Full Text Journal Articles by
Author Barry Lutz

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Long-term dry storage of enzyme-based reagents for isothermal nucleic acid amplification in a porous matrix for use in point-of-care diagnostic devices.

Sujatha Kumar, Ryan Gallagher, Josh Bishop, Enos Kline, Joshua Buser, Lisa Lafleur, Kamal Shah, Barry Lutz, Paul Yager,

Nucleic acid amplification test (NAAT)-based point-of-care (POC) devices are rapidly growing for use in low-resource settings. However, key challenges are the ability to store the enzyme-based reagents in dry form in the device and the long-term stability of those reagents at elevated temperatures, especially where ambient temperatures could be as ... Read more >>

Analyst (The Analyst)
[2020, 145(21):6875-6886]

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Urine Biomarker Assessment of Infant Adherence to Isoniazid Prophylaxis.

Sylvia M LaCourse, Daniel Leon, Nuttada Panpradist, Barbra A Richardson, Elizabeth Maleche-Obimbo, Jerphason Mecha, Daniel Matemo, Jaclyn N Escudero, John Kinuthia, Barry Lutz, Grace John-Stewart,

We assessed adherence in an infant tuberculosis prevention trial in Kenya with a urine isoniazid metabolite-detecting dipstick. Ninety-seven infants had 155 assays performed; 77 (49.7%) were found to be positive despite caregiver-reported adherence. Positive assays were associated with maternal secondary education, HIV suppression and no reported missed doses in past ... Read more >>

Pediatr Infect Dis J (The Pediatric infectious disease journal)
[2021, 40(1):e43-e45]

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Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

Ashley Kim, Elisabeth Brandstetter, Naomi Wilcox, Jessica Heimonen, Chelsey Graham, Peter Han, Lea Starita, Denise McCulloch, Amanda Casto, Deborah Nickerson, Margaret Van de Loo, Jennifer Mooney, Misja Ilcisin, Kairsten Fay, Jover Lee, Thomas Sibley, Victoria Lyon, Rachel Geyer, Matthew Thompson, Barry Lutz, Mark Rieder, Trevor Bedford, Michael Boeckh, Janet Englund, Helen Chu,

<h4>Introduction</h4> While influenza and other respiratory pathogens cause significant morbidity and mortality, the community-based burden of these infections remains incompletely understood. The development of novel methods to detect respiratory infections is essential for mitigating epidemics and developing pandemic-preparedness infrastructure. <h4>Methods</h4> From October 2019 to March 2020, we conducted a home-based ... Read more >>

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The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology.

Helen Y Chu, Michael Boeckh, Janet A Englund, Michael Famulare, Barry Lutz, Deborah A Nickerson, Mark Rieder, Lea M Starita, Amanda Adler, Elisabeth Brandstetter, Chris D Frazer, Peter D Han, Reena K Gulati, James Hadfield, Michael Jackson, Anahita Kiavand, Louise E Kimball, Kirsten Lacombe, Kira Newman, Thomas R Sibley, Jennifer K Logue, Victoria Rachel Lyon, Caitlin R Wolf, Monica Zigman Suchsland, Jay Shendure, Trevor Bedford,

<h4>Introduction</h4>Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterise, and potentially contain new and emerging influenza strains at both an individual and population level. The objective of this study is to use data gathered simultaneously from ... Read more >>

BMJ Open (BMJ open)
[2020, 10(10):e037295]

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Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

Nicola Felix Mueller, Cassia Wagner, Chris Frazar, Pavitra Roychoudhury, Jover Lee, Louise Moncla, Benjamin Pelle, Matthew Richardson, Erica Ryke, Hong Xie, Lasata Shrestha, Amin Addetia, Victoria Rachleff, Nicole Lieberman, Meei-Li Huang, Romesh Gautom, Geoff Melly, Brian Hiatt, Philip Dykema, Amanda Adler, Elisabeth Brandstetter, Peter Han, Kairsten Fay, Misja Ilcisin, Kirsten Lacombe, Thomas Sibley, Melissa Truong, Caitlin Wolf, Michael Boeckh, Janet Englund, Michael Famulare, Barry Lutz, Mark Rieder, Matthew Thompson, Jeffrey Duchin, Lea Starita, Helen Chu, Jay Shendure, Keith Jerome, Scott Lindquist, Alex Greninger, Deborah Nickerson, Trevor Bedford,

The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of ... Read more >>

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Cryptic transmission of SARS-CoV-2 in Washington state.

