Genome maps of structural variation across 26 human populations reveal population-specific patterns of variation

Large structural variations (>2 kb in size) have not been studied in detail in the human genome because they are difficult to detect by conventional sequencing technologies. By employing long-range genome analysis platforms, large structural variations can be identified across the entire genome in one experiment. We have generated genome maps with optical mapping for 154 individuals from the 26 populations sequenced in the 1000 Genomes Project and studied structural variation patterns in each individual and across multiple populations. Although population patterns of large structural variations are similar to those based on single nucleotide variations in 87% of the 3 Gb human genome, ~4% of the genome is highly variable and has very complicated but population-specific patterns. In addition, we identified ~60 Mb of new genome content not found in the reference genome sequence assembly. Our results show that population-specific reference genome assemblies will be needed to resolve structural variation patterns in complex regions in the genome.