@article{Park2020,

title = {Digital CRISPR/Cas‐Assisted Assay for Rapid and Sensitive Detection of SARS‐CoV‐2},

author = {J.S. Park and K. Hsieh and L. Chen and A. Kaushik and A.Y. Trick and T.H. Wang},

doi = {https://doi.org/10.1002/advs.202003564},

year  = {2021},

date = {2021-01-12},

urldate = {2020-11-20},

journal = {Advanced Science},

abstract = {The unprecedented demand for rapid diagnostics in response to the COVID‐19 pandemic has brought the spotlight onto clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated systems (Cas)‐assisted nucleic acid detection assays. Already benefitting from an elegant detection mechanism, fast assay time, and low reaction temperature, these assays can be further advanced via integration with powerful, digital‐based detection. Thus motivated, the first digital CRISPR/Cas‐assisted assay—coined digitization‐enhanced CRISPR/Cas‐assisted one‐pot virus detection (deCOViD)—is developed and applied toward SARS‐CoV‐2 detection. deCOViD is realized through tuning and discretizing a one‐step, fluorescence‐based, CRISPR/Cas12a‐assisted reverse transcription recombinase polymerase amplification assay into sub‐nanoliter reaction wells within commercially available microfluidic digital chips. The uniformly elevated digital concentrations enable deCOViD to achieve qualitative detection in <15 min and quantitative detection in 30 min with high signal‐to‐background ratio, broad dynamic range, and high sensitivity—down to 1 genome equivalent (GE) µL−1 of SARS‐CoV‐2 RNA and 20 GE µL−1 of heat‐inactivated SARS‐CoV‐2, which outstrips its benchtop‐based counterpart and represents one of the fastest and most sensitive CRISPR/Cas‐assisted SARS‐CoV‐2 detection to date. Moreover, deCOViD can detect RNA extracts from clinical samples. Taken together, deCOViD opens a new avenue for advancing CRISPR/Cas‐assisted assays and combating the COVID‐19 pandemic and beyond.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{park2021,

title = {Ligation-Enabled Fluorescence-Coding PCR for High-Dimensional Fluorescence-Based Nucleic Acid Detection},

author = { J.S. Park and T. Pisanic and Y. Zhang and T.H. Wang},

url = {https://pubmed.ncbi.nlm.nih.gov/33427441/},

doi = {https://doi.org/10.1021/acs.analchem.0c04221},

year  = {2021},

date = {2021-01-11},

journal = {Analytical Chemistry},

volume = {93},

number = {4},

pages = { 2351–2358},

abstract = {Polymerase chain reaction (PCR) is by far the most commonly used method of nucleic acid amplification and has likewise been employed for a plethora of diagnostic purposes. Nonetheless, multiplexed PCR-based detection schemes have hitherto been largely limited by technical challenges associated with nonspecific interactions and other limitations inherent to traditional fluorescence-based assays. Here, we describe a novel strategy for multiplexed PCR-based analysis called Ligation-eNabled fluorescence-Coding PCR (LiNC PCR) that exponentially enhances the multiplexing capability of standard fluorescence-based PCR assays. The technique relies upon a simple, preliminary ligation reaction in which target DNA sequences are converted to PCR template molecules with distinct endpoint fluorescence signatures. Universal TaqMan probes are used to create target-specific multicolor fluorescence signals that can be readily decoded to identify amplified targets of interest. We demonstrate the LiNC PCR technique by implementing a two-color-based assay for detection of 10 ovarian cancer epigenetic biomarkers at analytical sensitivities as low as 60 template molecules with no detectable target cross-talk. Overall, LiNC PCR provides a simple and inexpensive method for achieving high-dimensional multiplexing that can be implemented in manifold molecular diagnostic applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fan2020,

title = {Epigenomic Reprogramming toward Mesenchymal-Epithelial Transition in Ovarian-Cancer-Associated Mesenchymal Stem Cells Drives Metastasis},

author = {H. Fan and H.I. Atiya and Y. Wang and T.R. Pisanic and T.H. Wang and I.M. Shih and K.K. Foy and L. Frisbie and R.J. Buckanovich and A.A. Chomiak and R.L. Tiedemann and S.B. Rothbart and C. Chandler and H. Shen and L.G. Coffman},

url = {https://www.sciencedirect.com/science/article/pii/S2211124720314625},

doi = {https://doi.org/10.1016/j.celrep.2020.108473},

year  = {2020},

date = {2020-11-08},

journal = {Cell Reports},

volume = {33},

number = {10},

pages = {108473},

abstract = {A role for cancer cell epithelial-to-mesenchymal transition (EMT) in cancer is well established. Here, we show that, in addition to cancer cell EMT, ovarian cancer cell metastasis relies on an epigenomic mesenchymal-to-epithelial transition (MET) in host mesenchymal stem cells (MSCs). These reprogrammed MSCs, termed carcinoma-associated MSCs (CA-MSCs), acquire pro-tumorigenic functions and directly bind cancer cells to serve as a metastatic driver/chaperone. Cancer cells induce this epigenomic MET characterized by enhancer-enriched DNA hypermethylation, altered chromatin accessibility, and differential histone modifications. This phenomenon appears clinically relevant, as CA-MSC MET is highly correlated with patient survival. Mechanistically, mirroring MET observed in development, MET in CA-MSCs is mediated by WT1 and EZH2. Importantly, EZH2 inhibitors, which are clinically available, significantly inhibited CA-MSC-mediated metastasis in mouse models of ovarian cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Miller2020,

title = {Leveraging locus-specific epigenetic heterogeneity to improve the performance of blood-based DNA methylation biomarkers},

author = {B.F Miller and T.R. Pisanic II and G. Margolin and H.M. Petrykowska and P. Athamanolap and A. Goncearenco and A. Osei-Tutu and C.M. Annunziata and T.H. Wang and L. Elnitski},

url = {https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-020-00939-w},

doi = {https://doi.org/10.1101/579839.},

year  = {2020},

date = {2020-10-21},

journal = {Clinical Epigenetics},

volume = {12},

number = {1},

pages = {1-19},

abstract = {Background

Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based cancer testing. Here, we describe development and validation of a methylation density binary classification method called EpiClass (available for download at https://github.com/Elnitskilab/EpiClass) that can be used to predict and optimize the performance of methylation biomarkers, particularly in challenging, heterogeneous samples such as liquid biopsies. This approach is based upon leveraging statistical differences in single-molecule sample methylation density distributions to identify ideal thresholds for sample classification.



Results

We developed and tested the classifier using reduced representation bisulfite sequencing (RRBS) data derived from ovarian carcinoma tissue DNA and controls. We used these data to perform in silico simulations using methylation density profiles from individual epiallelic copies of ZNF154, a genomic locus known to be recurrently methylated in numerous cancer types. From these profiles, we predicted the performance of the classifier in liquid biopsies for the detection of epithelial ovarian carcinomas (EOC). In silico analysis indicated that EpiClass could be leveraged to better identify cancer-positive liquid biopsy samples by implementing precise thresholds with respect to methylation density profiles derived from circulating cell-free DNA (cfDNA) analysis. These predictions were confirmed experimentally using DREAMing to perform digital methylation density analysis on a cohort of low volume (1-ml) plasma samples obtained from 26 EOC-positive and 41 cancer-free women. EpiClass performance was then validated in an independent cohort of 24 plasma specimens, derived from a longitudinal study of 8 EOC-positive women, and 12 plasma specimens derived from 12 healthy women, respectively, attaining a sensitivity/specificity of 91.7%/100.0%. Direct comparison of CA-125 measurements with EpiClass demonstrated that EpiClass was able to better identify EOC-positive women than standard CA-125 assessment. Finally, we used independent whole genome bisulfite sequencing (WGBS) datasets to demonstrate that EpiClass can also identify other cancer types as well or better than alternative methylation-based classifiers.



