2 research outputs found
A New General Model for Predicting Melting Thermodynamics of Complementary and Mismatched B‑Form Duplexes Containing Locked Nucleic Acids: Application to Probe Design for Digital PCR Detection of Somatic Mutations
Advances in real-time polymerase
chain reaction (PCR), as well
as the emergence of digital PCR (dPCR) and useful modified nucleotide
chemistries, including locked nucleic acids (LNAs), have created the
potential to improve and expand clinical applications of PCR through
their ability to better quantify and differentiate amplification products,
but fully realizing this potential will require robust methods for
designing dual-labeled hydrolysis probes and predicting their hybridization
thermodynamics as a function of their sequence, chemistry, and template
complementarity. We present here a nearest-neighbor thermodynamic
model that accurately predicts the melting thermodynamics of a short
oligonucleotide duplexed either to its perfect complement or to a
template containing mismatched base pairs. The model may be applied
to pure-DNA duplexes or to duplexes for which one strand contains
any number and pattern of LNA substitutions. Perturbations to duplex
stability arising from mismatched DNA:DNA or LNA:DNA base pairs are
treated at the Gibbs energy level to maintain statistical significance
in the regressed model parameters. This approach, when combined with
the model’s accounting of the temperature dependencies of the
melting enthalpy and entropy, permits accurate prediction of <i>T</i><sub>m</sub> values for pure-DNA homoduplexes or LNA-substituted
heteroduplexes containing one or two independent mismatched base pairs.
Terms accounting for changes in solution conditions and terminal addition
of fluorescent dyes and quenchers are then introduced so that the
model may be used to accurately predict and thereby tailor the <i>T</i><sub>m</sub> of a pure-DNA or LNA-substituted hydrolysis
probe when duplexed either to its perfect-match template or to a template
harboring a noncomplementary base. The model, which builds on classic
nearest-neighbor thermodynamics, should therefore be of use to clinicians
and biologists who require probes that distinguish and quantify two
closely related alleles in either a quantitative PCR or dPCR assay.
This potential is demonstrated by using the model to design allele-specific
probes that completely discriminate and quantify clinically relevant
mutant alleles (<i>BRAF</i> V600E and <i>KIT</i> D816V) in a dPCR assay
Initial Diagnosis of <i>ALK</i>-Positive Non-Small-Cell Lung Cancer Based on Analysis of <i>ALK</i> Status Utilizing Droplet Digital PCR
We
describe a novel droplet digital PCR (ddPCR) assay capable of
detecting genomic alterations associated with inversion translocations.
It is applied here to detection of rearrangements in the anaplastic
lymphoma kinase (<i>ALK</i>) gene associated with <i>ALK</i>-positive non-small-cell lung cancer (NSCLC). NSCLC patients
may carry a nonreciprocal translocation on human chromosome 2, in
which synchronized double stranded breaks (DSB) within the echinoderm
microtubule-associated protein-like 4 (<i>EML4</i>) gene
and <i>ALK</i> lead to an inversion of genetic material
that forms the non-natural gene fusion <i>EML4-ALK</i> encoding
a constitutively active tyrosine kinase that is associated with 3
to 7% of all NSCLCs. Detection of <i>ALK</i> rearrangements
is currently achieved in clinics through direct visualization via
a fluorescent <i>in situ</i> hybridization (FISH) assay,
which can detect those rearrangements to a limit of detection (LOD)
of ca. 15%. We show that the ddPCR assay presented here provides a
LOD of 0.25% at lower cost and with faster turnaround times