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A tunable filter for high molecular weight DNA selection and linked-read sequencing

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Abstract

In third generation sequencing, the production of quality data requires the selection of molecules longer than ∼20 kbp, but the size selection threshold of most purification technologies is smaller than this target. Here, we describe a technology operated in a capillary with a tunable selection threshold in the range of 3 to 40 kbp controlled by an electric field. We demonstrate that the selection cut-off is sharp, the purification yield is high, and the purification throughput is scalable. We also provide an analytical model that the actuation settings of the filter. The selection of high molecular weight genomic DNA from the melon Cucumis melo L., a diploid organism of ∼0.45 Gbp, is then reported. Linked-read sequencing data show that the N50 phase block size, which scores the correct representation of two chromosomes, is enhanced by a factor of 2 after size selection, establishing the relevance and versatility of our technology.

Graphical abstract: A tunable filter for high molecular weight DNA selection and linked-read sequencing

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Publication details

The article was received on 27 Sep 2019, accepted on 22 Nov 2019 and first published on 25 Nov 2019


Article type: Paper
DOI: 10.1039/C9LC00965E
Lab Chip, 2020, Advance Article

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    A tunable filter for high molecular weight DNA selection and linked-read sequencing

    N. Milon, J. Fuentes Rojas, A. Castinel, L. Bigot, G. Bouwmans, K. Baudelle, A. Boutonnet, A. Gibert, O. Bouchez, C. Donnadieu, F. Ginot and A. Bancaud, Lab Chip, 2020, Advance Article , DOI: 10.1039/C9LC00965E

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