Trevor Bedford, Alexander L Greninger, Pavitra Roychoudhury, Lea M Starita, Michael Famulare, Meei-Li Huang, Arun Nalla, Gregory Pepper, Adam Reinhardt, Hong Xie, Lasata Shrestha, Truong N Nguyen, Amanda Adler, Elisabeth Brandstetter, Shari Cho, Danielle Giroux, Peter D Han, Kairsten Fay, Chris D Frazar, Misja Ilcisin, Kirsten Lacombe, Jover Lee, Anahita Kiavand, Matthew Richardson, Thomas R Sibley, Melissa Truong, Caitlin R Wolf, Deborah A Nickerson, Mark J Rieder, Janet A Englund, , James Hadfield, Emma B Hodcroft, John Huddleston, Louise H Moncla, Nicola F Müller, Richard A Neher, Xianding Deng, Wei Gu, Scot Federman, Charles Chiu, Jeffrey S Duchin, Romesh Gautom, Geoff Melly, Brian Hiatt, Philip Dykema, Scott Lindquist, Krista Queen, Ying Tao, Anna Uehara, Suxiang Tong, Duncan MacCannell, Gregory L Armstrong, Geoffrey S Baird, Helen Y Chu, Jay Shendure, Keith R Jerome,

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 ... Read more >>

Science (Science (New York, N.Y.))
[2020, 370(6516):571-575]

Cited: 1 time

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Two-Fluorophore Mobile Phone Imaging of Biplexed Real-Time NAATs Overcomes Optical Artifacts in Highly Scattering Porous Media.

Kamal G Shah, Sujatha Kumar, Vidhi Singh, Louise Hansen, Erin Heiniger, Joshua D Bishop, Barry Lutz, Paul Yager,

Nucleic acid amplification tests (NAATs) are common in laboratory and clinical settings because of their low time to result and exquisite sensitivity and specificity. Laboratory NAATs include onboard positive controls to reduce false negatives and specialized hardware to enable real-time fluorescence detection. Recent efforts to translate NAATs into at-home tests ... Read more >>

Anal Chem (Analytical chemistry)
[2020, 92(19):13066-13072]

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Near point-of-care, point-mutation test to detect drug resistance in HIV-1: a validation study in a Mexican cohort.

Nuttada Panpradist, Ingrid A Beck, Parker S Ruth, Santiago Ávila-Ríos, Claudia García-Morales, Maribel Soto-Nava, Daniela Tapia-Trejo, Margarita Matías-Florentino, Hector E Paz-Juarez, Silvia Del Arenal-Sanchez, Gustavo Reyes-Terán, Barry R Lutz, Lisa M Frenkel,

OBJECTIVE:Pretreatment HIV-drug resistance (PDR, HIVDR) to non-nucleoside reverse transcriptase inhibitors (NNRTIs) is increasing globally. NNRTIs continue to be used as first-line antiretroviral therapy (ART) in some communities due to the cost of dolutegravir-based ART or dolutegravir-associated adverse events. A simplified version of the oligonucleotide ligation assay (OLA) - 'OLA-Simple' - ... Read more >>

AIDS (AIDS (London, England))
[2020, 34(9):1331-1338]

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Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform.

