Genotyping run
A genotyping runs detects the single nucleotide polymorphism (SNP) variants of a
target nucleic acid sequence.
Genotyping experiments use preformulated TaqMan
™
SNP Genotyping Assays that
include the following components:
• Two sequence-specific primers for amplification of sequences containing the
SNP of interest
• Two allele-specific TaqMan
™
probes for Allele 1 and Allele 2
1. The software normalizes the fluorescence of the reporter dyes to the
fluorescence of the passive reference dye in each well.
2. The software plots the normalized reporter dye signal of each sample well on an
Allelic Discrimination Plot, which contrasts the reporter dye intensities of the
allele-specific probes.
3. The software algorithmically clusters the sample data, and assigns a genotype
call to the samples of each cluster according to its position on the plot.
Presence/absence run
Presence/absence run determines the presence or absence of a target nucleic acid
sequence in a sample.
The software calls the target present or absent based on an algorithmically
determined call threshold. (The call threshold is different from the C
t
threshold; the C
t
threshold is not used to make calls.)
Melt curve run
Melt curve runs determines the melting temperature (Tm) of the amplification
products of a PCR that used intercalating dyes.
In the software, melt curve analysis is included in the default run method for any
experiment type that uses intercalating dyes.
1. The software plots a melt curve based on the fluorescence of the dye with
respect to change in temperature.
2. Using the melt curve, the software calculates the melting temperature (T
m
).
Chapter 1
Product information
Types of runs
1
32
QuantStudio
™
6 Pro and 7 Pro Real-Time PCR Systems User Guide
