Genes of interest were captured and sequenced using an adaptation of the Multiplexed Direct Genomic Selection (MDiGS) assay (Alvarado et al. 2014 (link)). Using the same method as described in Alvarado et al, we pooled 48 indexed DNA samples. For BAC capture we used the clones RP11–652K3 (CFTR), RP11–1056O6 (CFTR), and RP11–268A15 (PLS3) obtained from the BACPAC Resource Center at Children’s Hospital Oakland Research Institute in Oakland, California. RP11–652K3 and RP11–1056O6 have approximately 88 kb of overlap and together cover the entire CFTR gene (Osoegawa et al. 2001 (link)). For the capture of SMN2 we used a 35.5 kb portion of the clone RP1–215P15. This portion contains the entire SMN2 gene flanked by BamHI that had previously been cloned into the BAC pIndigoBac5 (Epicentre) SMN26.6 (BAC5 SMN2) (Hao et al. 2011 (link)). Four cosmids (108F4, 121C9, 22A5, 30C9) flanking the SMN2 gene were used to block non-specific capture. We confirmed that the cosmids do not contain SMN2 by PCR (DiDonato et al. 1994 (link); DiDonato 1995 ; Thompson et al. 1995 (link)). The biotinylated captured BACs were then hybridized with the pooled indexed DNA library for more than 70 hours. The DNA library then contained only sequences hybridized to SMN, PLS3, or CFTR. The 48 samples were run on a single MiSeq lane and then decoded using the indices.