Conclusions

Our results indicate that assessment of intramolecular methylation density distributions calculated from cfDNA facilitates the use of methylation biomarkers for diagnostic applications. Furthermore, we demonstrated that EpiClass analysis of ZNF154 methylation was able to outperform CA-125 in the detection of etiologically diverse ovarian carcinomas, indicating broad utility of ZNF154 for use as a biomarker of ovarian cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hashemi2020,

title = {A Novel Platform Using RNA Signatures To Accelerate Antimicrobial Susceptibility Testing in Neisseria gonorrhoeae},

author = {M.M. Hashemi and N. Ram-Mohan and X. Yang and N. Andini and N. R. Gessner and K.C. Carroll and T.H. Wang and S. Yang

},

url = {https://jcm.asm.org/content/58/12/e01152-20},

doi = {DOI: 10.1128/JCM.01152-20},

year  = {2020},

date = {2020-09-23},

journal = {J Clin Microbiol.},

volume = {58},

number = {12},

pages = {e01152-20},

abstract = {The rise of antimicrobial-resistant pathogens can be attributed to the lack of a rapid pathogen identification (ID) or antimicrobial susceptibility testing (AST), resulting in delayed therapeutic decisions at the point of care. Gonorrhea is usually empirically treated, with no AST results available before treatment, thus contributing to the rapid rise in drug resistance. Here, we present a rapid AST platform using RNA signatures for Neisseria gonorrhoeae. Transcriptome sequencing (RNA-seq) followed by bioinformatic tools was applied to explore potential markers in the transcriptome profile of N. gonorrhoeae upon minutes of azithromycin exposure. Validation of candidate markers using quantitative real-time PCR (qRT-PCR) showed that two markers (arsR [NGO1562] and rpsO) can deliver accurate AST results across 14 tested isolates. Further validation of our susceptibility threshold in comparison to MIC across 64 more isolates confirmed the reliability of our platform. Our RNA markers combined with emerging molecular point-of-care systems has the potential to greatly accelerate both ID and AST to inform treatment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Yang2020b,

title = {RNA markers for ultra-rapid molecular antimicrobial susceptibility testing in fluoroquinolone-treated Klebsiella pneumoniae},

author = {X. Yang and M.M. Hashemi and N. Andini and M.M. Li and S. Kuang and K.C. Carroll and T.H. Wang and S. Yan},

url = {https://academic.oup.com/jac/article/75/7/1747/5810132},

year  = {2020},

date = {2020-09-03},

journal = {Journal of Antimicrobial Chemotherapy},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Li2020,

title = {Electrode-free Concentration and Recovery of DNA at Physiologically Relevant Ionic Concentrations},

author = {S. Li and A. Li and K. Hsieh and S.M. Friedrich and T.H. Wang},

url = {https://pubs.acs.org/doi/abs/10.1021/acs.analchem.0c00831},

year  = {2020},

date = {2020-09-03},

journal = {Analytical Chemistry},

volume = {92},

number = {8},

pages = {6150–6157},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bell2020,

title = {Single-cell lineage tracing of developing retinal systems},

author = {C. Bell and W. Fang and C. Berlinicke and A. Kaushik and P. Zhang and T.H. Wang and R. Kalhor and H. Ji and D.J. Zack},

url = {https://iovs.arvojournals.org/article.aspx?articleid=2768344},

year  = {2020},

date = {2020-09-03},

journal = {Investigative Ophthalmology & Visual Science},

volume = {61},

number = {7},

pages = {4014},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhang2020,

title = {ddRFC: A scalable multiplexed droplet digital nucleic acid amplification test platform},

author = {Y. Zhang and P. Zhang and L. Chen and A. Kaushik and K. Hu and T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S0956566320304917},

year  = {2020},

date = {2020-09-03},

journal = {Biosensors and Bioelectronics},

volume = {167},

number = {112499},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Beh2020,

title = {Microfluidic-prepared, monodisperse, X-ray-visible, embolic microspheres for non-oncological embolization applications},

author = {C.W. Beh and Y.i Fu and C.R. Weiss and C. Hu and A. Arepally and H.Q. Mao and T.H. Wang and D.L. Kraitchman},

url = {https://pubs.rsc.org/en/content/articlelanding/2020/lc/d0lc00098a#!divAbstract},

doi = {https://doi.org/10.1039/D0LC00098A},

year  = {2020},

date = {2020-09-01},

journal = {Lab on a Chip},

volume = {20},

pages = {3591-3600},

abstract = {Embolotherapy using particle embolics is normally performed with exogenous contrast to assist in visualization. However, the exact location of the embolics cannot be identified after contrast washout. We developed a novel, pseudo-check valve-integrated microfluidic device, that partitions barium- impregnated alginate from crosslinking solution, thereby preventing nozzle failure. This enables rapid and continuous generation of inherently X-ray-visible embolic microspheres (XEMs) with uniform size. The XEMs are visible under clinical X-ray and cone beam CT both in vitro and in vivo. In particular, we demonstrated the embolization properties of these XEMs in large animals, performing direct intra- and post-procedural assessment of embolic delivery. The persistent radiopacity of these XEMs enables real-time evaluation of embolization precision and offers great promise for non-invasive follow-up examination without exogenous contrast. We also demonstrated that bariatric arterial embolization with XEMs significantly suppresses weight gain in swine, as an example of a non-oncological application of embolotherapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gaddes2020,

title = {Facile Coupling of Droplet Magnetofluidic-Enabled Automated Sample Preparation to Digital Nucleic Acid Amplification Testing and Analysis},

author = {D.E. Gaddes and P,W. Lee and A.Y. Trick and P. Athamanolap and C.M. O’Keefe and C. Puleo and K. Hsieh and T.H. Wang},

doi = {https://doi.org/10.1021/acs.analchem.0c02454},

year  = {2020},

date = {2020-09-01},

journal = {Analytical Chemistry},

volume = {92},

number = {19},

pages = {13254-13261},

abstract = {Digital nucleic acid amplification testing (dNAAT) and analysis techniques, such as digital polymerase chain reaction (PCR), have become useful clinical diagnostic tools. However, nucleic acid (NA) sample preparation preceding dNAAT is generally laborious and performed manually, thus creating the need for a simple sample preparation technique and a facile coupling strategy for dNAAT. Therefore, we demonstrate a simple workflow which automates magnetic bead-based extraction of NAs with a one-step transfer to dNAAT. Specifically, we leverage droplet magnetofluidics (DM) to automate the movement of magnetic beads between small volumes of reagents commonly employed for NA extraction and purification. Importantly, the buffer typically used to elute the NAs off the magnetic beads is replaced by a carefully selected PCR solution, enabling direct transfer from sample preparation to dNAAT. Moreover, we demonstrate the potential for multiplexing using a digital high-resolution melt (dHRM) after the digital PCR (dPCR). The utility of this workflow is demonstrated with duplexed detection of bacteria in a sample imitating a coinfection. We first purify the bacterial DNA into a PCR solution using our DM-based sample preparation. We then transfer the purified bacterial DNA to our microfluidic nanoarray to amplify 16S rRNA using dPCR and then perform dHRM to identify the two bacterial species.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Liu2020,

title = {Detection of Promoter DNA Methylation in Urine and Plasma Aids the Detection of Non–Small Cell Lung Cancer},

author = {B. Liu and J. Ricarte-Filho and A. Mallisetty and C. Villani and A.E. Kottorou and K.P. Rodgers and C. Chen and T. Ito and K. Holmes and N. Gastala and K. Valyi-Nagy and O. David and R.C. Gaba and C. Ascoli and M. Pasquinelli and L.E. Feldman and M.G. Massad and T.H. Wang and I. Jusue-Torres and E. Benedetti and R.A. Winn and M.V. Brock and J.G. Herman and A. Hulbert},

url = {https://clincancerres.aacrjournals.org/content/26/16/4339.full},

doi = {DOI: 10.1158/1078-0432.CCR-19-2896},

year  = {2020},

date = {2020-08-12},

journal = {Clinical Cancer Research},

volume = {26},

number = {16},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pisanic2020,

title = {The methylomic landscape of fallopian tube lesions associated with ovarian high-grade serous carcinoma},

author = {T R Pisanic and Y Wang and H Sun and M Considine and L Li and T H Wang and T L Wang and Ie M Shih},

doi = {DOI: 10.1158/1078-0432.CCR-20-0270},

year  = {2020},

date = {2020-08-12},

journal = {Clinical Cancer Research},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hsieh2020,

title = {Applying Biosensor Development Concepts to Improve Preamplification-Free CRISPR/Cas12a-Dx},

author = {K. Hsieh and G. Zhao and T.H. Wang},

url = {https://pubs.rsc.org/en/content/articlelanding/2020/an/d0an00664e#!divAbstract},

year  = {2020},

date = {2020-05-27},

journal = {Analyst},

volume = {145},

pages = {4880-4888},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Yang2020,

title = {Investigating cone photoreceptor development using patient-derived NRL null retinal organoids},

author = {A. Kallman and E.E. Capowski and J. Wang and A.M. Kaushik and A.D. Jansen and K.L. Edwards and L. Chen and C.A. Berlinicke and M.J. Phillips and E.A. Pierce and J. Qian and T.H. Wang and D.M. Gamm and D.J. Zack},

url = {https://www.nature.com/articles/s42003-020-0808-5},

year  = {2020},

date = {2020-02-21},

journal = {Communications Biology},

volume = {3},

number = {1},

pages = {1-13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2019,

title = {Prognostic Value of Survival of MicroRNAs Signatures in Non-small Cell Lung Cancer},

author = {B Chen and T Gao and W Yuan and W Zhao and T H Wang and J Wu},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6843868/},

