Background: Our ultimate goal is to detect the entire human microbiome, in health and in disease, in a single\r\nreaction tube, and employing only commercially available reagents. To that end, we adapted molecular inversion\r\nprobes to detect bacteria using solely a massively multiplex molecular technology. This molecular probe\r\ntechnology does not require growth of the bacteria in culture. Rather, the molecular probe technology requires\r\nonly a sequence of forty sequential bases unique to the genome of the bacterium of interest. In this\r\ncommunication, we report the first results of employing our molecular probes to detect bacteria in clinical\r\nsamples.\r\nResults: While the assay on Affymetrix GenFlex Tag16K arrays allows the multiplexing of the detection of the\r\nbacteria in each clinical sample, one Affymetrix GenFlex Tag16K array must be used for each clinical sample. To\r\nmultiplex the clinical samples, we introduce a second, independent assay for the molecular probes employing\r\nSequencing by Oligonucleotide Ligation and Detection. By adding one unique oligonucleotide barcode for each\r\nclinical sample, we combine the samples after processing, but before sequencing, and sequence them together.\r\nConclusions: Overall, we have employed 192 molecular probes representing 40 bacteria to detect the bacteria in\r\ntwenty-one vaginal swabs as assessed by the Affymetrix GenFlex Tag16K assay and fourteen of those by the\r\nSequencing by Oligonucleotide Ligation and Detection assay. The correlations among the assays were excellent.
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