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

Nicolas Milon (1) , Juan-Luis Fuentes Rojas (1) , Adrien Castinel (2) , Laurent Bigot (3) , Géraud Bouwmans (3) , Karen Baudelle (3) , Audrey Boutonnet (4) , Audrey Gibert (2) , Olivier O. Bouchez (2) , Cécile Donnadieu (2) , Frédéric Ginot (4) , Aurélien Bancaud (1)

1 LAAS-MILE - Équipe Micro-Nanofluidique pour les sciences de la vie et de l’environnement
2 GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique
3 PhLAM - Laboratoire de Physique des Lasers, Atomes et Molécules - UMR 8523
4 Picometrics Technologies

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.

Domaines: Optique / photonique; Matériaux; Matière Condensée [cond-mat]

Nicolas Milon, Juan-Luis Fuentes Rojas, Adrien Castinel, Laurent Bigot, Géraud Bouwmans, et al.. A tunable filter for high molecular weight DNA selection and linked-read sequencing. Lab on a Chip, 2020, 20 (1), pp.175-184. ⟨10.1039/C9LC00965E⟩. ⟨hal-02400601⟩