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bioRxiv · 10.1101/2020.01.21.908897

Accurate CNV identification from only a few cells with low GC bias in a single-molecule sequencing platform

HU, L.·LIN, Q.·XIE, P.·ZENG, L.·LIU, L.·HUANG, M.·YAN, Q.·Zhang, M.·LIN, G.
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Abstract

A technical problem of characterizing copy number variation of several cells with next-generation sequencing is the whole genome amplification induced bias. The result of CNVs and mosaicism detection is affected by the GC bias. Here, we report a rapid non-WGA sample preparation strategy for a single-molecule sequencing platform GenoCare1600. This approach, combined with a single-molecule sequencing platform that avoids the use of WGA and bridge PCR processes, can provide higher reliability with its lower GC bias. By combining our optimized Tn5-based transposon insertion approach with GenoCare, we successfully detected CNVs as small as 1.29M and mosaicism as small as 20%, which is consistent with next-generation sequencing (NGS) data. Moreover, our GenoCare-TTI protocol showed less GC bias and less Mad of Diff. These results suggest that the optimized TTI approach, together with the GenoCare1600 sequencing platform, is a promising option for CNV characterization from maybe one single cell.

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HU, L., LIN, Q., XIE, P., ZENG, L., LIU, L., HUANG, M., YAN, Q., Zhang, M., LIN, G.. 2020-01-23. Accurate CNV identification from only a few cells with low GC bias in a single-molecule sequencing platform. https://doi.org/10.1101/2020.01.21.908897

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