A5045365994- SARS-CoV-2 detection and testing
- Cancer Genomics and Diagnostics
- Biosensors and Analytical Detection
- SARS-CoV-2 and COVID-19 Research
- Renal Transplantation Outcomes and Treatments
- Pancreatic and Hepatic Oncology Research
- Mycobacterium research and diagnosis
- Advanced biosensing and bioanalysis techniques
- Single-cell and spatial transcriptomics
- COVID-19 diagnosis using AI
- Respiratory viral infections research
- Blood groups and transfusion
- Lymphadenopathy Diagnosis and Analysis
- Diagnosis and treatment of tuberculosis
- Molecular Biology Techniques and Applications
- Genomics and Phylogenetic Studies
- Genetic factors in colorectal cancer
University of Washington
2019-2022
A unique four-plexed RT-LAMP test kit operated by health workers can provide faster, more sensitive results than laboratory tests.
BackgroundDetection of SARS-CoV-2 infections is important for treatment, isolation infected and exposed individuals, contact tracing. RT-qPCR the "gold-standard" method to sensitively detect RNA, but most laboratory-developed assays involve complex steps. Here, we aimed simplify by streamlining reaction setup, eliminating RNA extraction, proposing reduced-cost detection workflows that avoid need expensive qPCR instruments.MethodA low-cost RT-PCR based "kit" was developed faster turnaround...
The increasing prevalence of variant lineages during the COVID-19 pandemic has potential to disrupt molecular diagnostics due mismatches between primers and templates. Point-of-care diagnostics, which often lack complete functionality their high-throughput laboratory counterparts, are particularly susceptible this type disruption, can result in false-negative results. To address challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed...
Transrenal urine cell-free DNA (cfDNA) is a promising tuberculosis (TB) biomarker, but challenging to detect because of the short length (<100 bp) and low concentration TB-specific fragments. We aimed improve diagnostic sensitivity TB cfDNA by increasing recovery fragments during sample preparation.
Urine cell-free DNA (cfDNA) is a valuable non-invasive biomarker with broad potential clinical applications, but there no consensus on its optimal pre-analytical methodology, including the extraction step. Due to short length (majority of fragments <100 bp) and low concentration (ng/mL), urine cfDNA not efficiently recovered by conventional silica-based methods. To maximize sensitivity assays, we developed an ultrasensitive hybridization method that uses sequence-specific oligonucleotide...
The increasing prevalence of variant lineages during the COVID-19 pandemic has potential to disrupt molecular diagnostics due mismatches between primers and templates. Point-of-care diagnostics, which often lack complete functionality their high throughput laboratory counterparts, are particularly susceptible this type disruption, can result in false negative results. To address challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed...
BackgroundUrine cell-free DNA (cfDNA) is an attractive target for diagnosing pulmonary Mycobacterium tuberculosis (MTB) infection, but has not been thoroughly characterized as a biomarker.MethodsThis study was performed to investigate the size and composition of urine cfDNA from (TB) patients with minimal bias using next-generation sequencing (NGS). A combination extraction single-stranded sequence library preparation methods demonstrated recover short, highly degraded fragments employed....
ABSTRACT Transrenal urine cell-free DNA (cfDNA) is a promising tuberculosis (TB) biomarker, but challenging to detect because of the short length (<100 bp) and low concentration TB-specific fragments. We aimed improve diagnostic sensitivity TB cfDNA by increasing recovery fragments during sample preparation. developed highly sensitive sequence-specific purification method that uses hybridization probes immobilized on magnetic beads capture (50 with 91.8% average efficiency. Combined...
This new workflow enables co-extraction of HIV and SARS-CoV2 RNAs from clinical pooled plasma/nasal secretion samples that allows sensitive detection SARS-CoV-2 infections in the patients-living with HIV.
ABSTRACT RNA amplification tests allow sensitive detection of SARS-CoV-2 infection, but their complexity and cost are prohibitive for expanding COVID-19 testing. We developed “Harmony COVID-19”, a point-of-care test using inexpensive consumables, ready-to-use reagents, simple device that processes up to 4 samples simultaneously. Our lyophilized reverse-transcription, loop-mediated isothermal (RT-LAMP) can detect as little 15 copies per reaction, it report early 17 min with high viral load (2...
Abstract Background COVID-19 pandemic interrupted routine care for individuals living with HIV, putting them at risk of becoming virologically unsuppressed and ill. Often they are high exposure to SARS-CoV-2 infection severe disease once infected. For this population, it is urgent closely monitor HIV plasma viral load ( VL ) screen SARS-COV-2 infection. Method We have developed a non-proprietary method isolate RNA from plasma, nasal secretions NS ), or both. SARS-CoV-2, human RP targets in...
Overview: This protocol describes a method for highly sensitive sequence-specific purification of short tuberculosis (TB) urine cell-free DNA (cfDNA) from large-volume (10 mL) samples. Biotinylated oligonucleotide capture probes complementary to the target interest are immobilized on streptavidin-coated magnetic beads and used capture, concentrate, purify via hybridization. improves upon analytical performance both existing silica-based extraction methods cfDNA previous hybridization...
Overview: This protocol describes a method for highly sensitive sequence-specific purification of short tuberculosis (TB) urine cell-free DNA (cfDNA) from large-volume (10 mL) samples. Biotinylated oligonucleotide capture probes complementary to the target interest are immobilized on streptavidin-coated magnetic beads and used capture, concentrate, purify via hybridization. improves upon analytical performance both existing silica-based extraction methods cfDNA previous hybridization...
ABSTRACT Urine cell-free DNA (cfDNA) presents an attractive target for diagnosing pulmonary Mycobacterium tuberculosis (TB) infection but has not been thoroughly characterized. Here, we aimed to investigate the size and composition of TB-derived urine cfDNA with minimal bias using next-generation sequencing (NGS). To enable analysis highly fragmented cfDNA, used a combination extraction (Q sepharose) single-stranded sequence library preparation methods demonstrated recover short, degraded...