Optimization and clinical validation of a pathogen detection microarray.
DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.
Wong
Christopher W
CW
Genomic Technologies, Genome Institute of Singapore, Republic of Singapore. wongc@gis.a-star.edu.sg
Heng
Charlie Lee Wah
CL
Wan Yee
Leong
L
Soh
Shirlena W L
SW
Kartasasmita
Cissy B
CB
Simoes
Eric A F
EA
Hibberd
Martin L
ML
Sung
Wing-Kin
WK
Miller
Lance D
LD
D000465:Algorithms; D001419:Bacteria / Q000302:isolation & purification*; D001424:Bacterial Infections / Q000175:diagnosis; D001431:Bacteriological Techniques; D020635:Buchnera / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis* / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000302:isolation & purification; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D012680:Sensitivity and Specificity
D004269:DNA, Bacterial