year  = {2019},

date = {2019-10-06},

journal = {Journal of Cancer},

volume = {10},

number = {23},

pages = {5793-5804},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{B2019,

title = {Rab8 GTPase regulates Klotho-mediated inhibition of cell growth and progression by directly modulating its surface expression in human non-small cell lung cancer},

author = {B Chen and S Huang and T R Pisanic and A Stark and Y Tao and B Cheng and Y Li and Y Wei and W Zhao and T H Wang and J Wu},

url = {https://www.sciencedirect.com/science/article/pii/S2352396419307108},

year  = {2019},

date = {2019-09-17},

journal = {EBioMedicine},

volume = {49},

pages = {118-132},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Athamanolap2019,

title = {Nanoarray Digital Polymerase Chain Reaction with High-Resolution Melt for Enabling Broad Bacteria Identification and Pheno–Molecular Antimicrobial Susceptibility Test},

author = {P. Athamanolap and K. Hsieh and C.M. O’Keefe and Y. Zhang and S. Yang and T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acs.analchem.9b02344},

year  = {2019},

date = {2019-09-17},

journal = {Anal Chem},

volume = {91},

number = {20},

pages = {12784-12792},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Loo2019,

title = {Technological Advances in Multiscale Analysis of Single Cells in Biomedicine},

author = {J F C Loo and H P Ho and S K Kong and T H Wang and Y P Ho},

url = {https://onlinelibrary.wiley.com/doi/full/10.1002/adbi.201900138},

year  = {2019},

date = {2019-09-11},

journal = {Advanced Biosystems},

volume = {3},

number = {11},

pages = {1900138},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{O’Keefe2019,

title = {Highly Efficient Real-Time Droplet Analysis Platform for High-Throughput Interrogation of DNA Sequences by Melt},

author = {C.M. O’Keefe and A.M. Kaushik and and T.H. Wang},

url = {https://pubs.acs.org/doi/full/10.1021/acs.analchem.9b02346},

year  = {2019},

date = {2019-07-29},

journal = {Anal Chem},

volume = {91},

number = {17},

pages = {11275-11282},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN6701,

title = {Influence of Bioreceptor Layer Structure on Myelin Basic Protein Detection using Organic Field Effect Transistor-Based Biosensors},

author = { Jian Song and Jennifer Dailey and Hui Li and Hyun-June Jang and Luisa Russell and Pengfei Zhang and Peter C. Searson and Jeff Tza-Huei Wang and Allen D. Everett and Howard E. Katz},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adfm.201802605},

doi = {10.1002/adfm.201802605},

issn = {1616301X},

year  = {2018},

date = {2018-07-31},

journal = {Advanced Functional Materials},

volume = {28},

number = {37},

pages = {1802605},

abstract = {Abstract Organic field-effect transistor (OFET)-based biosensors with antibody receptors are widely considered for protein antigen detection. To the authors' knowledge, there are no comparative evaluations to date of different choices for the matrix polymer to which the antibodies are attached. Herein, multiple acrylic copolymers are studied as receptor layers with myelin basic protein and its corresponding antibody as an archetypal antibody–antigen pair. Stability against multiple washing steps and the capacity for immobilizing antibodies on polymers on device surfaces with the help of fluorescein isothiocyanate-labeled antibodies are compared. Electronic detection and selectivity are also observed. The conclusions provide guidance on the selection of bioreceptor material for increasing sensitivity and process stability of OFET biosensors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN6503,

title = {Sample-to-Answer Droplet Magnetofluidic Platform for Point-of-Care Hepatitis C Viral Load Quantitation},

author = { D. J. Shin and A. Y. Trick and Y. H. Hsieh and D. L. Thomas and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29955160},

doi = {10.1038/s41598-018-28124-3},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2018},

date = {2018-06-28},

journal = {Sci Rep},

volume = {8},

number = {1},

pages = {9793},

abstract = {Gold standard quantitative nucleic acid tests for diagnosis of viral diseases are currently limited to implementation in laboratories outside of the clinic. An instrument for conducting nucleic acid testing at the point-of-care (POC) that is easily operable by the clinician would reduce the required number of visits to the clinic and improve patient retention for proper treatment. Here we present a droplet magnetofluidic (DM) platform, which leverages functionalized magnetic particles to miniaturize and automate laboratory assays for use in the clinic at the POC. Our novel thermoformed disposable cartridge coupled to a portable multiaxial magnetofluidic instrument enables real-time PCR assays for quantitative and sensitive detection of nucleic acids from crude biosamples. Instead of laborious benchtop sample purification techniques followed by elution and spiking into PCR buffer, the user simply injects the biosample of interest into a cartridge with magnetic particles and loads the cartridge into the instrument. We demonstrate the utility of our platform with hepatitis C virus (HCV) RNA viral load quantitation from blood serum in approximately 1 hour. Clinical serum samples (n = 18) were directly processed on cartridges with no false positives and a limit of detection of 45 IU per 10 microl sample injection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN6505,

title = {Healthcare worker feedback on a prototype smartphone-based point-of-care test platform for use in episodic care},

author = { D. J. Shin and M. Lewis and Y. H. Hsieh and N. A. Rahmoun and C. A. Gaydos and T. H. Wang and R. Rothman},

url = {https://www.ncbi.nlm.nih.gov/pubmed/30245594},

doi = {10.1097/POC.0000000000000160},

issn = {1533-029X (Print) 

1533-029X (Linking)},

year  = {2018},

date = {2018-06-01},

journal = {Point Care},

volume = {17},

number = {2},

pages = {63-65},

abstract = {With a growing list of new platforms, end-user acceptability is an evolving topic in point-of-care (POC) test development. While technical reports of new experimental POC tests are common, it is rare to find reports which evaluate the end-user acceptability of such innovations. This work illustrates an example of bridging that gap by evaluating the end-user acceptability of an experimental POC test platform with novel technical features. A prototype smartphone-based STI tests was evaluated by ED technicians, followed by a survey of acceptability factors. Our findings suggest that the end-user acceptability of some design features implemented in the prototype.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5843,

title = {A sample-to-answer droplet magnetofluidic assay platform for quantitative methylation-specific PCR},

author = { A. Stark and D. J. Shin and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29594810},

doi = {10.1007/s10544-018-0276-6},

issn = {1572-8781 (Electronic) 

1387-2176 (Linking)},

year  = {2018},

date = {2018-03-28},

journal = {Biomed Microdevices},

volume = {20},

number = {2},

pages = {31},

abstract = {Dysregulation of DNA methylation has been identified as an epigenetic biomarker for numerous cancer types. Gene-specific identification techniques relying on methylation-specific PCR (MSP) require a lengthy manual benchtop process that is susceptible to human-error and contamination. This MSP assay requires a series of discrete sample processing steps including genomic DNA extraction, bisulfite conversion and readout via PCR. In this work, we present a streamlined assay platform utilizing droplet magnetofluidic principles for integration of all sample processing steps required to obtain quantitative MSP signal from raw biological samples. We present a streamlined protocol for solid-phase extraction and bisulfite conversion of genomic DNA, which minimizes reagent use and simplifies the sample preparation protocol for implementation on a compact assay platform. Furthermore, we present a thermally robust assay chip that enables DNA extraction, bisulfite conversion and quantitative PCR from biological samples on a single device. Technical improvements to facilitate DNA extraction and PCR on a single chip in addition to chip performance characterization data are presented.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5842,

title = {Programmable microfluidic genotyping of plant DNA samples for marker-assisted selection},

author = { Helena C. Zec and Tony Zheng and Lingshu Liu and Kuangwen Hsieh and Tushar D. Rane and Todd Pederson and Tza-Huei Wang},

url = {http://dx.doi.org/10.1038/micronano.2017.97},

doi = {10.1038/micronano.2017.97},

issn = {2055-7434},

year  = {2018},

date = {2018-03-26},

journal = {Microsystems & Nanoengineering},

volume = {4},

pages = {17097},

abstract = {As demands to maintain the global food production continue to mount, multinational seed companies are turning to new DNA marker technologies to accelerate the rate of plant breeding and crop improvement. The key to widespread adoption of molecular breeding is the availability of flexible and cost-effective tools that can perform combinatorial and high-throughput genotyping of single-nucleotide polymorphisms (SNPs) to guide the crop development process. Toward this end, we have developed a programmable, droplet-based microfluidic device for genotyping maize genomic DNA. A unique feature of the microfluidic platform is the nano sample processors (NSPs), which allow the device to sequentially load an unrestricted number of unique DNA samples using only two inlets, overcoming the current limitation to the number of sample inputs due to small device footprint. Direct and programmable droplet generation within the device allows each sample to be genotyped against a panel of markers on demand. Moreover, we have successfully implemented the Invader assay for SNP genotyping in flowing, 50-nL droplets, thus achieving significant reduction in consumption of reagents per reaction as compared with conventional genotyping platforms. As a demonstration, we performed 240 Invader reactions (testing 8 DNA samples against 10 SNP markers) and achieved greater than 93% accuracy in SNP calling of plant DNA samples in a single droplet-based experiment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5631,

title = {Accelerating bacterial growth detection and antimicrobial susceptibility assessment in integrated picoliter droplet platform},

author = { A. M. Kaushik and K. Hsieh and L. Chen and D. J. Shin and J. C. Liao and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28609716},

doi = {10.1016/j.bios.2017.06.006},

issn = {1873-4235 (Electronic) 

