Structural variants (SVs), including deletions, insertions, duplications and inversions, account for most varying base pairs (bp) among individual human genomes1. Numerous studies have implicated SVs in human health with associated phenotypes ranging from cognitive disabilities to predispositions to obesity, cancer and other maladies1,2. Discovery and genotyping of these variants remains challenging, however, since SVs are prone to arise in repetitive regions and internal SV structures can be complex3. This has created challenges for genome-wide association studies (GWAS)4,5. Despite recent methodological and technological advances6,7,8,9, efforts to perform discovery, genotyping, and statistical haplotype-block integration of all major SV classes have so far been lacking. Earlier SV surveys depended on microarrays10 as well as genomic and clone-based approaches limited to a small number of samples11,12,13,14,15. More recently, short-read DNA sequencing data from the initial phases of the 1000 Genomes Project8,9 enabled us to construct sets of SVs, genotyped across populations, with enhanced size and breakpoint resolution6,7. Previous 1000 Genomes Project SV set releases, however, encompassed fewer individuals and were largely6 or entirely8 limited to deletions, in spite of the relevance of other SV classes to human genetics1,2,4.
