The TruSeq Amplicon - Cancer Panel Library Preparation Kit can be used with 150 ng (minimum) to 250 ng (recommended) of high quality genomic DNA. For FFPE genomic DNA Illumina recommends 250 ng (minimum).
Input DNA Quantitation
Illumina strongly recommends quantifying the starting genomic material. Quantify the starting genomic material using a fluorescence-based quantification method, such as PicoGreen, rather than a UV-spectrometer-based method. Fluorescence-based methods, which employ a double-stranded DNA (dsDNA) specific dye, specifically and accurately quantitate dsDNA even in the presence of many common contaminants. In contrast, UV spectrometer methods based on 260 OD readings are prone to overestimating DNA concentrations due to the presence of RNA and other contaminants commonly found in gDNA preparations.
Assessing DNA Quality
The Illumina FFPE QC Kit is strongly recommended to determine if FFPE DNA is of sufficient quality for use in with the TruSeq Amplicon - Cancer Panel. In addition, absorbance measurements at 260 nm are commonly used to quantify DNA. The ratio of absorbance at 260 nm to absorbance at 280 nm is used as an indication of sample purity. This protocol is optimized for DNA with absorbance ratio values of 1.8–2.0.