High-throughput Detection of Clinically Relevant Mutations in Archived Tumor Samples By Multiplexed PCR and Next Generation Sequencing

Study ID Alternative Stable ID Type
EGAS00001000674 Other

Study Description

PURPOSE: 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. EXPERIMENTAL DESIGN: We first validated MMP-seq’s technical performance 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 (FF) tissue from the same tumors as benchmarks. To demonstrate the potential clinical utility of our methodology, we profiled FFPE tumor samples from 73 endometrial cancer patients. RESULTS: 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 ... (Show More)

Study Datasets 3 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
MMP-seq tumor samples, UDG treated (FASTQ)
Illumina MiSeq 16
MMP-seq cell lines (FASTQ)
Illumina Genome Analyzer IIx 154
MMP-seq tumor samples (FASTQ)
Illumina Genome Analyzer IIx 218

Who archives the data?