2015
Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments
Qi Y, Liu X, Liu CG, Wang B, Hess KR, Symmans WF, Shi W, Pusztai L. Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments. PLOS ONE 2015, 10: e0119230. PMID: 26136146, PMCID: PMC4489803, DOI: 10.1371/journal.pone.0119230.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsEuropean Genome-phenome ArchiveProtein kinase geneMillions of nucleotidesSame genomic DNANext-generation sequencing experimentsVariant callsGenomic locationNext-generation sequencingSequence dataSNV callsKinase geneGenomic DNANucleotide substitutionsSequencing experimentsHigh stringencyVariant allele frequencyNucleotide variantsTrue biological changeNucleotide alterationsGeneration sequencingAllele countsSequencing errorsBreast cancer samplesAllele frequencies
2013
Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, He J, Schnall-Levin M, White J, Sanford EM, An P, Sun J, Juhn F, Brennan K, Iwanik K, Maillet A, Buell J, White E, Zhao M, Balasubramanian S, Terzic S, Richards T, Banning V, Garcia L, Mahoney K, Zwirko Z, Donahue A, Beltran H, Mosquera JM, Rubin MA, Dogan S, Hedvat CV, Berger MF, Pusztai L, Lechner M, Boshoff C, Jarosz M, Vietz C, Parker A, Miller VA, Ross JS, Curran J, Cronin MT, Stephens PJ, Lipson D, Yelensky R. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nature Biotechnology 2013, 31: 1023-1031. PMID: 24142049, PMCID: PMC5710001, DOI: 10.1038/nbt.2696.Peer-Reviewed Original Research