Multiplex real-time PCR assays that measure the abundance of extremely rare mutations associated with cancer

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21 Scopus citations

Abstract

We describe the use of "SuperSelective" primers that enable the detection and quantitation of somatic mutations whose presence relates to cancer diagnosis, prognosis, and therapy, in real-time PCR assays that can potentially analyze rare DNA fragments present in blood samples (liquid biopsies). The design of these deoxyribonucleotide primers incorporates both a relatively long "5′ anchor sequence" that hybridizes strongly to target DNA fragments, and a very short, physically and functionally separate, "3′ foot sequence" that is perfectly complementary to the mutant target sequence, but mismatches the wild-type sequence. As few as ten mutant fragments can reliably be detected in the presence of 1,000,000 wild-type fragments, even when the difference between the mutant and the wild type is only a single nucleotide polymorphism. Multiplex PCR assays employing a set of SuperSelective primers, and a corresponding set of differently colored molecular beacon probes, can be used in situations where the different mutations, though occurring in different cells, are located in the same codon. These non-symmetric real-time multiplex PCR assays contain limited concentrations of each SuperSelective primer, thereby enabling the simultaneous determination of each mutation's abundance by comparing its threshold value to the threshold value of a reference gene present in the sample.

Original languageEnglish (US)
Article numbere0156546
JournalPloS one
Volume11
Issue number5
DOIs
StatePublished - May 2016

All Science Journal Classification (ASJC) codes

  • General

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