Jesse J. Salk

Ultra-deep duplex sequencing reveals unique features of somatic evolution in the normal tissues of a family with Li-Fraumeni syndrome

Duplex sequencing of a Li-Fraumeni family links germline TP53 p.R181H to higher neutral-region mutagenesis and weaker blood TP53 selection, plus recurrent p.R248Q/W hits across proband tissues.

Alignment between Duplex Sequencing and transgenic rodent mutation assay data in the assessment of in vivo NDMA-induced mutagenesis

This study aligns Duplex Sequencing with transgenic rodent mutation assay data to assess in vivo NDMA-induced mutagenesis, finding dose-dependent mutation frequency increases and concordant benchmark dose estimates.

Dose-related Mutagenic and Clastogenic Effects of Benzofluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay

This study assesses the mutagenic and clastogenic effects of benzo[b]fluoranthene in mice using Duplex Sequencing and the micronucleus assay, showing dose-dependent increases in mutation frequency and cancer-related mutation spectra.

Adopting Duplex Sequencing Technology for Genetic Toxicity Testing: A Proof-of-Concept Mutagenesis Experiment with N-Ethyl-N-Nitrosourea (ENU)-Exposed Rats

This paper evaluates a DuplexSeq-based mutagenesis assay in ENU-exposed rats, showing early detection of mutations and reproducible results across tissues and labs.

Duplex Sequencing Provides Detailed Characterization of Mutation Frequencies and Spectra in the Bone Marrow of MutaMouse Males Exposed to Procarbazine Hydrochloride

This study uses Duplex Sequencing to assess mutation frequencies and spectra in MutaMouse bone marrow after procarbazine exposure, showing its advantages over conventional assays.

Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging

The paper examines how mitochondrial haplotype and mito-nuclear matching influence somatic mutation and selection in aging mice across tissues.

Error-corrected Duplex Sequencing enables direct detection and quantification of mutations in human TK6 cells with remarkable inter-laboratory consistency

This study demonstrates that error-corrected Duplex Sequencing reliably detects and quantifies mutations in human TK6 cells across different laboratories and time points.

svCapture: Efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing

The paper introduces svCapture, a method for detecting rare structural variant junctions with high accuracy using error-minimized capture sequencing.

Direct Quantification of in vivo Mutagenesis and Carcinogenesis Using Duplex Sequencing

This paper demonstrates that Duplex Sequencing, an error-corrected NGS method, can accurately quantify in vivo mutagenesis and early signs of carcinogenesis in mice, outperforming traditional transgenic rodent assays.

Targeted genome fragmentation with CRISPR/Cas9 improves hybridization capture, reduces PCR bias, and enables efficient high-accuracy sequencing of small targets

This paper introduces CRISPR-DS, a targeted sequencing technique that improves hybridization capture, reduces PCR bias, and enables detection of ultra-low frequency mutations.