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 ResearchMeSH KeywordsAllelesHigh-Throughput Nucleotide SequencingHumansMutationOligonucleotide Array Sequence AnalysisSequence Analysis, DNAConceptsLow-frequency mutationsDuplex SequencingNumber of lociLow-frequency allelesWhole-genome sequencingHuman cell linesSingle nucleotide polymorphismsGenomic DNAWhole-exome sequencingMutation enrichmentParallel enrichmentBreast tumor samplesSequencingLociMutationsDistinct mutationsCell linesDNADetection of mutationsReads
2011
GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays
Li A, Liu Z, Lezon-Geyda K, Sarkar S, Lannin D, Schulz V, Krop I, Winer E, Harris L, Tuck D. GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays. Nucleic Acids Research 2011, 39: 4928-4941. PMID: 21398628, PMCID: PMC3130254, DOI: 10.1093/nar/gkr014.Peer-Reviewed Original Research
2002
Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression)
Seth P, Krop I, Porter D, Polyak K. Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression). Oncogene 2002, 21: 836-843. PMID: 11850811, DOI: 10.1038/sj.onc.1205113.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBreast NeoplasmsDioxygenasesEstrogen AntagonistsEstrogensFemaleGene Expression ProfilingHypoxia-Inducible Factor-Proline DioxygenasesIn Situ HybridizationMolecular Sequence DataNuclear ProteinsOligonucleotide Array Sequence AnalysisPhylogenyProcollagen-Proline DioxygenaseReceptors, EstrogenRNA, NeoplasmSequence Homology, Amino AcidTamoxifenTranscriptional ActivationTumor Cells, CulturedConceptsNovel nuclear proteinLigand-dependent transcription factorsDirect transcriptional targetGene expression profilesImmediate early genesTranscriptional targetsTranscription factorsEstrogen-dependent breast cancer cell linesNuclear proteinsSAGE technologyExpression profilesConstitutive expressionHuman breast cancer cellsBreast cancer cellsGenesBreast cancer cell linesCell growthCancer cell linesInitial characterizationNew memberColony growthCancer cellsCell linesNovel estrogenEstrogen receptor