Jesse J Salk
Affiliation: University of Washington
- Two-temperature LATE-PCR endpoint genotypingJ Aquiles Sanchez
Department of Biology, MS008, Brandeis University, Waltham, MA 02454, USA
BMC Biotechnol 6:44. 2006..Furthermore, the use of only a single colored probe for genotyping enhances the multiplex detection capacity of the assay...
- Passenger mutations as a marker of clonal cell lineages in emerging neoplasiaJesse J Salk
Department of Pathology, University of Washington School of Medicine MB 357705, 1959 NE Pacific St, Seattle, WA 98195, United States
Semin Cancer Biol 20:294-303. 2010..We discuss historical as well as contemporary approaches and consider ways in which powerful new genomic technologies might be harnessed to develop a future generation of early cancer diagnostics...
- Clonal expansions in ulcerative colitis identify patients with neoplasiaJesse J Salk
Department of Pathology, University of Washington School of Medicine, Seattle, WA 98105, USA
Proc Natl Acad Sci U S A 106:20871-6. 2009....
- Clonal expansions and short telomeres are associated with neoplasia in early-onset, but not late-onset, ulcerative colitisJesse J Salk
Department of Pathology, Department of Medicine, Department of Biostatistics, and Division of Gastroenterology, University of Washington, School of Medicine, Seattle, Washington Division of Anatomic Pathology, University of Utah, Salt Lake City, Utah and Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington
Inflamm Bowel Dis 19:2593-602. 2013..We have previously reported that cancer progression is associated with the presence of clonal expansions and shorter telomeres in nondysplastic mucosa. We sought to validate these findings in an independent case-control study...
- Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damageScott R Kennedy
Department of Pathology, University of Washington, Seattle, Washington, United States of America
PLoS Genet 9:e1003794. 2013....
- Detecting ultralow-frequency mutations by Duplex SequencingScott R Kennedy
Department of Pathology, University of Washington, Seattle, USA
Nat Protoc 9:2586-606. 2014..Here we provide a detailed protocol for efficient DS adapter synthesis, library preparation and target enrichment, as well as an overview of the data analysis workflow. The protocol typically takes 1-3 d. ..
- Detection of ultra-rare mutations by next-generation sequencingMichael W Schmitt
Departments of Pathology, Genome Sciences, and Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 109:14508-13. 2012..We apply the method to directly assess the frequency and pattern of random mutations in mitochondrial DNA from human cells...
- Decreased mitochondrial DNA mutagenesis in human colorectal cancerNolan G Ericson
Molecular Diagnostics Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
PLoS Genet 8:e1002689. 2012..Together these findings raise the intriguing possibility that fidelity of mitochondrial genome is, in fact, increased in cancer as a result of a decrease in reactive oxygen species-mediated mtDNA damage...
- Mutational heterogeneity in human cancers: origin and consequencesJesse J Salk
Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology, University of Washington, Seattle, Washington 98195, USA
Annu Rev Pathol 5:51-75. 2010..The impact of DNA sequencing on future cancer research and personalized therapy is likely to be profound and merits critical evaluation...
- Exploring the implications of distinct mutational signatures and mutation rates in aging and cancerEdward J Fox
Department of Pathology, University of Washington, Seattle, WA, 98195, USA
Genome Med 8:30. 2016..Significantly, cancer genomes are dominated by mutation signatures distinct from those that accumulate in normal tissues with age, with potentially important translational implications. ..
- Cancer genome sequencing--an interim analysisEdward J Fox
Joseph Gottstein Memorial Laboratory, Department of Pathology, University of Washington, Seattle, Washington 98195, USA
Cancer Res 69:4948-50. 2009..Most significantly, however, the cancer genome sequencing strategy, as currently applied, fails to characterize the most relevant genomic features of cancer-the mutational heterogeneity within individual tumors...
- Generation, function, and prognostic utility of somatic mitochondrial DNA mutations in cancerMariola Kulawiec
Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Environ Mol Mutagen 51:427-39. 2010..Finally, we discuss the potential clinical utility of mtDNA mutations for improving the sensitivity of early cancer diagnosis, rapidly detecting cancer recurrence, and predicting the disease outcome...
- Optimization of DNA polymerase mutation rates during bacterial evolutionErn Loh
Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology, University of Washington, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 107:1154-9. 2010..Our results indicate that under conditions where organism fitness is not yet maximized for a particular environment, competitive adaptation may be facilitated by enhanced mutagenesis...