0956-5663 (Linking)},

year  = {2017},

date = {2017-11-15},

journal = {Biosens Bioelectron},

volume = {97},

pages = {260-266},

abstract = {There remains an urgent need for rapid diagnostic methods that can evaluate antibiotic resistance for pathogenic bacteria in order to deliver targeted antibiotic treatments. Toward this end, we present a rapid and integrated single-cell biosensing platform, termed dropFAST, for bacterial growth detection and antimicrobial susceptibility assessment. DropFAST utilizes a rapid resazurin-based fluorescent growth assay coupled with stochastic confinement of bacteria in 20 pL droplets to detect signal from growing bacteria after 1h incubation, equivalent to 2-3 bacterial replications. Full integration of droplet generation, incubation, and detection into a single, uninterrupted stream also renders this platform uniquely suitable for in-line bacterial phenotypic growth assessment. To illustrate the concept of rapid digital antimicrobial susceptibility assessment, we employ the dropFAST platform to evaluate the antibacterial effect of gentamicin on E. coli growth.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5269,

title = {A Multiplex Ligation Assay for miRNA Copy Number Profiling},

author = { D. Kilburn and Y. Song and T. H. Wang and K. J. Liu},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27826928},

doi = {10.1007/978-1-4939-6524-3_17},

issn = {1940-6029 (Electronic) 

1064-3745 (Linking)},

year  = {2017},

date = {2017-11-09},

journal = {Methods Mol Biol},

volume = {1509},

pages = {185-193},

abstract = {Ligo-miR is an assay technology that can perform multiplexed detection of miRNAs from a wide range of biological sources. At its core are two sequential ligation steps. First in the capture ligation, template molecules are created by ligating a DNA adapter to the 3' end of all miRNA molecules. Then in the coding ligation these templates are used to generate, linearly amplified, DNA products encoded by length. The resultant number of each DNA product is proportional to the original number of miRNA molecules. The products and their corresponding miRNA can be identified and quantified using common DNA sizing methods such as electrophoresis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5648,

title = {Integrated Bacterial Identification and Antimicrobial Susceptibility Testing Using PCR and High-Resolution Melt},

author = { P. Athamanolap and K. Hsieh and L. Chen and S. Yang and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29027789},

doi = {10.1021/acs.analchem.7b02809},

issn = {1520-6882 (Electronic) 

0003-2700 (Linking)},

year  = {2017},

date = {2017-11-07},

journal = {Anal Chem},

volume = {89},

number = {21},

pages = {11529-11536},

abstract = {Accurate and timely diagnostics are critical for managing bacterial infections. The current gold standard, culture-based diagnostics, can provide clinicians with comprehensive diagnostic information including bacterial identity and antimicrobial susceptibility, but they often require several days of turnaround time, which leads to compromised clinical outcome and promotes the spread of antibiotic resistance. Nucleic acid amplification tests such as PCR have significantly accelerated the detection of specific bacteria but generally lack the capacities for broad-based bacterial identification or antimicrobial susceptibility testing. Here, we report an integrated assay based on PCR and high-resolution melt (HRM) for rapid diagnosis for bacterial infections. In our assay, we measure bacterial growth in the presence or absence of certain antibiotics with real-time quantitative PCR or digital PCR to determine antimicrobial susceptibility. In addition, we use HRM and a machine learning algorithm to identify bacterial species based on melt-curve profiles of the 16S rRNA gene in an automated fashion. As a demonstration, we correctly identified the bacterial species and their antimicrobial susceptibility profiles for multiple unknown samples in blinded tests within approximately 6.5 h.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5642,

title = {Molecular rheotaxis directs DNA migration and concentration against a pressure-driven flow},

author = { S. M. Friedrich and J. M. Burke and K. J. Liu and C. F. Ivory and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/29089494},

doi = {10.1038/s41467-017-01214-y},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2017},

date = {2017-10-31},

journal = {Nat Commun},

volume = {8},

number = {1},

pages = {1213},

abstract = {In-line preconcentration techniques are used to improve the sensitivity of microfluidic DNA analysis platforms. The most common methods are electrokinetic and require an externally applied electric field. Here we describe a microfluidic DNA preconcentration technique that does not require an external field. Instead, pressure-driven flow from a fluid-filled microcapillary into a lower ionic strength DNA sample reservoir induces spontaneous DNA migration against the direction of flow. This migratory phenomenon that we call Molecular Rheotaxis initiates in seconds and results in a concentrated DNA bolus at the capillary orifice. We demonstrate the ease with which this concentration method can be integrated into a microfluidic total analysis system composed of in-line DNA preconcentration, size separation, and single-molecule detection. Paired experimental and numerical simulation results are used to delineate the parameters required to induce Molecular Rheotaxis, elucidate the underlying mechanism, and optimize conditions to achieve DNA concentration factors exceeding 10,000 fold.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5625,

title = {Impedance feedback control of microfluidic valves for reliable post processing combinatorial droplet injection},

author = { B. Axt and Y. F. Hsieh and D. Nalayanda and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28681238},

doi = {10.1007/s10544-017-0203-2},

issn = {1572-8781 (Electronic) 

1387-2176 (Linking)},

year  = {2017},

date = {2017-09-01},

journal = {Biomed Microdevices},

volume = {19},

number = {3},

pages = {61},

abstract = {Droplet microfluidics has found use in many biological assay applications as a means of high-throughput sample processing. One of the challenges of the technology, however, is the ability to control and merge droplets on-demand as they flow through the microdevices. It is in the interest of developing lab-on-chip devices to be able to combinatorically program additive mixing steps for more complex multistep and multiplex assays. Existing technologies to merge droplets are either passive in nature or require highly predictable droplet movement for feedforward control, making them vulnerable to errors during high throughput operation. In this paper, we describe and demonstrate a microfluidic valve-based device for the purpose of combinatorial droplet injection at any stage in a multistep assay. Microfluidic valves are used to robustly control fluid flow, droplet generation, and droplet mixing in the device on-demand, while on-chip impedance measurements taken in real time are used as feedback to accurately time the droplet injections. The presented system is contrasted to attempts without feedback, and is shown to be 100% reliable over long durations. Additionally, content detection and discretionary injections are explored and successfully executed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5621,

title = {Determination of absolute expression profiles using multiplexed miRNA analysis},

author = { Y. Song and D. Kilburn and J. H. Song and Y. Cheng and C. T. Saeui and D. G. Cheung and C. M. Croce and K. J. Yarema and S. J. Meltzer and K. J. Liu and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28704432},

doi = {10.1371/journal.pone.0180988},

issn = {1932-6203 (Electronic) 

1932-6203 (Linking)},

year  = {2017},

date = {2017-07-13},

journal = {PLoS One},

volume = {12},

number = {7},

pages = {e0180988},

abstract = {Accurate measurement of miRNA expression is critical to understanding their role in gene expression as well as their application as disease biomarkers. Correct identification of changes in miRNA expression rests on reliable normalization to account for biological and technological variance between samples. Ligo-miR is a multiplex assay designed to rapidly measure absolute miRNA copy numbers, thus reducing dependence on biological controls. It uses a simple 2-step ligation process to generate length coded products that can be quantified using a variety of DNA sizing methods. We demonstrate Ligo-miR's ability to quantify miRNA expression down to 20 copies per cell sensitivity, accurately discriminate between closely related miRNA, and reliably measure differential changes as small as 1.2-fold. Then, benchmarking studies were performed to show the high correlation between Ligo-miR, microarray, and TaqMan qRT-PCR. Finally, Ligo-miR was used to determine copy number profiles in a number of breast, esophageal, and pancreatic cell lines and to demonstrate the utility of copy number analysis for providing layered insight into expression profile changes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5632,

title = {Mobile nucleic acid amplification testing (mobiNAAT) for Chlamydia trachomatis screening in hospital emergency department settings},

author = { D. J. Shin and P. Athamanolap and L. Chen and J. Hardick and M. Lewis and Y. H. Hsieh and R. E. Rothman and C. A. Gaydos and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28674410},

doi = {10.1038/s41598-017-04781-8},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2017},

date = {2017-07-03},

journal = {Sci Rep},

volume = {7},

number = {1},

pages = {4495},

abstract = {Management of curable sexually-transmitted infections (STI) such as Chlamydia can be revolutionized by highly sensitive nucleic acid testing that is deployable at the point-of-care (POC). Here we report the development of a mobile nucleic acid amplification testing (mobiNAAT) platform utilizing a mobile phone and droplet magnetofluidics to deliver NAAT in a portable and accessible format. By using magnetic particles as a mobile substrate for nucleic acid capture and transport, fluid handling is reduced to particle translocation on a simple magnetofluidic cartridge assembled with reagents for nucleic acid purification and amplification. A mobile phone user interface operating in tandem with a portable Bluetooth-enabled cartridge-processing unit facilitates process integration. We tested 30 potentially Chlamydia trachomatis (CT)-infected patients in a hospital emergency department and confirmed that mobiNAAT showed 100% concordance with laboratory-based NAAT. Concurrent evaluation by a nontechnical study coordinator who received brief training via an embedded mobile app module demonstrated ease of use and reproducibility of the platform. This work demonstrates the potential of mobile nucleic acid testing in bridging the diagnostic gap between centralized laboratories and hospital emergency departments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5273,

title = {New and developing diagnostic technologies for urinary tract infections},

author = { M. Davenport and K. E. Mach and L. M. D. Shortliffe and N. Banaei and T. H. Wang and J. C. Liao},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28248946},

doi = {10.1038/nrurol.2017.20},

issn = {1759-4820 (Electronic) 

