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3
Sample Preparation
Step 5. Validate enrichment and quantify enriched target DNA
Analysis of Electropherogram Results
• Check that the electropherogram shows a peak fragment size between
approximately 225 to 525 bp.
• Determine the concentration of enriched target DNA in the sample by
integration under the peak between 175 and 625 bp. Peaks at
<150 bp may be observed, but should be excluded from quantitation.
• Some designs may generate a peak at about 125 bp. This peak is
associated with an adaptor-dimer product which will cluster and
generate sequence that does not map to the genome. If the molar
fraction of the 125 bp peak is greater than 10%, do another round of
AMPure purification after pooling samples. First, pool equimolar
amounts of libraries to be multiplexed, using concentrations
determined for the 175–625 peak of each sample. Using 40 µL of the
pooled libraries, purify the DNA using AMPure XP beads according to
the protocol starting on page 77.
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HaloPlex Target Enrichment System Automation Protocol