A5078642801- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Advanced biosensing and bioanalysis techniques
- Cancer Research and Treatments
- Protist diversity and phylogeny
- Evolution and Genetic Dynamics
- DNA Repair Mechanisms
- Environmental DNA in Biodiversity Studies
- Amoebic Infections and Treatments
- Renal and related cancers
- Genomics and Rare Diseases
- Microtubule and mitosis dynamics
Broad Institute
2021-2024
Massachusetts Institute of Technology
2023
University of Pittsburgh
1987
Liquid biopsies enable early detection and monitoring of diseases such as cancer, but their sensitivity remains limited by the scarcity analytes cell-free DNA (cfDNA) in blood. Improvements to have primarily relied on enhancing sequencing technology ex vivo. We sought transiently augment level circulating tumor (ctDNA) a blood draw attenuating its clearance report two intravenous priming agents given 1 2 hours before recover more ctDNA. Our consist nanoparticles that act cells responsible...
Abstract Detecting mutations from single DNA molecules is crucial in many fields but challenging. Next-generation sequencing (NGS) affords tremendous throughput cannot directly sequence double-stranded (‘single duplexes’) to discern the true on both strands. Here we present Concatenating Original Duplex for Error Correction (CODEC), which confers duplex resolution NGS. CODEC 1,000-fold higher accuracy than NGS, using up 100-fold fewer reads sequencing. revealed mutation frequencies of 2.72 ×...
Blood-based, or "liquid," biopsies enable minimally invasive diagnostics but have limits on sensitivity due to scarce cell-free DNA (cfDNA). Improvements primarily relied enhancing sequencing technology ex vivo . Here, we sought augment the level of circulating tumor (ctDNA) detected in a blood draw by attenuating clearance cfDNA We report first-in-class intravenous DNA-binding priming agent given 2 hours prior recover more cfDNA. The antibody minimizes nuclease digestion and organ uptake...
Abstract Accurate DNA sequencing is crucial in biomedicine. Underlying the most accurate methods assumption that a mutation true if altered bases are present on both strands of duplex. We now show this can be wrong. establish current to prepare for sequencing, via ‘End Repair/dA-Tailing,’ may substantially resynthesize strands, leading amplifiable lesions or alterations one strand become indiscernible from mutations strands. Indeed, we discovered 7–17% and 32–57% interior ‘duplex base pairs’...
Three of four mRNAs that are specific to the differentiation Naegleria gruberi amebae into flagellates (Mar, J., J. H. Lee, D. Shea, and C. Walsh, 1986, Cell Biol., 102:353-361) have been identified as coding for flagellar proteins. The products these mRNAs, which coordinately regulated during differentiation, were by in vitro translation hybrid-selected RNA followed two-dimensional gel electrophoresis antibody binding. Six cross-hybridizing clones complementary a 1.7-kb (class II) all...
We have examined the nature of requirement for RNA synthesis during differentiation Naegleria gruberi amebae into flagellates (Fulton, C., and C. Walsh, 1980, J. Cell Biol., 85:346-360) by looking poly(A)+RNAs that are specific to differentiating cells. A cDNA library prepared from poly(A)+RNA extracted cells 40 min after initiation (40-min RNA), time when formation flagella becomes insensitive inhibitors synthesis, was cloned pBR322. Recombinant clones were screened sequences complementary...
Abstract The ability to assay large numbers of low-abundance mutations is crucial in biomedicine. Yet, the technical hurdles sequencing multiple at extremely high depth and accuracy remain daunting. For low-level mutations, it’s either ‘depth or breadth’ but not both. Here, we report a simple powerful approach accurately track thousands distinct with minimal reads. Our technique called MAESTRO ( m inor llele e nriched s equencing t hrough r ecognition o ligonucleotides) employs...
Abstract Liquid biopsies using cell-free DNA (cfDNA) enable non-invasive detection and characterization of disease. Advances in sequencing methods have significantly improved the performance liquid biopsies. Yet, despite these advances, sensitivity remains a fundamental challenge. In oncology, circulating tumor (ctDNA) screening tests only detect 20-40% stage I tumors for minimal residual disease 25-50% after surgery. The major barrier to better is intrinsic low level ctDNA plasma. Physical...
Abstract Detecting mutations as rare a single molecule is crucial in many fields such cancer diagnostics and aging research but remains challenging. Third generation sequencers can read double-stranded DNA (a ‘single duplex’) whole to identify true on both strands apart from false either strand with limited accuracy throughput. Although next sequencing (NGS) track dissociated Duplex Sequencing, the need sequence each independently severely diminishes its Here, we developed hybrid method...
ABSTRACT Accurate DNA sequencing is crucial in biomedicine. Underlying the most accurate methods assumption that a mutation true if altered bases are present on both strands of duplex. We now show this can be wrong. establish current to prepare for sequencing, via ‘End Repair/dA-Tailing,’ may substantially resynthesize strands, leading amplifiable lesions or alterations one strand become indiscernible from mutations strands. Indeed, we discovered 7-17% and 32-57% interior ‘duplex base pairs’...
Abstract Liquid biopsy measurements, such as analysis of circulating tumor DNA (ctDNA) shed by cancer cells, have garnered significant attention for their potential to empower the field precision oncology. Given that ctDNA tests could enable minimally invasive monitoring and molecular profiling disease, they are being investigated use in earlier detection via pan-cancer screening tests, tracking evolution inform therapy selection, making treatment decisions during minimal residual disease...
Liquid biopsies are enabling minimally invasive monitoring and molecular profiling of diseases across medicine, but their sensitivity remains limited by the scarcity cell-free DNA (cfDNA) in blood. Here, we report an intravenous priming agent that is given prior to a blood draw increase abundance cfDNA circulation. Our consists nanoparticles act on cells responsible for clearance slow down uptake. In tumor-bearing mice, this increases recovery circulating tumor (ctDNA) up 60-fold improves...