Jumping library
These libraries allow the analysis of large areas of the genome and overcome distance limitations in common cloning techniques.
The stretch of DNA located between these two "ends" is deleted by a series of biochemical manipulations carried out at the start of this cloning technique.
A DNA marker (such as the amber suppressor tRNA gene supF) can be included at this time point within the covalently linked circle to allow for selection of junction fragments.
Circles are subsequently fully digested with a second restriction enzyme (such as EcoRI) to generate a large number of fragments.
[1] The next step is to screen this library with a probe that represents a "starting point" of the desired "chromosome hop", i.e. determining the location of the genome that is being interrogated.
This approach included the use of two separate λ vectors for library construction, and a partial filling-in reaction that removes the need for a selectable marker.
This filling-in reaction worked by destroying the specific cohesive ends (resulting from restriction digests) of the DNA fragments that were nonligated and noncircularized, thus preventing them from cloning into the vectors, in a more energy-efficient and accurate manner.
Furthermore, this improved technique required less DNA to start with, and also produced a library that could be transferred into a plasmid form, making it easier to store and replicate.
[4] Second-generation or "Next-Gen" (NGS) techniques have evolved radically: the sequencing capacity has increased more than ten thousandfold and the cost has dropped by over one million-fold since 2007(National Human Genome Research Institute).
[7] Alternatively, a jumping library can be used with NGS for the mapping of structural variation and scaffolding of de novo assemblies.
In addition, the fosmids can be modified to facilitate the conversion into jumping library compatible with certain next generation sequencers.
[8][10] The segments resulting from circularization during constructing jumping library are cleaved, and DNA fragments with markers will be enriched and subjected to paired-end sequencing.
DELLY was developed to discover genomic structural variants and "integrates short insert paired-ends, long-range mate-pairs and split-read alignments" to detect rearrangements at sequence level.
In the early days, chromosome walking from genetically linked DNA markers was used to identify and clone disease genes.
Chromosome jumping helped reduce the mapping "steps" and bypass the highly repetitive regions in the mammalian genome.
Karyotyping and FISH can identify balanced translocations and inversions but are labor-intensive and provide low resolution (small genomic changes are missed).
For example, Slade et al. applied this method to fine map a de novo balanced translocation in a child with Wilms' tumor.
[15] 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.
[9] Conventional cytogenetic testing cannot offer the gene-level resolution required to predict the outcome of a pregnancy and whole genome deep sequencing is not practical for routine prenatal diagnosis.
By using a longer-jump library, Ribeiro et al. demonstrated that the assemblies of bacterial genomes were of high quality while reducing both cost and time.
