RT Journal
A1 Lin, Baochuan
A1 Wang, Zheng
A1 Vora, Gary J.
A1 Thornton, Jennifer A.
A1 Schnur, Joel M.
A1 Thach, Dzung C.
A1 Blaney, Kate M.
A1 Ligler, Adam G.
A1 Malanoski, Anthony P.
A1 Santiago, Jose
A1 Walter, Elizabeth A.
A1 Agan, Brian K.
A1 Metzgar, David
A1 Seto, Donald
A1 Daum, Luke T.
A1 Kruzelock, Russell
A1 Rowley, Robb K.
A1 Hanson, Eric H.
A1 Tibbetts, Clark
A1 Stenger, David A.
T1 Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays
JF Genome Research 
JO Genome Research 
YR 2006 
FD April 01 
VO 16 
IS 4 
SP 527 
OP 535 
DO 10.1101/gr.4337206 
UL http://genome.cshlp.org/content/16/4/527.abstract 
AB The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of interest. However, to achieve the practical attainment of this potential, numerous technical issues, especially nucleic acid amplification, probe specificity, and interpretation strategies of sequence detection, need to be addressed. In this report, we demonstrate an approach that combines the use of a custom-designed Affymetrix resequencing Respiratory Pathogen Microarray (RPM v.1) with methods for microbial nucleic acid enrichment, random nucleic acid amplification, and automated sequence similarity searching for broad-spectrum respiratory pathogen surveillance. Successful proof-of-concept experiments, utilizing clinical samples obtained from patients presenting adenovirus or influenza virus-induced febrile respiratory illness (FRI), demonstrate the ability of this approach for correct species- and strain-level identification with unambiguous statistical interpretation at clinically relevant sensitivity levels. Our results underscore the feasibility of using this approach to expedite the early surveillance of diseases, and provide new information on the incidence of multiple pathogens.