Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA

@article{Forshew2012NoninvasiveIA,
  title={Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA},
  author={Tim Forshew and Muhammed Murtaza and Christine A. Parkinson and Davina Gale and Dana Wai Yi Tsui and Fiona Kaper and Sarah-Jane Dawson and Anna M Piskorz and Mercedes Jimenez-Linan and D. R. Bentley and James Hadfield and Andrew P. May and Carlos Caldas and James D. Brenton and Nitzan Rosenfeld},
  journal={Science Translational Medicine},
  year={2012},
  volume={4},
  pages={136ra68 - 136ra68}
}
Sizable genomic regions were screened and low-frequency mutations were identified in circulating DNA of cancer patients using tagged-amplicon deep sequencing (TAm-Seq). Deep Sequencing Tumor DNA in Plasma Five liters of circulating blood contain millions of copies of the genome, broken into short fragments; in cancer patients, a small fraction is circulating tumor DNA (ctDNA). An even smaller number harbor mutations that affect cancer outcome. Looking for diagnostic answers in circulating DNA… 
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References

SHOWING 1-10 OF 53 REFERENCES
Detection of tumor mutations in the presence of excess amounts of normal DNA
TLDR
A screening method, termed PPEM (PNA-directed PCR, primer extension, MALDI-TOF), that can detect as few as 3 copies of mutant alleles in the presence of a 10,000-fold excess of normal allele in a robust and specific manner and is amenable to high-throughput automation.
Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing
TLDR
With an improved performance when run on the Illumina Miseq, the UDT-Seq assay is well suited for clinical applications to guide therapy and study clonal selection in heterogeneous samples.
High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.
TLDR
A sequencingbased approach to identifying genomic alterations in FFPE tumor samples is described, affirm the feasibility and clinical utility of targeted sequencing in the oncology arena and provide a foundation for genomics-based stratification of cancer patients.
High Throughput Interrogation of Somatic Mutations in High Grade Serous Cancer of the Ovary
TLDR
Sequenom analysis using OncoMap on DNA extracted from FFPE ovarian cancer samples is feasible and leads to the detection of potentially druggable mutations.
Circulating mutant DNA to assess tumor dynamics
TLDR
It is found that ctDNA measurements could be used to reliably monitor tumor dynamics in subjects with cancer who were undergoing surgery or chemotherapy, and it is suggested that this personalized genetic approach could be generally applied to individuals with other types of cancer.
Detection of mutations in EGFR in circulating lung-cancer cells.
TLDR
Molecular analysis of circulating tumor cells from the blood of patients with lung cancer offers the possibility of monitoring changes in epithelial tumor genotypes during the course of treatment, and shows that a reduction in the number of captured cells was associated with a radiographic tumor response; an increase in theNumber of cells wasassociated with tumor progression, with the emergence of additional EGFR mutations in some cases.
Detection and quantification of mutations in the plasma of patients with colorectal tumors.
  • F. Diehl, M. Li, B. Vogelstein
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 2005
TLDR
Patients with advanced colorectal cancers consistently contained mutant adenomatous polyposis coli (APC) DNA molecules in their plasma, which has implications for the mechanisms through which tumor DNA is released into the circulation and for diagnostic tests based on this phenomenon.
Single-Molecule Detection of Epidermal Growth Factor Receptor Mutations in Plasma by Microfluidics Digital PCR in Non–Small Cell Lung Cancer Patients
TLDR
The sensitive detection and accurate quantification of low abundance EGFR mutations in tumor tissues and plasma by microfluidics digital PCR would be useful for predicting treatment response, monitoring disease progression and early detection of treatment failure associated with acquired drug resistance.
Replacing PCR with COLD-PCR enriches variant DNA sequences and redefines the sensitivity of genetic testing
TLDR
Co-amplification at lower denaturation temperature PCR (COLD-PCR), a novel form of PCR that amplifies minority alleles selectively from mixtures of wild-type and mutation-containing sequences irrespective of the mutation type or position on the sequence, is described.
...
...