2023
Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer
Budhraja K, McDonald B, Stephens M, Contente-Cuomo T, Markus H, Farooq M, Favaro P, Connor S, Byron S, Egan J, Ernst B, McDaniel T, Sekulic A, Tran N, Prados M, Borad M, Berens M, Pockaj B, LoRusso P, Bryce A, Trent J, Murtaza M. Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer. Science Translational Medicine 2023, 15: eabm6863. PMID: 36630480, PMCID: PMC10080578, DOI: 10.1126/scitranslmed.abm6863.Peer-Reviewed Original ResearchConceptsGenome-wide analysisNucleotide frequenciesDNA fragmentsGenome-wide differencesFragment endsNovel cancer diagnosticsCopy number amplificationChromatin accessibilityGenomic regionsGenomic positionsGC contentDNA sequencesSequencing dataDifferent cancer typesNumber amplificationCell typesCellular originSomatic mutationsCancer cellsFragment lengthCell-free DNADNACancer typesFragmentsSequence
2014
AN INTEGRATED FRAMEWORK FOR REPORTING CLINICALLY RELEVANT BIOMARKERS FROM PAIRED TUMOR/NORMAL GENOMIC AND TRANSCRIPTOMIC SEQUENCING DATA IN SUPPORT OF CLINICAL TRIALS IN PERSONALIZED MEDICINE
Altman R, Dunker A, Hunter L, Ritchie M, Murray T, Klein T, NASSER S, KURDOGLU A, IZATT T, ALDRICH J, RUSSELL M, CHRISTOFORIDES A, TEMBE W, KIEFER J, CORNEVEAUX J, BYRON S, FORMAN K, ZUCCARO C, KEATS J, LORUSSO P, CARPTEN J, TRENT J, CRAIG D. AN INTEGRATED FRAMEWORK FOR REPORTING CLINICALLY RELEVANT BIOMARKERS FROM PAIRED TUMOR/NORMAL GENOMIC AND TRANSCRIPTOMIC SEQUENCING DATA IN SUPPORT OF CLINICAL TRIALS IN PERSONALIZED MEDICINE. Biocomputing 2014, 56-67. PMID: 25592568, DOI: 10.1142/9789814644730_0007.Peer-Reviewed Original ResearchConceptsTranscriptomic sequencing dataHigh-throughput genomic dataRelational database systemsTerabytes of dataTumor/normal samplesSingle nucleotide changeDiversity of usersReal-time mannerIndividual genomesAnnotation databasesDatabase systemsFlexible computational frameworkChromosomal rearrangementsGenomic dataGene expressionSequencing dataData structureComputational architectureGene fusionsNucleotide changesMultiple trackersBase pairsSmall insertionsTime mannerClinical genomic testing