Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region

Fuyang Qu; Rongjie Zhao; Xiaolan Ma; Yifang Chen; Luoquan Li; Meng Yan; Yi-Ping Ho

doi:10.1109/NANOMED59780.2023.10404501

Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region

Fuyang Qu
, Rongjie Zhao
, Xiaolan Ma
, Yifang Chen
, Luoquan Li
, Meng Yan^*
, Yi-Ping Ho^*

^*Corresponding author for this work

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

3 Citations (Scopus)

Abstract

Low-cost and convenient methodologies to produce uniform droplets are demanded for the detection and quantification of environmental DNA (eDNA). In this work, we demonstrate that hydrogel-beads templated emulsification is applicable to generate monodispersed droplets within one minute via vortexing and pipetting. Compartmentalized reactions via the beads-templated digital PCR (bdPCR) have been further conducted to amplify the targeted region of a seahorse species genome. The results from bdPCR have shown a similar limit of detection compared with the traditional water-in-oil based droplet digital PCR (ddPCR). SYBR green staining results further demonstrated the successful amplification of target templates through bdPCR. Finally, the bdPCR platform was adopted to amplify eDNA from marine water and the results showcased the successful detection of a seahorse species. © 2023 IEEE.

Original language	English
Title of host publication	The 16th IEEE International Conference on Nano/Molecular Medicine & Engineering, IEEE-NANOMED 2023
Publisher	IEEE
Pages	79-82
ISBN (Electronic)	979-8-3503-4370-0
ISBN (Print)	979-8-3503-4371-7
DOIs	https://doi.org/10.1109/NANOMED59780.2023.10404501
Publication status	Published - Dec 2023
Event	16th IEEE International Conference on Nano/Molecular Medicine & Engineering (IEEE-NANOMED 2023) - Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan Duration: 5 Dec 2023 → 8 Dec 2023 https://ieee-nanomed.org/2023/

Publication series

Name	IEEE International Conference on Nano/Molecular Medicine and Engineering, NANOMED
ISSN (Print)	2159-6964
ISSN (Electronic)	2159-6972

Conference

Conference	16th IEEE International Conference on Nano/Molecular Medicine & Engineering (IEEE-NANOMED 2023)
Abbreviated title	NANOMED 2023
Place	Japan
City	Okinawa
Period	5/12/23 → 8/12/23
Internet address	https://ieee-nanomed.org/2023/

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10.1109/NANOMED59780.2023.10404501

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Qu, F., Zhao, R., Ma, X., Chen, Y., Li, L., Yan, M., & Ho, Y.-P. (2023). Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region. In The 16th IEEE International Conference on Nano/Molecular Medicine & Engineering, IEEE-NANOMED 2023 (pp. 79-82). (IEEE International Conference on Nano/Molecular Medicine and Engineering, NANOMED). IEEE. https://doi.org/10.1109/NANOMED59780.2023.10404501

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title = "Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region",

abstract = "Low-cost and convenient methodologies to produce uniform droplets are demanded for the detection and quantification of environmental DNA (eDNA). In this work, we demonstrate that hydrogel-beads templated emulsification is applicable to generate monodispersed droplets within one minute via vortexing and pipetting. Compartmentalized reactions via the beads-templated digital PCR (bdPCR) have been further conducted to amplify the targeted region of a seahorse species genome. The results from bdPCR have shown a similar limit of detection compared with the traditional water-in-oil based droplet digital PCR (ddPCR). SYBR green staining results further demonstrated the successful amplification of target templates through bdPCR. Finally, the bdPCR platform was adopted to amplify eDNA from marine water and the results showcased the successful detection of a seahorse species. {\textcopyright} 2023 IEEE.",

author = "Fuyang Qu and Rongjie Zhao and Xiaolan Ma and Yifang Chen and Luoquan Li and Meng Yan and Yi-Ping Ho",

year = "2023",

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doi = "10.1109/NANOMED59780.2023.10404501",

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series = "IEEE International Conference on Nano/Molecular Medicine and Engineering, NANOMED",