1759-4812 (Linking)},

year  = {2017},

date = {2017-05-01},

journal = {Nat Rev Urol},

volume = {14},

number = {5},

pages = {296-310},

abstract = {Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5160,

title = {Early Detection of Lung Cancer Using DNA Promoter Hypermethylation in Plasma and Sputum},

author = { A. Hulbert and I. Jusue-Torres and A. Stark and C. Chen and K. Rodgers and B. Lee and C. Griffin and A. Yang and P. Huang and J. Wrangle and S. A. Belinsky and T. H. Wang and S. C. Yang and S. B. Baylin and M. V. Brock and J. G. Herman},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27729459},

doi = {10.1158/1078-0432.CCR-16-1371},

issn = {1078-0432 (Print) 

1078-0432 (Linking)},

year  = {2017},

date = {2017-04-15},

journal = {Clin Cancer Res},

volume = {23},

number = {8},

pages = {1998-2005},

abstract = {Purpose: CT screening can reduce death from lung cancer. We sought to improve the diagnostic accuracy of lung cancer screening using ultrasensitive methods and a lung cancer-specific gene panel to detect DNA methylation in sputum and plasma.Experimental Design: This is a case-control study of subjects with suspicious nodules on CT imaging. Plasma and sputum were obtained preoperatively. Cases (n = 150) had pathologic confirmation of node-negative (stages I and IIA) non-small cell lung cancer. Controls (n = 60) had non-cancer diagnoses. We detected promoter methylation using quantitative methylation-specific real-time PCR and methylation-on-beads for cancer-specific genes (SOX17, TAC1, HOXA7, CDO1, HOXA9, and ZFP42).Results: DNA methylation was detected in plasma and sputum more frequently in people with cancer compared with controls (P < 0.001) for five of six genes. The sensitivity and specificity for lung cancer diagnosis using the best individual genes was 63% to 86% and 75% to 92% in sputum, respectively, and 65% to 76% and 74% to 84% in plasma, respectively. A three-gene combination of the best individual genes has sensitivity and specificity of 98% and 71% using sputum and 93% and 62% using plasma. Area under the receiver operating curve for this panel was 0.89 [95% confidence interval (CI), 0.80-0.98] in sputum and 0.77 (95% CI, 0.68-0.86) in plasma. Independent blinded random forest prediction models combining gene methylation with clinical information correctly predicted lung cancer in 91% of subjects using sputum detection and 85% of subjects using plasma detection.Conclusions: High diagnostic accuracy for early-stage lung cancer can be obtained using methylated promoter detection in sputum or plasma. Clin Cancer Res; 23(8); 1998-2005. (c)2016 AACR.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5145,

title = {Defining, distinguishing and detecting the contribution of heterogeneous methylation to cancer heterogeneity},

author = { T. R. 2nd Pisanic and P. Athamanolap and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27582426},

doi = {10.1016/j.semcdb.2016.08.030},

issn = {1096-3634 (Electronic) 

1084-9521 (Linking)},

year  = {2017},

date = {2017-04-01},

journal = {Semin Cell Dev Biol},

volume = {64},

pages = {5-17},

abstract = {DNA methylation is a fundamental means of epigenetic gene regulation that occurs in virtually all cell types. In many higher organisms, including humans, it plays vital roles in cell differentiation and homeostatic maintenance of cell phenotype. The control of DNA methylation has traditionally been attributed to a highly coordinated, linear process, whose dysregulation has been associated with numerous pathologies including cancer, where it occurs early in, and even prior to, the development of neoplastic tissues. Recent experimental evidence has demonstrated that, contrary to prevailing paradigms, methylation patterns are actually maintained through inexact, dynamic processes. These processes normally result in minor stochastic differences between cells that accumulate with age. However, various factors, including cancer itself, can lead to substantial differences in intercellular methylation patterns, viz. methylation heterogeneity. Advancements in molecular biology techniques are just now beginning to allow insight into how this heterogeneity contributes to clonal evolution and overall cancer heterogeneity. In the current review, we begin by presenting a didactic overview of how the basal bimodal methylome is established and maintained. We then provide a synopsis of some of the factors that lead to the accrual of heterogeneous methylation and how this heterogeneity may lead to gene silencing and impact the development of cancerous phenotypes. Lastly, we highlight currently available methylation assessment techniques and discuss their suitability to the study of heterogeneous methylation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5274,

title = {Microbial Typing by Machine Learned DNA Melt Signatures},

author = { N. Andini and B. Wang and P. Athamanolap and J. Hardick and B. J. Masek and S. Thair and A. Hu and G. Avornu and S. Peterson and S. Cogill and R. E. Rothman and K. C. Carroll and C. A. Gaydos and J. T. Wang and S. Batzoglou and S. Yang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28165067},

doi = {10.1038/srep42097},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2017},

date = {2017-02-06},

journal = {Sci Rep},

volume = {7},

pages = {42097},

abstract = {There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naive Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5270,

title = {Erythrocyte Membrane-Coated Upconversion Nanoparticles with Minimal Protein Adsorption for Enhanced Tumor Imaging},

author = { L. Rao and Q. F. Meng and L. L. Bu and B. Cai and Q. Huang and Z. J. Sun and W. F. Zhang and A. Li and S. S. Guo and W. Liu and T. H. Wang and X. Z. Zhao},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28050902},

doi = {10.1021/acsami.6b14450},

issn = {1944-8252 (Electronic) 

1944-8244 (Linking)},

year  = {2017},

date = {2017-01-25},

journal = {ACS Appl Mater Interfaces},

volume = {9},

number = {3},

pages = {2159-2168},

abstract = {Upconversion nanoparticles (UCNPs) with superior optical and chemical features have been broadly employed for in vivo cancer imaging. Generally, UCNPs are surface modified with ligands for cancer active targeting. However, nanoparticles in biological fluids are known to form a long-lived "protein corona", which covers the targeting ligands on nanoparticle surface and dramatically reduces the nanoparticle targeting capabilities. Here, for the first time, we demonstrated that by coating UCNPs with red blood cell (RBC) membranes, the resulting cell membrane-capped nanoparticles (RBC-UCNPs) adsorbed virtually no proteins when exposed to human plasma. We further observed in various scenarios that the cancer targeting ability of folic acid (FA)-functionalized nanoparticles (FA-RBC-UCNPs) was rescued by the cell membrane coating. Next, the FA-RBC-UCNPs were successfully utilized for enhanced in vivo tumor imaging. Finally, blood parameters and histology analysis suggested that no significant systematic toxicity was induced by the injection of biomimetic nanoparticles. Our method provides a new angle on the design of targeted nanoparticles for biomedical applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5144,

title = {A Simple Thermoplastic Substrate Containing Hierarchical Silica Lamellae for High-Molecular-Weight DNA Extraction},

author = { Y. Zhang and Y. Zhang and J. M. Burke and K. Gleitsman and S. M. Friedrich and K. J. Liu and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27862402},

doi = {10.1002/adma.201603738},

issn = {1521-4095 (Electronic) 

0935-9648 (Linking)},

year  = {2016},

date = {2016-12-01},

journal = {Adv Mater},

volume = {28},

number = {48},

pages = {10630-10636},

abstract = {An inexpensive, magnetic thermoplastic nanomaterial is developed utilizing a hierarchical layering of micro- and nanoscale silica lamellae to create a high-surface-area and low-shear substrate capable of capturing vast amounts of ultrahigh-molecular-weight DNA. Extraction is performed via a simple 45 min process and is capable of achieving binding capacities up to 1 000 000 times greater than silica microparticles.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5183,

title = {Continuous Production of Discrete Plasmid DNA-Polycation Nanoparticles Using Flash Nanocomplexation},

author = { J. L. Santos and Y. Ren and J. Vandermark and M. M. Archang and J. M. Williford and H. W. Liu and J. Lee and T. H. Wang and H. Q. Mao},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27717227},

doi = {10.1002/smll.201601425},

issn = {1613-6829 (Electronic) 