Helen Y Chu, Janet A Englund, Lea M Starita, Michael Famulare, Elisabeth Brandstetter, Deborah A Nickerson, Mark J Rieder, Amanda Adler, Kirsten Lacombe, Ashley E Kim, Chelsey Graham, Jennifer Logue, Caitlin R Wolf, Jessica Heimonen, Denise J McCulloch, Peter D Han, Thomas R Sibley, Jover Lee, Misja Ilcisin, Kairsten Fay, Roy Burstein, Beth Martin, Christina M Lockwood, Matthew Thompson, Barry Lutz, Michael Jackson, James P Hughes, Michael Boeckh, Jay Shendure, Trevor Bedford, ,

N Engl J Med (The New England journal of medicine)
[2020, 383(2):185-187]

Cited: 12 times

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Leveraging UMLS-driven NLP to enhance identification of influenza predictors derived from electronic medical record data

Kari Stephens, Margaret Au, Meliha Yetisgen, Barry Lutz, Monica Zigman Suchsland, Mark Ebell, Matthew Thompson,

<h4>ABSTRACT</h4> <h4>Objective</h4> Multiple clinical prediction rules have been developed, but lack validation. This study aims to identify a set of prediction algorithms for influenza, based on electronic health record (EHR) structured data and clinical notes derived data using Unified Medical Language System (UMLS) driven natural language processing (NLP). <h4>Materials and ... Read more >>

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The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

, Helen Chu, Michael Boeckh, Janet Englund, Michael Famulare, Barry Lutz, Deborah Nickerson, Mark Rieder, Lea Starita, Jay Shendure, Trevor Bedford, Amanda Adler, Elisabeth Brandstetter, Chris Frazar, Peter Han, Reena Gulati, James Hadfield, Michael Jackson, Anahita Kiavand, Louise Kimball, Kirsten Lacombe, Jennifer Logue, Victoria Lyon, Kira Newman, Thomas Sibley, Monica Zigman Suchsland, Caitlin Wolf, ,

<h4>Introduction</h4> Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterize, and potentially contain new and emerging influenza strains at a population level. The objective of this study is to use data gathered simultaneously from community and ... Read more >>

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Diagnostic accuracy of an app-guided, self-administered test for influenza among individuals presenting to general practice with influenza-like illness: study protocol

Victoria Lyon, Monica Zigman Suchsland, Monique Chilver, Nigel Stocks, Barry Lutz, Philip Su, Shawna Cooper, Chunjong Park, Libby Rose Lavitt, Alex Mariakakis, Shwetak Patel, Chelsey Graham, Mark Rieder, Cynthia LeRouge, Matthew Thompson,

Introduction Diagnostic tests for influenza in Australia are currently only authorised for use in clinical settings. At-home diagnostic testing for influenza could reduce the need for patient contact with healthcare services, which potentially could contribute to symptomatic improvement and reduced spread of influenza. We aim to determine the accuracy of ... Read more >>

BMJ Open (BMJ open)
[2020, 10(11):]

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1775. A Community-wide Study to Evaluate the Accuracy of Self-testing for Influenza: Works in Progress.

Matthew Thompson, Monica L Zigman Suchsland, Victoria Lyon, Enos Kline, ShiChu Huang, Helen Y Chu, Mark Rieder, Lea Starita, Jeris Bosua, Barry R Lutz,

AbstractBackgroundSeasonal influenza (flu) occurs annually, causing disease with substantial morbidity and mortality. Currently, flu is suspected from clinical features, but requires a laboratory test to confirm infection. No influenza tests in the United States are approved for use outside of clinical settings. We aimed to determine the accuracy of influenza ... Read more >>

Open Forum Infect Dis (Open forum infectious diseases)
[2019, 6(Suppl 2):S654-S654]

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OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories.

Nuttada Panpradist, Ingrid A Beck, Justin Vrana, Nikki Higa, David McIntyre, Parker S Ruth, Isaac So, Enos C Kline, Ruth Kanthula, Annie Wong-On-Wing, Jonathan Lim, Daisy Ko, Ross Milne, Theresa Rossouw, Ute D Feucht, Michael Chung, Gonzague Jourdain, Nicole Ngo-Giang-Huong, Laddawan Laomanit, Jaime Soria, James Lai, Eric D Klavins, Lisa M Frenkel, Barry R Lutz,

<h4>Background</h4>HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels.<h4>Methods</h4>The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated ... Read more >>

EBioMedicine (EBioMedicine)
[2019, 50:34-44]

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LB21. The Seattle Flu Study: A Community-Based Study of Influenza.

