Population structure, stratification, and introgression of human structural variation

Mohamed A. Almarri, Anders Bergström, Javier Prado-Martinez, Fengtang Yang, Beiyuan Fu, Alistair S. Dunham, Yuan Chen, Matthew E. Hurles, Chris Tyler-Smith, Yali Xue

Research output: Contribution to journalArticlepeer-review

48 Citations (Scopus)


Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.
Original languageEnglish
Pages (from-to)189-199.e15
Number of pages11
Issue number1
Early online date11 Jun 2020
Publication statusPublished - 9 Jul 2020

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