1613-6810 (Linking)},

year  = {2016},

date = {2016-12-01},

journal = {Small},

volume = {12},

number = {45},

pages = {6214-6222},

abstract = {Despite successful demonstration of linear polyethyleneimine (lPEI) as an effective carrier for a wide range of gene medicine, including DNA plasmids, small interfering RNAs, mRNAs, etc., and continuous improvement of the physical properties and biological performance of the polyelectrolyte complex nanoparticles prepared from lPEI and nucleic acids, there still exist major challenges to produce these nanocomplexes in a scalable manner, particularly for lPEI/DNA nanoparticles. This has significantly hindered the progress toward clinical translation of these nanoparticle-based gene medicine. Here the authors report a flash nanocomplexation (FNC) method that achieves continuous production of lPEI/plasmid DNA nanoparticles with narrow size distribution using a confined impinging jet device. The method involves the complex coacervation of negatively charged DNA plasmid and positive charged lPEI under rapid, highly dynamic, and homogeneous mixing conditions, producing polyelectrolyte complex nanoparticles with narrow distribution of particle size and shape. The average number of plasmid DNA packaged per nanoparticles and its distribution are similar between the FNC method and the small-scale batch mixing method. In addition, the nanoparticles prepared by these two methods exhibit similar cell transfection efficiency. These results confirm that FNC is an effective and scalable method that can produce well-controlled lPEI/plasmid DNA nanoparticles.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5268,

title = {National Institute of Biomedical Imaging and Bioengineering Point-of-Care Technology Research Network: Advancing Precision Medicine},

author = { P. Ford Carleton and S. Schachter and J. A. Parrish and J. M. Collins and J. B. Crocker and R. F. Dixon and S. Edgman-Levitan and K. B. Lewandrowski and J. E. Stahl and C. Klapperich and M. Cabodi and C. A. Gaydos and A. M. Rompalo and Y. Manabe and T. H. Wang and R. Rothman and C. D. Geddes and L. Widdice and J. Jackman and R. A. Mathura and T. B. Lash},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27730014},

doi = {10.1109/JTEHM.2016.2598837},

issn = {2168-2372 (Print) 

2168-2372 (Linking)},

year  = {2016},

date = {2016-10-13},

journal = {IEEE J Transl Eng Health Med},

volume = {4},

pages = {2800614},

abstract = {To advance the development of point-of-care technology (POCT), the National Institute of Biomedical Imaging and Bioengineering established the POCT Research Network (POCTRN), comprised of Centers that emphasize multidisciplinary partnerships and close facilitation to move technologies from an early stage of development into clinical testing and patient use. This paper describes the POCTRN and the three currently funded Centers as examples of academic-based organizations that support collaborations across disciplines, institutions, and geographic regions to successfully drive innovative solutions from concept to patient care.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5184,

title = {Signal-on Protein Detection via Dye Translocation between Aptamer and Quantum Dot},

author = { Y. H. Lao and C. W. Chi and S. M. Friedrich and K. Peck and T. H. Wang and K. W. Leong and L. C. Chen},

url = {https://www.ncbi.nlm.nih.gov/pubmed/27101438},

doi = {10.1021/acsami.6b02871},

issn = {1944-8252 (Electronic) 

1944-8244 (Linking)},

year  = {2016},

date = {2016-05-18},

journal = {ACS Appl Mater Interfaces},

volume = {8},

number = {19},

pages = {12048-55},

abstract = {A unique interaction between the cyanine dye and negatively charged quantum dot is used to construct a signal-on biaptameric quantum dot (QD) Forster resonance energy transfer (FRET) beacon for protein detection and distinct aptamer characterization. The beacon comprises a pair of aptamers, one intercalated with the cyanine dye (YOYO-3) and the other conjugated to a negatively charged, carboxyl-QD. When the target protein is present, structural folding and sandwich association of the two aptamers take place. As a consequence, YOYO-3 is displaced from the folded aptamer and transferred to the unblocked QD surface to yield a target concentration-dependent FRET signal. As a proof-of-principle, we demonstrate the detection of thrombin ranging from nanomolar to submicromolar concentrations and confirm the dye translocation using cylindrical illumination confocal spectroscopy (CICS). The proposed beacon provides a simple, rapid, signal-on FRET detection for protein as well as a potential platform for distinct aptamer screening.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5130,

title = {Cancer Cell Membrane-Coated Upconversion Nanoprobes for Highly Specific Tumor Imaging},

author = { L. Rao and L. L. Bu and B. Cai and J. H. Xu and A. Li and W. F. Zhang and Z. J. Sun and S. S. Guo and W. Liu and T. H. Wang and X. Z. Zhao},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26970518},

doi = {10.1002/adma.201506086},

issn = {1521-4095 (Electronic) 

0935-9648 (Linking)},

year  = {2016},

date = {2016-05-01},

journal = {Adv Mater},

volume = {28},

number = {18},

pages = {3460-6},

abstract = {Cancer cell membrane-coated upconversion nanoprobes (CC-UCNPs) with immune escape and homologous targeting capabilities are used for highly specific tumor imaging. The combination of UCNPs with biomimetic cancer cell membranes embodies a novel materials design strategy and presents a compelling class of advanced materials.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5005,

title = {Analysis of single nucleic acid molecules in micro- and nano-fluidics},

author = { S. M. Friedrich and H. C. Zec and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26818700},

doi = {10.1039/c5lc01294e},

issn = {1473-0189 (Electronic) 

1473-0189 (Linking)},

year  = {2016},

date = {2016-03-07},

journal = {Lab Chip},

volume = {16},

number = {5},

pages = {790-811},

abstract = {Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5009,

title = {A parallelized microfluidic DNA bisulfite conversion module for streamlined methylation analysis},

author = { A. Stark and D. J. Shin and T. 2nd Pisanic and K. Hsieh and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26759004},

doi = {10.1007/s10544-015-0029-8},

issn = {1572-8781 (Electronic) 

1387-2176 (Linking)},

year  = {2016},

date = {2016-02-01},

journal = {Biomed Microdevices},

volume = {18},

number = {1},

pages = {5},

abstract = {Aberrant methylation of DNA has been identified as an epigenetic biomarker for numerous cancer types. The vast majority of techniques aimed at detecting methylation require bisulfite conversion of the DNA sample prior to analysis, which until now has been a benchtop process. Although microfluidics has potential benefits of simplified operation, sample and reagent economy, and scalability, bisulfite conversion has yet to be implemented in this format. Here, we present a novel droplet microfluidic design that facilitates rapid bisulfite conversion by reducing the necessary processing steps while retaining comparable performance to existing methods. This new format has a reduced overall processing time and is readily scalable for use in high throughput DNA methylation analysis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5007,

title = {Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping},

author = { S. I. Fraley and P. Athamanolap and B. J. Masek and J. Hardick and K. C. Carroll and Y. H. Hsieh and R. E. Rothman and C. A. Gaydos and T. H. Wang and S. Yang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26778280},

doi = {10.1038/srep19218},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2016},

date = {2016-01-18},

journal = {Sci Rep},

volume = {6},

pages = {19218},

abstract = {High Resolution Melt (HRM) is a versatile and rapid post-PCR DNA analysis technique primarily used to differentiate sequence variants among only a few short amplicons. We recently developed a one-vs-one support vector machine algorithm (OVO SVM) that enables the use of HRM for identifying numerous short amplicon sequences automatically and reliably. Herein, we set out to maximize the discriminating power of HRM + SVM for a single genetic locus by testing longer amplicons harboring significantly more sequence information. Using universal primers that amplify the hypervariable bacterial 16 S rRNA gene as a model system, we found that long amplicons yield more complex HRM curve shapes. We developed a novel nested OVO SVM approach to take advantage of this feature and achieved 100% accuracy in the identification of 37 clinically relevant bacteria in Leave-One-Out-Cross-Validation. A subset of organisms were independently tested. Those from pure culture were identified with high accuracy, while those tested directly from clinical blood bottles displayed more technical variability and reduced accuracy. Our findings demonstrate that long sequences can be accurately and automatically profiled by HRM with a novel nested SVM approach and suggest that clinical sample testing is feasible with further optimization.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5013,

title = {Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution},

author = { S. M. Friedrich and K. J. Liu and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26684193},

doi = {10.1021/jacs.5b10983},

issn = {1520-5126 (Electronic) 