Helen Y Chu, Helen Y Chu, Michael Boeckh, Michael Boeckh, Janet A Englund, Janet A Englund, Michael Famulare, Barry R Lutz, Barry R Lutz, Deborah A Nickerson, Mark Rieder, Mark Rieder, Lea Starita, Lea Starita, Matthew Thompson, Matthew Thompson, Jay Shendure, Trevor Bedford, Amanda Adler, Elisabeth Brandstetter, Elisabeth Brandstetter, Jeris Bosua, Jeris Bosua, Christian D Frazar, Peter D Han, Reena Gulati, James Hadfield, ShiChu Huang, Michael L Jackson, Michael L Jackson, Anahita Kiavand, Louise E Kimball, Louise E Kimball, Kirsten Lacombe, Kirsten Lacombe, Jennifer Logue, Jennifer Logue, Victoria Lyon, Thomas R Sibley, Monica L Zigman Suchsland, Monica L Zigman Suchsland, Caitlin R Wolf, Caitlin R Wolf,

AbstractBackgroundInfluenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect and contain new and emerging flu strains at a population level. The objective of this study was to use data gathered simultaneously from community and hospital sites to ... Read more >>

Open Forum Infect Dis (Open forum infectious diseases)
[2019, 6(Suppl 2):S1002-S1002]

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Analytical Comparison of Methods for Extraction of Short Cell-Free DNA from Urine.

Amy Oreskovic, Norman D Brault, Nuttada Panpradist, James J Lai, Barry R Lutz,

Urine cell-free DNA (cfDNA) is a valuable noninvasive biomarker for cancer mutation detection, infectious disease diagnosis (eg, tuberculosis), organ transplantation monitoring, and prenatal screening. Conventional silica DNA extraction does not efficiently capture urine cfDNA, which is dilute (ng/mL) and highly fragmented [30 to 100 nucleotides (nt)]. The clinical sensitivity of ... Read more >>

J Mol Diagn (The Journal of molecular diagnostics : JMD)
[2019, 21(6):1067-1078]

Cited: 2 times

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Threshold-Based Quantification in a Multiline Lateral Flow Assay via Computationally Designed Capture Efficiency.

David J Gasperino, Daniel Leon, Barry Lutz, David M Cate, Kevin P Nichols, David Bell, Bernhard H Weigl,

Lateral flow assays (LFAs) are widely used for yes/no detection of analytes, but they are not well-suited for quantification. We show that the sensitivity of the test line in a lateral flow assay can be tuned to appear at a specific sample concentration by varying the density of capture molecules ... Read more >>

Anal Chem (Analytical chemistry)
[2018, 90(11):6643-6650]

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Frequency tuning allows flow direction control in microfluidic networks with passive features.

Rahil Jain, Barry Lutz,

Frequency tuning has emerged as an attractive alternative to conventional pumping techniques in microfluidics. Oscillating (AC) flow driven through a passive valve can be rectified to create steady (DC) flow, and tuning the excitation frequency to the characteristic (resonance) frequency of the underlying microfluidic network allows control of flow magnitude ... Read more >>

Lab Chip (Lab on a chip)
[2017, 17(9):1552-1558]

Cited: 1 time

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A rapid, instrument-free, sample-to-result nucleic acid amplification test.

Lisa K Lafleur, Joshua D Bishop, Erin K Heiniger, Ryan P Gallagher, Maxwell D Wheeler, Peter Kauffman, Xiaohong Zhang, Enos C Kline, Joshua R Buser, Sujatha Kumar, Samantha A Byrnes, Nicolaas M J Vermeulen, Noah K Scarr, Yevgeniy Belousov, Walt Mahoney, Bhushan J Toley, Paula D Ladd, Barry R Lutz, Paul Yager,

The prototype demonstrated here is the first fully integrated sample-to-result diagnostic platform for performing nucleic acid amplification tests that requires no permanent instrument or manual sample processing. The multiplexable autonomous disposable nucleic acid amplification test (MAD NAAT) is based on two-dimensional paper networks, which enable sensitive chemical detection normally reserved ... Read more >>

Lab Chip (Lab on a chip)
[2016, 16(19):3777-3787]

Cited: 29 times

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Flow control using audio tones in resonant microfluidic networks: towards cell-phone controlled lab-on-a-chip devices.

