,8
- 1Department of Ophthalmology and Visual Science, Washington University, St. Louis, Missouri 63110, USA;
- 2Department of Ophthalmology, University of Washington, Seattle, Washington 98195, USA;
- 3Department of Pathology, University of Washington, Seattle, Washington 98195, USA;
- 4Department of Genomic Sciences, University of Washington, Seattle, Washington 98195, USA;
- 5Department of Genetics, Washington University, St. Louis, Missouri 63110, USA;
- 6Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA
-
↵7 These authors contributed equally to this work.
Abstract
Metagenomic characterization of complex biomes remains challenging. Here we describe a modification of digital karyotyping—biome representational in silico karyotyping (BRISK)—as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. Application to normal human tissue demonstrated linear recovery of tags by chromosome. We apply this technique to the biome of the oral mucosa and find that greater than 25% of recovered DNA is nonhuman. DNA from 41 microbial species could be identified from oral mucosa of two subjects. Of recovered nonhuman sequences, fewer than 30% are currently annotated. We characterized seven prevalent unknown sequences by chromosome walking and find these represent novel microbial sequences including two likely derived from novel phage genomes. Application of BRISK to archival tissue from a nasopharyngeal carcinoma resulted in identification of Epstein-Barr virus infection. These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery.
Footnotes
-
↵8 Corresponding author.
E-mail russvg{at}u.washington.edu; fax: (206) 543-4414.
-
[Supplemental material is available for this article. The sequencing data from this study have been submitted to GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) under accession nos. FI185049.1, FI185051.1, FI185052.1, FI185053.1, FI185054.1, and FI185056.1.]
-
Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.115758.110.
- Received September 23, 2010.
- Accepted January 20, 2011.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
