EGAGenomicsIllumina MiSeq;https://ega-archive.org/datasets/EGAD0000100110416EGA dataset EGAD00001001104EGA<h4>Purpose</h4>Tailoring cancer treatment to tumor molecular characteristics promises to make personalized medicine a reality. However, reliable genetic profiling of archived clinical specimens has been hindered by limited sensitivity and high false-positive rates. Here, we describe a novel methodology, MMP-seq, which enables sensitive and specific high-throughput, high-content genetic profiling in archived clinical samples.<h4>Experimental design</h4>We first validated the technical performance of MMP-seq in 66 cancer cell lines and a Latin square cross-dilution of known somatic mutations. We next characterized the performance of MMP-seq in 17 formalin-fixed paraffin-embedded (FFPE) clinical samples using matched fresh-frozen tissue from the same tumors as benchmarks. To demonstrate the potential clinical utility of our methodology, we profiled FFPE tumor samples from 73 patients with endometrial cancer.<h4>Results</h4>We demonstrated that MMP-seq enabled rapid and simultaneous profiling of a panel of 88 cancer genes in 48 samples, and detected variants at frequencies as low as 0.4%. We identified DNA degradation and deamination as the main error sources and developed practical and robust strategies for mitigating these issues, and dramatically reduced the false-positive rate. Applying MMP-seq to a cohort of endometrial tumor samples identified extensive, potentially actionable alterations in the PI3K (phosphoinositide 3-kinase) and RAS pathways, including novel PIK3R1 hotspot mutations that may disrupt negative regulation of PIK3CA.<h4>Conclusions</h4>MMP-seq provides a robust solution for comprehensive, reliable, and high-throughput genetic profiling of clinical tumor samples, paving the way for the incorporation of genomic-based testing into clinical investigation and practice.High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next-generation sequencing.Bourgon Richard R, Lu Shan S, Yan Yibing Y, Lackner Mark R MR, Wang Weiru W, Weigman Victor V, Wang David D, Guan Yinghui Y, Ryner Lisa L, Koeppen Hartmut H, Patel Rajesh R, Hampton Garret M GM, Amler Lukas C LC, Wang Yulei YfalseMMP-seq tumor samples, UDG treated (FASTQ) - samplesMMP-seq tumor samples, UDG treated (FASTQ)2017-07-26 15:39:25EGAD00001001104960624573554EGAC00001000055EGAS00001000674