One individual, scy006, underwent whole-genome capture using 7 μl of previously screened library. Hybridization capture reaction was performed using commercially biotinylated probes for human from MYcroarray (www.mycroarray.com). The reactions conducted at 60°C for 40 hours in a final volume of 30 μl. Captured library was purified with Dynabeads MyOne Streptavidin C1 magnetic beads (Invitrogen) following the manufacturer’s protocol (version 3.1) and was subsequently eluted in 30 μl of 1× tris-EDTA buffer with 0.05% Tween 20 (TET) buffer. Postcapture amplification was performed in five separate reactions with 1 μl of each 10 μM PCR primer (IS5 and IS6), 10 μl of 5× Herculase II amplification buffer, 1 μl of Herculase II Fusion DNA Polymerase (Agilent Technologies), 0.5 μl of deoxynucleotide triphosphates (dNTPs) (25 mM), 32.5 μl of ddH2O, and 5 μl of captured DNA library. The thermocycling conditions consisted of an initial denaturation at 98°C for 30 s, 16 cycles of 98°C for 20 s, 60°C for 30 s, 72°C for 30 s, and a final extension at 72°C for 5 min. After postcapture amplification, the five amplified samples per reaction were pooled and purified with the use of MinElute spin columns (Qiagen) following the manufacturer’s instructions. Despite successful library preparation, we did not observe much improvement in terms of single-nucleotide polymorphism (SNP) yield in the capture library. The screening results from captured library were merged with previous results obtained from conventional blunt-end libraries to increase the final coverage to the level used in this paper.

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