A5054082017- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- Acute Myeloid Leukemia Research
- DNA Repair Mechanisms
- Molecular Biology Techniques and Applications
- Genetic factors in colorectal cancer
- Carcinogens and Genotoxicity Assessment
- Genomics and Phylogenetic Studies
- Advanced biosensing and bioanalysis techniques
- Mitochondrial Function and Pathology
- Evolution and Genetic Dynamics
- Chronic Myeloid Leukemia Treatments
- Acute Lymphoblastic Leukemia research
- Colorectal Cancer Treatments and Studies
- Lung Cancer Treatments and Mutations
- Multiple Myeloma Research and Treatments
- CAR-T cell therapy research
- Genomic variations and chromosomal abnormalities
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- Cancer, Hypoxia, and Metabolism
- Epigenetics and DNA Methylation
- bioluminescence and chemiluminescence research
- Hematopoietic Stem Cell Transplantation
Blaze Bioscience (United States)
2017-2025
University of Washington
2009-2024
University of Washington Medical Center
2014-2024
Fred Hutch Cancer Center
2006-2023
Seattle University
2014
Apath (United States)
2009-2012
Brandeis University
2006
Microscale (United States)
2006
Next-generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity generate hundreds of billions nucleotides sequence in a single experiment, error rate ∼1% results millions mistakes. These scattered errors can be tolerated some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations accuracy, we...
Mitochondrial DNA (mtDNA) is believed to be highly vulnerable age-associated damage and mutagenesis by reactive oxygen species (ROS). However, somatic mtDNA mutations have historically been difficult study because of technical limitations in accurately quantifying rare mutations. We applied the sensitive Duplex Sequencing methodology, which can detect a single mutation among >107 wild type molecules, sequence purified from human brain tissue both young old individuals with unprecedented...
Persistence of FLT3 internal tandem duplication (ITD) in adults with acute myeloid leukemia (AML) first complete remission (CR) prior to allogeneic hematopoietic cell transplant (HCT) is associated increased relapse and death after transplant, but the association between level measurable residual disease (MRD) detected clinical outcome unknown.
Significance Error-corrected next-generation sequencing (ecNGS) can be used to rapidly detect and quantify the in vivo mutagenic impact of environmental exposures or endogenous processes any tissue, from species, at genomic location. The greater speed, higher scalability, richer data outputs, cross-species cross-locus applicability ecNGS compared existing methods make it a powerful new tool for mutational research, regulatory safety testing, emerging clinical applications.
High-accuracy next-generation DNA sequencing promises a paradigm shift in early cancer detection by enabling the identification of mutant molecules minimally invasive body fluid samples. We demonstrate 80% sensitivity for ovarian using ultra-accurate Duplex Sequencing to identify TP53 mutations uterine lavage. However, addition tumor DNA, we also detect low-frequency nearly all lavages from women with and without cancer. These increase age share selection traits clonal commonly found human...
Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in female germline. Here we investigate how mismatching between mitochondrial ancestry impacts somatic evolution of different tissues throughout ageing. We used ultrasensitive duplex sequencing to profile ~2.5 million across five haplotypes three young aged mice, cataloguing ~1.2 ultralow-frequency inherited mutations, which 81,097 unique. identify haplotype-specific mutational...
Genome instability is regarded as a hallmark of cancer. Human tumors frequently carry clonally expanded mutations in their mitochondrial DNA (mtDNA), some which may drive cancer progression and metastasis. The high prevalence clonal tumor mtDNA has commonly led to the assumption that genome genetically unstable, yet this hypothesis not been experimentally tested. In study, we directly measured frequency non-clonal (random) de novo single base substitutions human colorectal cancers....
Exposure to environmental mutagens increases the risk of cancer and genetic disorders. We used Duplex Sequencing (DS), a high-accuracy error-corrected sequencing technology, analyze mutation induction across twenty 2.4 kb intergenic genic targets in bone marrow MutaMouse males exposed benzo(a)pyrene (BaP), widespread pollutant. DS revealed linear dose-related mutations all with low intra-group variability. Heterochromatic regions exhibited highest frequencies (MF). C:G > A:T transversions at...
