A5021740624- Advanced biosensing and bioanalysis techniques
- SARS-CoV-2 detection and testing
- Biosensors and Analytical Detection
- SARS-CoV-2 and COVID-19 Research
- CRISPR and Genetic Engineering
- COVID-19 Clinical Research Studies
- COVID-19 epidemiological studies
- Immune Cell Function and Interaction
- Dental Research and COVID-19
- Single-cell and spatial transcriptomics
- Diabetes and associated disorders
- T-cell and B-cell Immunology
- Pancreatic function and diabetes
- Thermal Regulation in Medicine
- COVID-19 diagnosis using AI
- Infant Nutrition and Health
- Genomics and Phylogenetic Studies
- Climate Change and Health Impacts
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Immunotherapy and Immune Responses
- Diet and metabolism studies
- Viral gastroenteritis research and epidemiology
- Hepatitis C virus research
- Diabetes Management and Research
University of California, Berkeley
2019-2022
Innovative Genomics Institute
2020-2022
QB3
2019
San Francisco State University
2016
The primary associations of the HLA class II genes, HLA-DRB1 and HLA-DQB1, I HLA-A HLA-B, with type 1 diabetes (T1D) are well established. However, role polymorphism at HLA-DRB3, HLA-DRB4, HLA-DRB5 loci remains unclear. In two separate studies, one 500 subjects control 366 DRB1*03:01-positive samples from selected multiplex T1D families, we used Roche 454 sequencing Conexio Genomics ASSIGN ATF genotyping software analysis to analyze sequence variation these three HLA-DRB loci. Association...
Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, measurements rely on PCR followed by next-generation sequencing. However, amplification can introduce significant quantitative error. We describe REcount, a novel PCR-free direct counting method. Comparing defined plasmid pools to droplet digital data demonstrates that REcount is highly accurate and reproducible. use...
Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to outbreak prevention on college and university campuses. Here we describe the voluntary saliva program instituted at University California, Berkeley during an early period pandemic in 2020. The was administered as a research study ahead clinical implementation, enabling us launch while continuing optimize assay. Results both protocol itself participants’ experience show how succeeded providing routine,...
Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease collection and demonstrated utility detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce sensitivity. To improve test sensitivity while maintaining speed, we developed robotic method SARS-CoV-2 saliva samples with high throughput. Using this assay, the Free...
Abstract Background Many persons with active SARS-CoV-2 infection experience mild or no symptoms, presenting barriers to COVID-19 prevention. Regular temperature screening is nonetheless used in some settings, including university campuses, reduce transmission potential. We evaluated the potential impact of this strategy using a prospective university-affiliated cohort. Methods Between June and August 2020, 2912 participants were enrolled tested for by PCR at least once (median: 3, range:...
Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease collection and demonstrated utility detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce sensitivity. To improve test sensitivity while maintaining speed, we developed robotic method SARS-CoV-2 saliva samples with high throughput. Using this assay, the Free...
Stable dry-state storage of DNA is desirable to minimize required space and reduce electrical shipping costs. purified from various commercially available stabilization matrices has been used successfully in downstream molecular applications (e.g., quantitative polymerase chain reaction [qPCR], microarray, sequence-based genotyping). However, standard conditions still include freezing eluted aqueous buffers or nuclease-free water. Broad implementation dry-state, long-term requires...
Summary Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has played a vital role in outbreak prevention on college and university campuses. Here we describe the voluntary saliva program instituted at University California, Berkeley during an early period pandemic 2020. The was administered as research study ahead clinical implementation, enabling us to launch while continuing optimize assay. Results both protocol itself participants’ experience show how succeeded...
Clinical and surveillance testing for the SARS-CoV-2 virus relies overwhelmingly on RT-qPCR-based diagnostics, yet several popular assays require 2–3 separate reactions or rely detection of a single viral target, which adds significant time, cost, risk false-negative results. Furthermore, multiplexed RT-qPCR tests that detect at least two genes in reaction are typically not affordable large scale clinical adaptable to multiple PCR machines plate layouts. We developed assay using Luna Probe...
Hepatitis B virus (HBV) vaccine escape mutants (VEM) are increasingly described, threatening progress in control of this worldwide. Here we studied the relationship between host genetic variation, immunogenicity and viral sequences implicating VEM emergence. In a cohort 1,096 Bangladeshi children, identified human leukocyte antigen (HLA) variants associated with response antigens. Using an HLA imputation panel 9,448 south Asian individuals
Abstract Commonly used RT-qPCR-based SARS-CoV-2 diagnostics require 2-3 separate reactions or rely on detection of a single viral target, adding time and cost risk false-negative results. Currently, no test combines widely E- N-gene targets sample control in single, multiplexed reaction. We developed the IGI-LuNER RT-qPCR assay using Lu na Probe Universal One-Step master mix with publicly available primers probes to detect N gene, E human RNase P ( NER ). This combined, cost-effective can be...
ABSTRACT Background Many persons with active SARS-CoV-2 infection experience mild or no symptoms, presenting barriers to COVID-19 prevention. Regular temperature screening is nonetheless used in some settings, including University campuses, reduce transmission potential. We evaluated the potential impact of this strategy using a prospective University-affiliated cohort. Methods Between June and August 2020, 2,912 participants were enrolled tested for by PCR at least once (median: 3, range:...
Backgroundgenetic susceptibility to infection is mediated by numerous host factors, including the highly diverse, classical human leukocyte antigen (HLA) genes, which are critical genetic determinants of immunity. We systematically evaluated effect HLA alleles and haplotypes on 12 common enteric infections in children during first year life an urban slum Dhaka, Bangladesh.Methodsa birth cohort 601 Bangladeshi infants was prospectively monitored for diarrhoeal disease. Each stool sample...
Turnover is a fact of life for any project, and academic research teams can face particularly high levels people who come go through the duration project. In this article, we discuss challenges turnover some potential practices helping manage it, computational- data-intensive projects. The topics include establishing implementing data management plans, file format standardization, workflow process documentation, clear team roles, check-in check-out procedures.
Abstract Quantification of DNA sequence tags associated with engineered genetic constructs underlies many genomics measurements. Typically, such measurements are done using PCR to enrich and add adapters, followed by next-generation sequencing (NGS). However, amplification can introduce significant quantitative error into these Here we describe REcount, a novel PCR-free direct counting method for NGS-based quantification constructs. By comparing defined plasmid pools droplet digital data,...
Abstract The cellular composition of tumors is now recognized as an essential phenotype, with implications to diagnostic, progression and therapy efficacy. A tool for accurate profiling the tumor microenvironment lacking, single-cell methods computational approaches are not applicable or suffer from low accuracy. Here we present EpiSort , a novel strategy based on targeted bisulfite sequencing, which allows enumeration 23 cell types may be cancer studies.