Cantsilieris, Stuart, Stessman, Holly A, Shendure, Jay, Eichler, Evan E, Stuart Cantsilieris, Holly A. Stessman, Jay Shendure, Evan E. Eichler, Stessman, Holly A., Eichler, Evan E.

Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.