To re-call CNVs in the Bulgarian controls, we used the same filtering criteria and accepted only those considered highly suggestive by the MeZOD. Although we did not validate these on Agilent arrays, our calls have a demonstrable low false positive rate (<1%, Supplementary Section 4). This is much less than the corresponding false positive rate for de novos whose rarity confers more unfavourable signal-to-noise characteristics.
