Proximity, maps and conflict: New measures, New maps and New findings

This article introduces two new datasets. The first is a new interstate distance dataset. It is recognized that different theories regarding distance and conflict will call for different understandings of “distance” and accordingly, ten different types of distance measurement are presented. Moreover, it is argued that in order for a distance dataset to contain accurate distances, it is necessary for it to be based on maps reflecting state border changes over time. As such, a new map dataset is presented, including annualized maps for all states, stored in KML format. It will be shown that the frequent border changes experienced by states can have large impacts on distance calculations. The significance of the relationship between distance and conflict will be tested for the ten different types of distance measurement, not with the aim of finding a “best measure” but in order to demonstrate that distance remains an important variable and that each different form of distance measure can be significant

Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

Despite developments in targeted gene sequencing and whole-genome analysis techniques, the robust detection of all genetic variation, including structural variants, in and around genes of interest and in an allele-specific manner remains a challenge. Here we present targeted locus amplification (TLA), a strategy to selectively amplify and sequence entire genes on the basis of the crosslinking of physically proximal sequences. We show that, unlike other targeted re-sequencing methods, TLA works without detailed prior locus information, as one or a few primer pairs are sufficient for sequencing tens to hundreds of kilobases of surrounding DNA. This enables robust detection of single nucleotide variants, structural variants and gene fusions in clinically relevant genes, including BRCA1 and BRCA2, and enables haplotyping. We show that TLA can also be used to uncover insertion sites and sequences of integrated transgenes and viruses. TLA therefore promises to be a useful method in genetic research and diagnostics when comprehensive or allele-specific genetic information is needed