A5041479083- Genetic factors in colorectal cancer
- Cancer Genomics and Diagnostics
- Colorectal Cancer Treatments and Studies
- DNA and Biological Computing
- Cellular Automata and Applications
- Single-cell and spatial transcriptomics
- Gut microbiota and health
- Algorithms and Data Compression
- Advanced Data Storage Technologies
- Colorectal Cancer Screening and Detection
- Lymphoma Diagnosis and Treatment
- T-cell and B-cell Immunology
- Error Correcting Code Techniques
- Virus-based gene therapy research
- Bacteriophages and microbial interactions
- Immune Cell Function and Interaction
- Respiratory viral infections research
- Molecular Biology Techniques and Applications
- Pancreatic and Hepatic Oncology Research
- Cancer-related molecular mechanisms research
- Gastric Cancer Management and Outcomes
- Cancer Cells and Metastasis
- Genomic variations and chromosomal abnormalities
Stanford University
2017-2022
Palo Alto University
2018
Abstract Cancer cell lines are not homogeneous nor they static in their genetic state and biological properties. Genetic, transcriptional phenotypic diversity within contributes to the lack of experimental reproducibility frequently observed tissue-culture-based studies. While cancer line heterogeneity has been generally recognized, there no studies which quantify number clones that coexist distinguishing characteristics. We used a single-cell DNA sequencing approach characterize cellular...
With the amount of data being stored increasing rapidly, there is significant interest in exploring alternative storage technologies. In this context, DNA-based systems can offer significantly higher densities (petabytes/gram) and durability (thousands years) than current Specifically, DNA has been found to be stable over extended periods time which demonstrated analysis organisms long since extinct. Recent advances sequencing synthesis pipelines have made a promising candidate for...
As magnetization and semiconductor based storage technologies approach their limits, bio-molecules, such as DNA, have been identified promising media for future systems, due to high density (petabytes/gram) long-term durability (thousands of years). Furthermore, nanopore DNA sequencing enables high-throughput using devices small a USB thumb drive thus is ideally suited applications. Due the insertion/deletion error rates associated with base-called reads, current approaches rely heavily on...
ABSTRACT Sequencing the genomes of individual cancer cells provides highest resolution intratumoral heterogeneity. To enable high throughput single cell DNA-Seq across thousands per sample, we developed a droplet-based, automated partitioning technology for whole genome sequencing. We applied this approach on set gastric lines and primary tumor. In parallel, conducted separate RNA-Seq analysis these same cancers used copy number to compare results. This joint study, covering transcriptomes,...
Dysbioisis is an imbalance of organ's microbiome and plays a role in colorectal cancer pathogenesis. Characterizing the bacteria microenvironment through genome sequencing has advantages compared to culture-based profiling. However, there are notable technical analytical challenges characterizing universal features tumor microbiomes. Colorectal tumors demonstrate variation among different studies across individual patients. To address these issues, we conducted computational study determine...
DNA copy number aberrations (CNA) are frequently observed in colorectal cancers (CRC). There is an urgent need for CNA-based biomarkers clinics,. n For Stage III CRC, if combined with imaging or pathologic evidence, these markers promise more precise care. We conducted this specific biomarker discovery a cohort of 134 CRCs, and newly developed high-efficiency CNA profiling protocol. Specifically, we the protocol tumor-normal matched tissue samples based on low-coverage clinical whole-genome...
New approaches for genomic DNA/RNA detection are in high demand order to provide controls existing enzymatic technologies and create alternatives emerging applications. In particular, there is an unmet need rapid, reliable of short RNA regions which could open up new opportunities transcriptome analysis, virology, other fields. Herein, we report the first time a "click" chemistry approach oligonucleotide probe elongation as novel specifically detect viral sequence. We hybridized library...
Abstract With the amount of data being stored increasing rapidly, there is significant interest in exploring alternative storage technologies. In this context, DNA-based systems can offer significantly higher densities (petabytes/gram) and durability (thousands years) than current Specifically, DNA has been found to be stable over extended periods time which demonstrated analysis organisms long since extinct. Recent advances sequencing synthesis pipelines have made a promising candidate for...
ABSTRACT As magnetization and semiconductor based storage technologies approach their limits, bio-molecules, such as DNA, have been identified promising media for future systems, due to high density (petabytes/gram) long-term durability (thousands of years). Furthermore, nanopore DNA sequencing enables high-throughput using devices small a USB thumb drive thus is ideally suited applications. Due the insertion/deletion error rates associated with basecalled reads, current approaches rely...
Abstract Formalin-fixed, paraffin-embedded (FFPE) storage is a universally-adopted, cost-effective and long-term solution for tissue storage. Given the abundance of FFPE clinical samples, they provide good source genome sequencing studies. However, extraction nucleic acids from tissues yield highly fragmented DNA variable quality. The poor quality low make it difficult to generate adequate libraries genomic For population cancer study, we optimized procedure whole-genome on tumor normal...
Abstract Colorectal cancers with loss of DNA mismatch repair display microsatellite instability (MSI). These tumors have a better prognosis and an improved response rate to immune check point therapies compared non-MSI tumors. MSI-positive demonstrate surprising range somatic alterations in repetitive sequence tracts. For example, elevated at selected tetranucleotide repeats (EMAST) that may be related functional MSH3. Current MSI tests are based on PCR capillary electrophoresis. This...
ABSTRACT Recent evidence suggests that dysbiosis, an imbalance of microbiota, is associated with increased risk colorectal cancer. Diverse microbial organisms are physically the cells found in tumor biopsies. Characterizing this mucosa-associated microbiome through genome sequencing has advantages compared to culture-based profiling. However, there notable challenges accurately characterizing features microbiomes methods like transcriptome sequencing. Most sequence reads originate from host....
ABSTRACT DNA copy number aberrations (CNA) were frequently observed in colorectal cancers (CRC) . There is an urgent call for CNA-based biomarkers clinics, particular Stage III CRC, if combined with imaging or pathologic evidence, promise more precise care at the timing. We conducted this specific biomarker discovery a cohort of 134 CRCs, and newly developed high-efficiency CNA profiling protocol. Specifically, we protocol tumor-normal matched tissue samples based on low-coverage clinical...
ABSTRACT Background Gastric cancer (GC) is a leading cause of global morbidity and mortality. Developing information systems which integrate clinical genomic data may accelerate discoveries to improve prevention, detection, treatment. To support translational research in GC, we developed the GC Registry (GCR) , North American repository genomics data. Methods GCR national registry with online self-enrollment. Entry criteria into included following: (1) diagnosis (2) history first-or...
Gastric cancer is a leading cause of morbidity and mortality. Developing information systems which integrate clinical genomic data may accelerate discoveries to improve prevention, detection, treatment. To support translational research in gastric cancer, we developed the Cancer Registry (GCR), North American repository genomics data.Participants self-enrolled online. Entry criteria into GCR included following: (i) diagnosis (ii) history first- or second-degree relative, (iii) known germline...