2022
Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth
Gydush G, Nguyen E, Bae JH, Blewett T, Rhoades J, Reed SC, Shea D, Xiong K, Liu R, Yu F, Leong KW, Choudhury AD, Stover DG, Tolaney SM, Krop IE, Christopher Love J, Parsons HA, Mike Makrigiorgos G, Golub TR, Adalsteinsson VA. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth. Nature Biomedical Engineering 2022, 6: 257-266. PMID: 35301450, PMCID: PMC9089460, DOI: 10.1038/s41551-022-00855-9.Peer-Reviewed Original ResearchConceptsLow-frequency mutationsDuplex SequencingNumber of lociLow-frequency allelesWhole-genome sequencingHuman cell linesSingle nucleotide polymorphismsGenomic DNAWhole-exome sequencingMutation enrichmentParallel enrichmentBreast tumor samplesSequencingLociMutationsDistinct mutationsCell linesDNADetection of mutationsReads
2019
Mitochondrial DNA somatic mutation burden and heteroplasmy are associated with chronological age, smoking, and HIV infection
Ziada AS, Lu MY, Ignas‐Menzies J, Paintsil E, Li M, Ogbuagu O, Saberi S, Hsieh AYY, Sattha B, Harrigan PR, Kalloger S, Côté HCF, Pick N, Murray M, Money D, Soudeyns H, Kakkar F, Bitnun A, Brophy J, Janssen P, Singer J, Lapointe N, Prior J, Silverman M, Smith M, Macdonald H. Mitochondrial DNA somatic mutation burden and heteroplasmy are associated with chronological age, smoking, and HIV infection. Aging Cell 2019, 18: e13018. PMID: 31407474, PMCID: PMC6826146, DOI: 10.1111/acel.13018.Peer-Reviewed Original ResearchConceptsHIV infectionSomatic mutationsMtDNA mutationsOxidative damageSomatic mutation burdenHIV viremiaTobacco smokingMutation burdenSmokingMtDNA point mutationsDNA oxidative damageDe novo mutationsMitochondrial DNA mutationsInfectionNext-generation sequencingAgeSmokersRecent reportsSomatic mtDNA mutationsPrimer IDNovo mutationsLow-frequency mutationsChronological ageHeteroplasmic mutationsDNA mutations
2016
Carcinogenesis: UV Radiation
Brash D, Heffernan T, Nghiem P, Cho R. Carcinogenesis: UV Radiation. 2016, 887-902. DOI: 10.1007/978-3-662-47398-6_56.ChaptersLarge-scale sequencing projectsUV-damaged cellsSequencing projectsDNA repairTumor suppressorSomatic point mutationsSurveillance mechanismClonal growthLow-frequency mutationsDNA damageBase changesCell behaviorPoint mutationsMutationsSomatic mutationsFree radical clearanceHuman skin cancerFrequency mutationsSpecific somatic mutationsUltraviolet radiationPTCH mutationsGenetic factorsNOTCH1 mutationsCellsVast number
2015
Carcinogenesis: UV Radiation
Brash D, Heffernan T, Nghiem P, Cho R. Carcinogenesis: UV Radiation. 2015, 1-17. DOI: 10.1007/978-3-642-27814-3_56-2.ChaptersLarge-scale sequencing projectsUV-damaged cellsSequencing projectsDNA repairTumor suppressorSomatic point mutationsSurveillance mechanismClonal growthLow-frequency mutationsDNA damageBase changesCell behaviorPoint mutationsMutationsSomatic mutationsFree radical clearanceHuman skin cancerFrequency mutationsSpecific somatic mutationsUltraviolet radiationPTCH mutationsGenetic factorsNOTCH1 mutationsCellsVast number
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