Balanced chromosomal rearrangements can have a significant contribution to diseases, as demonstrated by the studies of leukemia. However, many of them are undetected by chromosomal microarray. Karyotyping and FISH can identify balanced translocations and inversions but are labor-intensive and provide low resolution (small genomic changes are missed).
A jumping library NGS combined approach can be applied to identify such genomic changes. For example, Slade et al. applied this method to fine map a de novo balanced translocation in a child with Wilms' tumor. For this study, 50 million reads were generated, but only 11.6% of these could be mapped uniquely to the reference genome, which represents approximately a sixfold coverage.
Talkowski et al. compared different approaches to detect balanced chromosome alterations, and showed that modified jumping library in combination with next generation DNA sequencing is an accurate method for mapping chromosomal breakpoints. Two varieties of jumping libraries (short-jump libraries and custom barcoded jumping libraries) were tested and compared to standard sequencing libraries.
For standard NGS, 200-500bp fragments are generated. About 0.03%–0.54% of fragments represent chimeric pairs, which are pairs of end-reads that are mapped to two different chromosomes. Therefore, very few fragments cover the breakpoint area.
When using short-jump libraries with fragments of 3.2–3.8kb, the percentage of chimeric pairs increased to 1.3%. With Custom Barcoded Jumping Libraries, the percentage of chimeric pairs further increased to 1.49%.