Abstract
Next-generation sequencing is an important and efficient tool for the identification of structural variation, particularly balanced chromosomal rearrangements, because such events are not routinely detected by microarray and localization of altered regions by karyotype is imprecise. Indeed, the degree of resolution that can be obtained through next-generation technologies enables elucidation of precise breakpoints and has facilitated the discovery of numerous pathogenic loci in human disease and congenital anomalies. The protocol described here explains one type of large-insert "jumping library" and the steps required to generate such a library for multiplexed sequencing using Illumina sequencing technology. This approach allows for cost-efficient multiplexing of samples and provides a very high yield of fragments with large inserts, or "jumping" fragments.