Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

By G. Frampton, Alex M. Fichtenholtz, G. Otto, Kai Wang, S. Downing, Jié He, Michael Schnall-Levin, Jared White, Eric M. Sanford, Peter An and 35 more. Nature Biotechnology, 2013

2,044 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology, Pathology and Forensic Medicine

View Paper: https://www.semanticscholar.org/paper/70c6e45a9511178fa4dfb08fa2acb626195232ed

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Citations in the corpus

Genomic features of response to combination immunotherapy in patients with advanced non-small cell lung cancer (2018, methodology): “…et al., 2017; Zehir et al., 2017), we found that limiting variants to the 468 genes represented in our institutional MSKIMPACT panel (Zehir et al., 2017) or the 315 genes in the FoundationOne panel (Frampton et al., 2013) maintained similar predictive fidelity for efficacy (Figures S3G–S3H).”
Haplotyping germline and cancer genomes using high-throughput linked-read sequencing (2016, neutral): “Exome sequencing does not detect gene fusions for which the breakpoint is more than a few hundred base pairs from an exon without custom targeting assays and extremely high sequencing coverage 22, 23 .”
Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers (2017, neutral): “The methods have been previously described (20).”
Comprehensive Characterization of Cancer Driver Genes and Mutations (2018, background): “Among the 299 genes we identified 59 novel genes that were not previously identified in 6 previous PanCancer publications (Frampton et al., 2013; Kandoth et al., 2013; Lawrence et al., 2014; Pritchard et al., 2014; Tamborero et al., 2013b; Vogelstein et al., 2013) or the cancer gene census list…”
Comprehensive Analysis of Hypermutation in Human Cancer (2017, positive): “Targeted regions of the genome were deeply sequenced using a validated cancer gene panel (Frampton et al., 2013).”
Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA (2015, methodology): “8% assay success rate for the Guardant360 panel starkly contrasts with tissue-based NGS assay failure rates of about 25% (20% because tissue is unavailable or QNS plus a 5% NGS assay failure rate), sparing repeat invasive biopsies [68].”
Feasibility of Large-Scale Genomic Testing to Facilitate Enrollment Onto Genomically Matched Clinical Trials. (2015, background): “Such larger panels may demonstrate potentially actionable alterations in many more patients.(3-6) We noted several challenges in linking genomic testing to genomically matched trials.”
Co-occurring genomic alterations define major subsets of KRAS - mutant lung adenocarcinoma with distinct biology, immune profiles, and therapeutic vulnerabilities (2015, neutral): “0 array profiling was performed by Foundation Medicine, as previously described (56).”
Precision Cancer Medicine: Challenges and Opportunities (2019, background): “For example, highly sensitive and quantitative RT-PCR to detect BCR-ABL fusion transcripts in peripheral blood is routinely used for post-treatment monitoring of CML. Treatment response is well defined by a grading system based not only on the absolute tumor load reduction, but also the dynamic spee”
Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden (2017, methodology): “CGP was performed using the FoundationOne assay (Cambridge, MA, USA), as previously described in detail [55, 56].”