Selective Whole Genome Amplification for Contamination Minimization

Selective whole genome amplification (SWGA) was performed according to published protocols^{27 (link)}. All SWGA reactions were carried out in the UV Cabinet for PCR Operations (UV-B-AR, Grant-Bio) to minimize contamination. SWGA reactions were performed containing a maximum of 50 ng of total input genomic DNA (and a minimum of 5 ng), 5 µl of 10 x Phi29 DNA Polymerase Reaction Buffer (New England BioLabs), 0.5 µl of Purified 100x BSA (New England BioLabs), 0.5 µl of 250 µM Primer mix of Pkset1, 5 µl 10 mM dNTP (Roche), 30 units Phi29 DNA Polymerase (New England BioLabs) and Nuclease-Free Water (Ambion, The RNA Company) to reach a final reaction volume of 50 µl. The reaction was carried out on a thermocycler with the following step-down program: 5 minutes at 35 °C, 10 minutes at 34 °C, 15 minutes at 33 °C, 20 minutes at 32 °C, 25 min 31 °C, 16 hours at 30 °C and 10 minutes at 65 °C. The SWGA samples were diluted 1:1 with EB buffer (Qiagen) and the reaction was purified using the AMPure XP beads (Beckman-Coulter), using a sample to beads ratio of 1:1 according to the protocol.