Reid H Phillips, Rahil Jain, Yoni Browning, Rachana Shah, Peter Kauffman, Doan Dinh, Barry R Lutz,

Fluid control remains a challenge in development of portable lab-on-a-chip devices. Here, we show that microfluidic networks driven by single-frequency audio tones create resonant oscillating flow that is predicted by equivalent electrical circuit models. We fabricated microfluidic devices with fluidic resistors (R), inductors (L), and capacitors (C) to create RLC ... Read more >>

Lab Chip (Lab on a chip)
[2016, 16(17):3260-3267]

Cited: 1 time

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Comparison of point-of-care-compatible lysis methods for bacteria and viruses.

Erin K Heiniger, Joshua R Buser, Lillian Mireles, Xiaohong Zhang, Paula D Ladd, Barry R Lutz, Paul Yager,

Nucleic acid sample preparation has been an especially challenging barrier to point-of-care nucleic acid amplification tests in low-resource settings. Here we provide a head-to-head comparison of methods for lysis of, and nucleic acid release from, several pathogenic bacteria and viruses-methods that are adaptable to point-of-care usage in low-resource settings. Digestion ... Read more >>

J Microbiol Methods (Journal of microbiological methods)
[2016, 128:80-87]

Cited: 5 times

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A physical framework for implementing virtual models of intracranial pressure and cerebrospinal fluid dynamics in hydrocephalus shunt testing.

Pranav Venkataraman, Samuel R Browd, Barry R Lutz,

OBJECTIVE The surgical placement of a shunt designed to resolve the brain's impaired ability to drain excess CSF is one of the most common treatments for hydrocephalus. The use of a dynamic testing platform is an important part of shunt testing that can faithfully reproduce the physiological environment of the ... Read more >>

J Neurosurg Pediatr (Journal of neurosurgery. Pediatrics)
[2016, 18(3):296-305]

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Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation.

Nuttada Panpradist, Ingrid A Beck, Michael H Chung, James N Kiarie, Lisa M Frenkel, Barry R Lutz,

Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug ... Read more >>

PLoS One (PloS one)
[2016, 11(1):e0145962]

Cited: 8 times

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Isothermal strand displacement amplification (iSDA): a rapid and sensitive method of nucleic acid amplification for point-of-care diagnosis.

Bhushan J Toley, Isabela Covelli, Yevgeniy Belousov, Sujatha Ramachandran, Enos Kline, Noah Scarr, Nic Vermeulen, Walt Mahoney, Barry R Lutz, Paul Yager,

We present a method of rapid isothermal amplification of DNA without initial heat denaturation of the template, and methods and probes for (a) real-time fluorescence detection and (b) lateral flow detection of amplicons. Isothermal strand displacement amplification (iSDA) can achieve >10(9)-fold amplification of the target sequence in <20 minutes at ... Read more >>

Analyst (The Analyst)
[2015, 140(22):7540-7549]

Cited: 21 times

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An update on research priorities in hydrocephalus: overview of the third National Institutes of Health-sponsored symposium "Opportunities for Hydrocephalus Research: Pathways to Better Outcomes".

James P McAllister, Michael A Williams, Marion L Walker, John R W Kestle, Norman R Relkin, Amy M Anderson, Paul H Gross, Samuel R Browd, ,

Building on previous National Institutes of Health-sponsored symposia on hydrocephalus research, "Opportunities for Hydrocephalus Research: Pathways to Better Outcomes" was held in Seattle, Washington, July 9-11, 2012. Plenary sessions were organized into four major themes, each with two subtopics: Causes of Hydrocephalus (Genetics and Pathophysiological Modifications); Diagnosis of Hydrocephalus (Biomarkers ... Read more >>

J Neurosurg (Journal of neurosurgery)
[2015, 123(6):1427-1438]

Cited: 24 times

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