Microfluidics for Genome-wide Studies Involving Next Generation Sequencing

Overview

Journal Biomicrofluidics

Publisher American Institute of Physics

Specialty Biomedical Engineering

Date 2017 Apr 12

PMID 28396707

Citations 13

Authors

Sai Ma

Travis W Murphy

Chang Lu

Affiliations

Soon will be listed here.

Abstract

Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine.

Citing Articles

Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing.

Heydari A, Sindi S Biophys Rev (Melville). 2024; 4(1):011306.

PMID: 38505815 PMC: 10903438. DOI: 10.1063/5.0091135.

Microsystem Advances through Integration with Artificial Intelligence.

Tsai H, Podder S, Chen P Micromachines (Basel). 2023; 14(4).

PMID: 37421059 PMC: 10141994. DOI: 10.3390/mi14040826.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices.

Rahman M, Islam K, Islam M, Islam M, Kaysir M, Akter M Micromachines (Basel). 2022; 13(6).

PMID: 35744582 PMC: 9229244. DOI: 10.3390/mi13060968.

Liquid Biopsy: A Distinctive Approach to the Diagnosis and Prognosis of Cancer.

Hirahata T, Quraish R, Quraish A, Ul Quraish S, Naz M, Razzaq M Cancer Inform. 2022; 21:11769351221076062.

PMID: 35153470 PMC: 8832574. DOI: 10.1177/11769351221076062.

Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start.

Conchouso D, Al-Maabadi A, Behzad H, Alarawi M, Hosokawa M, Nishikawa Y Genomics Proteomics Bioinformatics. 2021; 19(3):504-518.

PMID: 34952209 PMC: 8864243. DOI: 10.1016/j.gpb.2021.03.010.

References

Nicklas J, Buel E . Quantification of DNA in forensic samples. Anal Bioanal Chem. 2003; 376(8):1160-7. DOI: 10.1007/s00216-003-1924-z. View

Ma S, Schroeder B, Sun C, Loufakis D, Cao Z, Sriranganathan N . Electroporation-based delivery of cell-penetrating peptide conjugates of peptide nucleic acids for antisense inhibition of intracellular bacteria. Integr Biol (Camb). 2014; 6(10):973-8. DOI: 10.1039/c4ib00172a. View

Harismendy O, Schwab R, Bao L, Olson J, Rozenzhak S, Kotsopoulos S . Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing. Genome Biol. 2011; 12(12):R124. PMC: 3334619. DOI: 10.1186/gb-2011-12-12-r124. View

Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P . Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res. 2016; 26(3):304-19. PMC: 4783472. DOI: 10.1038/cr.2016.23. View

Jebrail M, Sinha A, Vellucci S, Renzi R, Ambriz C, Gondhalekar C . World-to-digital-microfluidic interface enabling extraction and purification of RNA from human whole blood. Anal Chem. 2014; 86(8):3856-62. DOI: 10.1021/ac404085p. View

Horsman K, Bienvenue J, Blasier K, Landers J . Forensic DNA analysis on microfluidic devices: a review. J Forensic Sci. 2007; 52(4):784-99. DOI: 10.1111/j.1556-4029.2007.00468.x. View

Sun C, Hsieh Y, Ma S, Geng S, Cao Z, Li L . Immunomagnetic separation of tumor initiating cells by screening two surface markers. Sci Rep. 2017; 7:40632. PMC: 5225414. DOI: 10.1038/srep40632. View

Hiatt J, Pritchard C, Salipante S, ORoak B, Shendure J . Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Res. 2013; 23(5):843-54. PMC: 3638140. DOI: 10.1101/gr.147686.112. View

Streets A, Zhang X, Cao C, Pang Y, Wu X, Xiong L . Microfluidic single-cell whole-transcriptome sequencing. Proc Natl Acad Sci U S A. 2014; 111(19):7048-53. PMC: 4024894. DOI: 10.1073/pnas.1402030111. View

10.

Zheng Y, Wang N, Li L, Jin F . Whole genome amplification in preimplantation genetic diagnosis. J Zhejiang Univ Sci B. 2011; 12(1):1-11. PMC: 3017410. DOI: 10.1631/jzus.B1000196. View

11.

Telenius H, Carter N, Bebb C, Nordenskjold M, Ponder B, Tunnacliffe A . Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics. 1992; 13(3):718-25. DOI: 10.1016/0888-7543(92)90147-k. View

12.

Wang J, Bao N, Paris L, Wang H, Geahlen R, Lu C . Detection of kinase translocation using microfluidic electroporative flow cytometry. Anal Chem. 2007; 80(4):1087-93. PMC: 2814306. DOI: 10.1021/ac702065e. View

13.

Nelson C, Fuller C, Fordyce P, Greninger A, Li H, DeRisi J . Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets. Nucleic Acids Res. 2013; 41(12):5991-6004. PMC: 3695516. DOI: 10.1093/nar/gkt259. View

14.

Hashimshony T, Wagner F, Sher N, Yanai I . CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2012; 2(3):666-73. DOI: 10.1016/j.celrep.2012.08.003. View

15.

Esteban J, Salas M, Blanco L . Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J Biol Chem. 1993; 268(4):2719-26. View

16.

Komori H, LaMere S, Torkamani A, Hart G, Kotsopoulos S, Warner J . Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res. 2011; 21(10):1738-45. PMC: 3202290. DOI: 10.1101/gr.116863.110. View

17.

Stark A, Shin D, Pisanic 2nd T, Hsieh K, Wang T . A parallelized microfluidic DNA bisulfite conversion module for streamlined methylation analysis. Biomed Microdevices. 2016; 18(1):5. PMC: 6586411. DOI: 10.1007/s10544-015-0029-8. View

18.

Geng T, Bao N, Gall O, Lu C . Modulating DNA adsorption on silica beads using an electrical switch. Chem Commun (Camb). 2009; (7):800-2. DOI: 10.1039/b817034g. View

19.

Morley A . Digital PCR: A brief history. Biomol Detect Quantif. 2016; 1(1):1-2. PMC: 5129430. DOI: 10.1016/j.bdq.2014.06.001. View

20.

Giresi P, Kim J, McDaniell R, Iyer V, Lieb J . FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2006; 17(6):877-85. PMC: 1891346. DOI: 10.1101/gr.5533506. View