0002-7863 (Linking)},

year  = {2016},

date = {2016-01-13},

journal = {J Am Chem Soc},

volume = {138},

number = {1},

pages = {319-27},

abstract = {Limited tools exist that are capable of monitoring nucleic acid conformations, fluctuations, and distributions in free solution environments. Single molecule free solution hydrodynamic separation enables the unique ability to quantitatively analyze nucleic acid biophysics in free solution. Single molecule fluorescent burst data and separation chromatograms can give layered insight into global DNA conformation, binding interactions, and molecular distributions. First, we show that global conformation of individual DNA molecules can be directly visualized by examining single molecule fluorescent burst shapes and that DNA exists in a dynamic equilibrium of fluctuating conformations as it is driven by Poiseuille flow through micron-sized channels. We then show that this dynamic equilibrium of DNA conformations is reflected as shifts in hydrodynamic mobility that can be perturbed using salt and ionic strength to affect packing density. Next, we demonstrate that these shifts in hydrodynamic mobility can be used to investigate hybridization thermodynamics and binding interactions. We distinguish and classify multiple interactions within a single sample, and demonstrate quantification amidst large concentration differences for the detection of rare species. Finally, we demonstrate that these differences can resolve perfect complement, 2 bp mismatched, and 3 bp mismatched sequences. Such a system can be used to garner diverse information about DNA conformation and structure, and potentially be extended to other molecules and mixed-species interactions, such as between nucleic acids and proteins or synthetic polymers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3200,

title = {DREAMing: a simple and ultrasensitive method for assessing intratumor epigenetic heterogeneity directly from liquid biopsies},

author = { T. R. 2nd Pisanic and P. Athamanolap and W. Poh and C. Chen and A. Hulbert and M. V. Brock and J. G. Herman and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26304549},

doi = {10.1093/nar/gkv795},

issn = {1362-4962 (Electronic) 

0305-1048 (Linking)},

year  = {2015},

date = {2015-12-15},

journal = {Nucleic Acids Res},

volume = {43},

number = {22},

pages = {e154},

abstract = {Many cancers comprise heterogeneous populations of cells at primary and metastatic sites throughout the body. The presence or emergence of distinct subclones with drug-resistant genetic and epigenetic phenotypes within these populations can greatly complicate therapeutic intervention. Liquid biopsies of peripheral blood from cancer patients have been suggested as an ideal means of sampling intratumor genetic and epigenetic heterogeneity for diagnostics, monitoring and therapeutic guidance. However, current molecular diagnostic and sequencing methods are not well suited to the routine assessment of epigenetic heterogeneity in difficult samples such as liquid biopsies that contain intrinsically low fractional concentrations of circulating tumor DNA (ctDNA) and rare epigenetic subclonal populations. Here we report an alternative approach, deemed DREAMing (Discrimination of Rare EpiAlleles by Melt), which uses semi-limiting dilution and precise melt curve analysis to distinguish and enumerate individual copies of epiallelic species at single-CpG-site resolution in fractions as low as 0.005%, providing facile and inexpensive ultrasensitive assessment of locus-specific epigenetic heterogeneity directly from liquid biopsies. The technique is demonstrated here for the evaluation of epigenetic heterogeneity at p14(ARF) and BRCA1 gene-promoter loci in liquid biopsies obtained from patients in association with non-small cell lung cancer (NSCLC) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN), respectively.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3198,

title = {Red Blood Cell Membrane as a Biomimetic Nanocoating for Prolonged Circulation Time and Reduced Accelerated Blood Clearance},

author = { L. Rao and L. L. Bu and J. H. Xu and B. Cai and G. T. Yu and X. Yu and Z. He and Q. Huang and A. Li and S. S. Guo and W. F. Zhang and W. Liu and Z. J. Sun and H. Wang and T. H. Wang and X. Z. Zhao},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26488923},

doi = {10.1002/smll.201502388},

issn = {1613-6829 (Electronic) 

1613-6810 (Linking)},

year  = {2015},

date = {2015-12-01},

journal = {Small},

volume = {11},

number = {46},

pages = {6225-36},

abstract = {For decades, poly(ethylene glycol) (PEG) has been widely incorporated into nanoparticles for evading immune clearance and improving the systematic circulation time. However, recent studies have reported a phenomenon known as äccelerated blood clearance (ABC)" where a second dose of PEGylated nanomaterials is rapidly cleared when given several days after the first dose. Herein, we demonstrate that natural red blood cell (RBC) membrane is a superior alternative to PEG. Biomimetic RBC membrane-coated Fe(3)O(4) nanoparticles (Fe(3)O(4) @RBC NPs) rely on CD47, which is a "don't eat me" marker on the RBC surface, to escape immune clearance through interactions with the signal regulatory protein-alpha (SIRP-alpha) receptor. Fe(3)O(4) @RBC NPs exhibit extended circulation time and show little change between the first and second doses, with no ABC suffered. In addition, the administration of Fe(3)O(4) @RBC NPs does not elicit immune responses on neither the cellular level (myeloid-derived suppressor cells (MDSCs)) nor the humoral level (immunoglobulin M and G (IgM and IgG)). Finally, the in vivo toxicity of these cell membrane-camouflaged nanoparticles is systematically investigated by blood biochemistry, hematology testing, and histology analysis. These findings are significant advancements toward solving the long-existing clinical challenges of developing biomaterials that are able to resist both immune response and rapid clearance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3197,

title = {Efficient synthesis of stably adenylated DNA and RNA adapters for microRNA capture using T4 RNA ligase 1},

author = { Y. Song and K. J. Liu and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26500066},

doi = {10.1038/srep15620},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2015},

date = {2015-10-26},

journal = {Sci Rep},

volume = {5},

pages = {15620},

abstract = {MicroRNA profiling methods have become increasingly important due to the rapid rise of microRNA in both basic and translational sciences. A critical step in many microRNA profiling assays is adapter ligation using pre-adenylated adapters. While pre-adenylated adapters can be chemically or enzymatically prepared, enzymatic adenylation is preferred due to its ease and high yield. However, previously reported enzymatic methods either require tedious purification steps or use thermostable ligases that can generate side products during the subsequent ligation step. We have developed a highly efficient, template- and purification-free, adapter adenylation method using T4 RNA ligase 1. This method is capable of adenylating large amounts of adapter at ~100% efficiency and can efficiently adenylate both DNA and RNA bases. We find that the adenylation reaction speed can differ between DNA and RNA and between terminal nucleotides, leading to bias if reactions are not allowed to run to completion. We further find that the addition of high PEG levels can effectively suppress these differences.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3199,

title = {Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification},

author = { W. Guan and L. Chen and T. D. Rane and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26333806},

doi = {10.1038/srep13795},

issn = {2045-2322 (Electronic) 

2045-2322 (Linking)},

year  = {2015},

date = {2015-09-03},

journal = {Sci Rep},

volume = {5},

pages = {13795},

abstract = {We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN5129,

title = {Enhancing Throughput of Combinatorial Droplet Devices via Droplet Bifurcation, Parallelized Droplet Fusion, and Parallelized Detection},

author = { Kuangwen Hsieh and Helena Zec and Polly Ma and Tushar Rane and Tza-Huei Wang},

url = {http://www.mdpi.com/2072-666X/6/10/1434},

issn = {2072-666X},

year  = {2015},

date = {2015-08-03},

journal = {Micromachines},

volume = {6},

number = {10},

pages = {1434},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3201,

title = {High-resolution quantification by charge-dominant electrophoretic mobility shift of quantum dots},

author = { Y. Zhang and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25546004},

doi = {10.1002/elps.201400577},

issn = {1522-2683 (Electronic) 

0173-0835 (Linking)},

year  = {2015},

date = {2015-04-01},

journal = {Electrophoresis},

volume = {36},

number = {7-8},

pages = {1011-5},

abstract = {Conjugation of biomolecules to colloidal nanoparticles, such as quantum dots (QDs), often leads to change in mobility. We discover that linking DNA molecules to quantum dots alters their surface charge density without significantly increasing the hydrodynamic radius, causing a prominent shift in electrophoretic mobility. In this study, a high-resolution molecular quantification method named quantification by QDs electrophoretic mobility shift (qQEMS) is developed based on the charge-dominant transformation that closely associates DNA quantity to QDs electrophoretic mobility. The versatility of qQEMS is demonstrated by a number of quantification assays in which DNA molecules functioned as enzyme substrates, target-specific probes, and competitive charge carriers. qQEMS shows a great potential as a generic and versatile quantification platform for a wide range of applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3203,

title = {Microfluidic continuous flow digital loop-mediated isothermal amplification (LAMP)},

author = { T. D. Rane and L. Chen and H. C. Zec and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25431886},

doi = {10.1039/c4lc01158a},

issn = {1473-0189 (Electronic) 

