RT Journal
A1 Muthappan, Valliammai
A1 Lee, Aaron Y.
A1 Lamprecht, Tamara L.
A1 Akileswaran, Lakshmi
A1 Dintzis, Suzanne M.
A1 Lee, Choli
A1 Magrini, Vincent
A1 Mardis, Elaine R.
A1 Shendure, Jay
A1 Van Gelder, Russell N.
T1 Biome representational in silico karyotyping
JF Genome Research 
JO Genome Research 
YR 2011 
FD April 01 
VO 21 
IS 4 
SP 626 
OP 633 
DO 10.1101/gr.115758.110 
UL http://genome.cshlp.org/content/21/4/626.abstract 
AB 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.