Chunk #5 — Online Methods — Phasing de novo mutation in MAGEL2 (also see Supplementary Figure 2)

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Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism.

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Wells in which SNP regions were amplified by qPCR were assumed to contain DNA fragments spanning the amplified SNP and the de novo deletion. A subset of these wells were chosen for PCR with primers magel11f and magel11r (Supplementary Table 2) using KAPA HiFi HotStart ReadyMix (Kapa Biosystems, Woburn, MA) according to the manufacturer’s instructions and the cycling conditions described above to amplify the de novo deletion region. ~40 ng of MDA product was used as template for the KAPA PCRs.