1473-0189 (Linking)},

year  = {2015},

date = {2015-02-07},

journal = {Lab Chip},

volume = {15},

number = {3},

pages = {776-82},

abstract = {Digital nucleic acid detection is rapidly becoming a popular technique for ultra-sensitive and quantitative detection of nucleic acid molecules in a wide range of biomedical studies. Digital polymerase chain reaction (PCR) remains the most popular way of conducting digital nucleic acid detection. However, due to the need for thermocycling, digital PCR is difficult to implement in a streamlined manner on a single microfluidic device, leading to complex fragmented workflows and multiple separate devices and instruments. Loop-mediated isothermal amplification (LAMP) is an excellent isothermal alternative to PCR with potentially better specificity than PCR because of the use of multiple primer sets for a nucleic acid target. Here we report a microfluidic droplet device implementing all the steps required for digital nucleic acid detection including droplet generation, incubation and in-line detection for digital LAMP. As compared to microchamber or droplet array-based digital assays, the continuous flow operation of this device eliminates the constraints on the number of total reactions imposed by the footprint of the device and the analysis throughput caused by the time for lengthy incubation and transfer of materials between instruments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3202,

title = {A barcode-free combinatorial screening platform for matrix metalloproteinase screening},

author = { T. D. Rane and H. C. Zec and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25543856},

doi = {10.1021/ac504330x},

issn = {1520-6882 (Electronic) 

0003-2700 (Linking)},

year  = {2015},

date = {2015-02-03},

journal = {Anal Chem},

volume = {87},

number = {3},

pages = {1950-6},

abstract = {Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3209,

title = {Magnetic droplet manipulation platforms for nucleic acid detection at the point of care},

author = { D. J. Shin and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25008142},

doi = {10.1007/s10439-014-1060-2},

issn = {1573-9686 (Electronic) 

0090-6964 (Linking)},

year  = {2014},

date = {2014-11-01},

journal = {Ann Biomed Eng},

volume = {42},

number = {11},

pages = {2289-302},

abstract = {This review summarizes recent developments in the use of magnetically actuated droplets in point-of-care molecular diagnostic platforms. We discuss the fundamentals of magnetic droplet manipulation and the various modes of actuation. The balance of forces acting on a droplet during transport and particle extraction, as well as the devices and instrumentation developed to perform these operations will be presented and discussed. Furthermore, we review some of the recent advances on the diagnostic applications of platforms utilizing magnetic manipulation for genetic assessment of biological samples.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3205,

title = {Trainable high resolution melt curve machine learning classifier for large-scale reliable genotyping of sequence variants},

author = { P. Athamanolap and V. Parekh and S. I. Fraley and V. Agarwal and D. J. Shin and M. A. Jacobs and T. H. Wang and S. Yang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25275518},

doi = {10.1371/journal.pone.0109094},

issn = {1932-6203 (Electronic) 

1932-6203 (Linking)},

year  = {2014},

date = {2014-10-03},

journal = {PLoS One},

volume = {9},

number = {9},

pages = {e109094},

abstract = {High resolution melt (HRM) is gaining considerable popularity as a simple and robust method for genotyping sequence variants. However, accurate genotyping of an unknown sample for which a large number of possible variants may exist will require an automated HRM curve identification method capable of comparing unknowns against a large cohort of known sequence variants. Herein, we describe a new method for automated HRM curve classification based on machine learning methods and learned tolerance for reaction condition deviations. We tested this method in silico through multiple cross-validations using curves generated from 9 different simulated experimental conditions to classify 92 known serotypes of Streptococcus pneumoniae and demonstrated over 99% accuracy with 8 training curves per serotype. In vitro verification of the algorithm was tested using sequence variants of a cancer-related gene and demonstrated 100% accuracy with 3 training curves per sequence variant. The machine learning algorithm enabled reliable, scalable, and automated HRM genotyping analysis with broad potential clinical and epidemiological applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3206,

title = {The promise of methylation on beads for cancer detection and treatment},

author = { A. A. Guzzetta and T. R. Pisanic Ii and P. Sharma and J. M. Yi and A. Stark and T. H. Wang and N. Ahuja},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25136840},

doi = {10.1586/14737159.2014.943665},

issn = {1744-8352 (Electronic) 

1473-7159 (Linking)},

year  = {2014},

date = {2014-09-01},

journal = {Expert Rev Mol Diagn},

volume = {14},

number = {7},

pages = {845-52},

abstract = {Despite numerous technical hurdles, the realization of true personalized medicine is becoming a progressive reality for the future of patient care. With the development of new techniques and tools to measure the genetic signature of tumors, biomarkers are increasingly being used to detect occult tumors, determine the choice of treatment and predict outcomes. Methylation of CpG islands at the promoter region of genes is a particularly exciting biomarker as it is cancer-specific. Older methods to detect methylation were cumbersome, operator-dependent and required large amounts of DNA. However, a newer technique called methylation on beads has resulted in a more uniform, streamlined and efficient assay. Furthermore, methylation on beads permits the extraction and processing of miniscule amounts of methylated tumor DNA in the peripheral blood. Such a technique may aid in the clinical detection and treatment of cancers in the future.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3207,

title = {Novel droplet platforms for the detection of disease biomarkers},

author = { H. Zec and D. J. Shin and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25109704},

doi = {10.1586/14737159.2014.945437},

issn = {1744-8352 (Electronic) 

1473-7159 (Linking)},

year  = {2014},

date = {2014-09-01},

journal = {Expert Rev Mol Diagn},

volume = {14},

number = {7},

pages = {787-801},

abstract = {Personalized medicine - healthcare based on individual genetic variation - has the potential to transform the way healthcare is delivered to patients. The promise of personalized medicine has been predicated on the predictive and diagnostic power of genomic and proteomic biomarkers. Biomarker screening may help improve health outcomes, for example, by identifying individuals' susceptibility to diseases and predicting how patients will respond to drugs. Microfluidic droplet technology offers an exciting opportunity to revolutionize the accessibility of personalized medicine. A framework for the role of droplet microfluidics in biomarker detection can be based on two main themes. Emulsion-based microdroplet platforms can provide new ways to measure and detect biomolecules. In addition, microdroplet platforms facilitate high-throughput screening of biomarkers. Meanwhile, surface-based droplet platforms provide an opportunity to develop miniaturized diagnostic systems. These platforms may function as portable benchtop environments that dramatically shorten the transition of a benchtop assay into a point-of-care format.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3208,

title = {Direct interrogation of DNA content distribution in nanoparticles by a novel microfluidics-based single-particle analysis},

author = { C. W. Beh and D. Pan and J. Lee and X. Jiang and K. J. Liu and H. Q. Mao and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25054542},

doi = {10.1021/nl5018404},

issn = {1530-6992 (Electronic) 

1530-6984 (Linking)},

year  = {2014},

date = {2014-08-13},

journal = {Nano Lett},

volume = {14},

number = {8},

pages = {4729-35},

abstract = {Nonviral gene delivery holds great promise not just as a safer alternative to viral vectors in traditional gene therapy applications, but also for regenerative medicine, induction of pluripotency in somatic cells, and RNA interference for gene silencing. Although it continues to be an active area of research, there remain many challenges to the rational design of vectors. Among these, the inability to characterize the composition of nanoparticles and its distribution has made it difficult to probe the mechanism of gene transfection process, since differences in the nanoparticle-mediated transfection exist even when the same vector is used. There is a lack of sensitive methods that allow for full characterization of DNA content in single nanoparticles and its distribution among particles in the same preparation. Here we report a novel spectroscopic approach that is capable of interrogating nanoparticles on a particle-by-particle basis. Using PEI/DNA and PEI-g-PEG/DNA nanoparticles as examples, we have shown that the distribution of DNA content among these nanoparticles was relatively narrow, with the average numbers of DNA of 4.8 and 6.7 per particle, respectively, in PEI/DNA and PEI-g-PEG/DNA nanoparticles. This analysis enables a more accurate description of DNA content in polycation/DNA nanoparticles. It paves the way toward comparative assessments of various types of gene carriers and provides insights into bridging the efficiency gap between viral and nonviral vehicles.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN3204,

title = {A droplet microfluidic approach to single-stream nucleic acid isolation and mutation detection},

author = { D. J. Shin and Y. Zhang and T. H. Wang},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25386112},

doi = {10.1007/s10404-013-1305-7},

issn = {1613-4982 (Print) 

1613-4982 (Linking)},

year  = {2014},

date = {2014-08-01},

journal = {Microfluid Nanofluidics},

volume = {17},

number = {2},

pages = {425-430},

abstract = {In this work, a droplet microfluidic platform for genetic mutation detection from crude biosample is described. Single-stream integration of nucleic acid isolation and amplification is realized on a simple fluidic cartridge. Subsequent DNA melting curve is employed with signal normalizing algorithm to differentiate heterozygous K-ras codon 12 c.25G>A mutant from the wildtype. This technique showcases an alternative to modular bench-top approaches for genetic mutation screening, which is of interest to decentralized diagnostic platforms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}