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booktitle = "The 16th IEEE International Conference on Nano/Molecular Medicine \& Engineering, IEEE-NANOMED 2023",

address = "United States",

note = "16th IEEE International Conference on Nano/Molecular Medicine \& Engineering (IEEE-NANOMED 2023), NANOMED 2023 ; Conference date: 05-12-2023 Through 08-12-2023",

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}

Qu, F, Zhao, R, Ma, X, Chen, Y, Li, L, Yan, M & Ho, Y-P 2023, Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region. in The 16th IEEE International Conference on Nano/Molecular Medicine & Engineering, IEEE-NANOMED 2023. IEEE International Conference on Nano/Molecular Medicine and Engineering, NANOMED, IEEE, pp. 79-82, 16th IEEE International Conference on Nano/Molecular Medicine & Engineering (IEEE-NANOMED 2023), Okinawa, Japan, 5/12/23. https://doi.org/10.1109/NANOMED59780.2023.10404501

Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region. / Qu, Fuyang; Zhao, Rongjie; Ma, Xiaolan et al.
The 16th IEEE International Conference on Nano/Molecular Medicine & Engineering, IEEE-NANOMED 2023. IEEE, 2023. p. 79-82 (IEEE International Conference on Nano/Molecular Medicine and Engineering, NANOMED).

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

TY - GEN

T1 - Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region

AU - Qu, Fuyang

AU - Zhao, Rongjie

AU - Ma, Xiaolan

AU - Chen, Yifang

AU - Li, Luoquan

AU - Yan, Meng

AU - Ho, Yi-Ping

PY - 2023/12

Y1 - 2023/12

N2 - Low-cost and convenient methodologies to produce uniform droplets are demanded for the detection and quantification of environmental DNA (eDNA). In this work, we demonstrate that hydrogel-beads templated emulsification is applicable to generate monodispersed droplets within one minute via vortexing and pipetting. Compartmentalized reactions via the beads-templated digital PCR (bdPCR) have been further conducted to amplify the targeted region of a seahorse species genome. The results from bdPCR have shown a similar limit of detection compared with the traditional water-in-oil based droplet digital PCR (ddPCR). SYBR green staining results further demonstrated the successful amplification of target templates through bdPCR. Finally, the bdPCR platform was adopted to amplify eDNA from marine water and the results showcased the successful detection of a seahorse species. © 2023 IEEE.

AB - Low-cost and convenient methodologies to produce uniform droplets are demanded for the detection and quantification of environmental DNA (eDNA). In this work, we demonstrate that hydrogel-beads templated emulsification is applicable to generate monodispersed droplets within one minute via vortexing and pipetting. Compartmentalized reactions via the beads-templated digital PCR (bdPCR) have been further conducted to amplify the targeted region of a seahorse species genome. The results from bdPCR have shown a similar limit of detection compared with the traditional water-in-oil based droplet digital PCR (ddPCR). SYBR green staining results further demonstrated the successful amplification of target templates through bdPCR. Finally, the bdPCR platform was adopted to amplify eDNA from marine water and the results showcased the successful detection of a seahorse species. © 2023 IEEE.

UR - https://www.scopus.com/pages/publications/85185227092

UR - https://www.scopus.com/pages/publications/85185227092#tab=impact

U2 - 10.1109/NANOMED59780.2023.10404501

DO - 10.1109/NANOMED59780.2023.10404501

M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 979-8-3503-4371-7

T3 - IEEE International Conference on Nano/Molecular Medicine and Engineering, NANOMED

SP - 79

EP - 82

BT - The 16th IEEE International Conference on Nano/Molecular Medicine & Engineering, IEEE-NANOMED 2023

PB - IEEE

T2 - 16th IEEE International Conference on Nano/Molecular Medicine & Engineering (IEEE-NANOMED 2023)

Y2 - 5 December 2023 through 8 December 2023

ER -

Qu F, Zhao R, Ma X, Chen Y, Li L, Yan M et al. Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region. In The 16th IEEE International Conference on Nano/Molecular Medicine & Engineering, IEEE-NANOMED 2023. IEEE. 2023. p. 79-82. (IEEE International Conference on Nano/Molecular Medicine and Engineering, NANOMED). doi: 10.1109/NANOMED59780.2023.10404501

Hydrogel Beads-Templated Emulsification-based Droplet Digital PCR of Targeted Genome Region

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