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bioRxiv · 10.1101/2020.09.21.304006

Two-target quantitative PCR to predict library composition for shallow shotgun sequencing

Cho, M. Y.·Oliva, M.·Spreafico, A.·Chen, B.·Wei, X.·Choi, Y.·Kaul, R.·Siu, L. L.·Coburn, B.·Schneeberger, P. H. H.
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Abstract

Shotgun sequencing enables retrieving high resolution information 40 from complex microbial communities. However, the technique is limited by missing information about host-to-microbe ratios observed in different sample types. This makes it challenging to plan sequencing experiments, especially in the context of high sample multiplexing and/or limited sequencing output. We evaluated a qPCR-based assay to predict host-to microbe ratio prior to sequencing. Using a two-target assay aimed at conserved human and bacterial genes, we predicted human-to-microbe ratios in two sample types and validated it on independently collected samples. The assay enabled accurate prediction for a broad range of sample compositions.

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Cho, M. Y., Oliva, M., Spreafico, A., Chen, B., Wei, X., Choi, Y., Kaul, R., Siu, L. L., Coburn, B., Schneeberger, P. H. H.. 2020-09-21. Two-target quantitative PCR to predict library composition for shallow shotgun sequencing. https://doi.org/10.1101/2020.09.21.304006

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