Mutagenicity testing is an essential component of health safety assessment. Duplex Sequencing (DS), emerging high-accuracy DNA sequencing technology, may provide substantial advantages over conventional mutagenicity assays. DS could be used to eliminate reliance on standalone reporter assays and mechanistic information alongside mutation frequency (MF) data. However, the performance must thoroughly assessed before it can routinely implemented for standard testing. We study spontaneous...
The presence of measurable residual disease (MRD) is strongly associated with treatment outcomes in acute myeloid leukemia (AML). Despite the correlation clinical outcomes, MRD assessment has yet to be standardized or routinely incorporated into trials and discrepancies have been observed between different techniques for assessment. In 62 patients AML, aged 18-60 years, first complete remission after intensive induction therapy on randomized phase III SWOG-S0106 trial (clinicaltrials gov....
Mutation rate is an important determinant of evolvability. The optimal mutation for different organisms during evolution has been modeled in silico and tested vivo, predominantly through pairwise comparisons. To characterize the fitness landscape across a broad range rates, we generated panel 66 DNA polymerase I mutants Escherichia coli with comparable growth properties, yet differing replication fidelities, spanning 10 3 -fold higher lower than that wild type. These strains were competed...
With the publishing of first complete whole genome a human cancer and its paired normal, we have passed key milestone in sequencing strategy. The generation such data will, thanks to technical advances, soon become commonplace. As significant number proof-of-concept studies been published, it is important analyze now likely implications these how this information might frame research near future. diversity genes mutated within individual tumor types, most striking feature all reported date,...
Human colorectal cancers (CRCs) contain both clonal and subclonal mutations. Clonal driver mutations are positively selected, present in most cells, drive malignant progression. Subclonal randomly dispersed throughout the genome, providing a vast reservoir of mutant cells that can expand, repopulate tumor, result rapid emergence resistance, as well being major contributor to tumor heterogeneity. Here, we apply duplex sequencing (DS) methodology quantify CRC with unprecedented depth (10
Next-generation sequencing methods suffer from low recovery, uneven coverage, and false mutations. DNA fragmentation by sonication is a major contributor to these problems because it produces randomly sized fragments, PCR amplification bias, end artifacts. In addition, oligonucleotide-based hybridization capture, common target enrichment method, has limited efficiency for small genomic regions, contributing recovery. This becomes critical problem in clinical applications, which value...
Chronic inflammation predisposes to a variety of human cancers. Affected tissues slowly accumulate mutations, some which affect growth regulation and drive successive waves clonal evolution, whereas far greater number are functionally neutral serve only passively mark expanding clones. Ulcerative colitis (UC) is an inflammatory bowel disease, in up 10% patients eventually develop colon cancer. Here we have mapped mutations hypermutable intergenic intronic polyguanine tracts with UC delineate...
The organotypic human air-liquid-interface (ALI) airway tissue model has been used as an in vitro cell culture system for evaluating the toxicity of inhaled substances. ALI cultures are highly differentiated, which made it challenging to evaluate genetic toxicology endpoints. In current study, we assayed DNA damage with high-throughput CometChip assay and quantified mutagenesis Duplex Sequencing, error-corrected next-generation sequencing method capable detecting a single mutation per 107...
Error-corrected duplex sequencing (DS) enables direct quantification of low-frequency mutations and offers tremendous potential for chemical mutagenicity assessment. We investigated the utility DS to quantify induced mutation frequency (MF) spectrum in human lymphoblastoid TK6 cells exposed a prototypical DNA alkylating agent, N-ethyl-N-nitrosourea (ENU). Furthermore, we explored appropriate experimental parameters this application, assessed inter-laboratory reproducibility. In two...