Segmental duplications and their variation in a complete human genome

Despite their importance in disease and evolution, highly identical segmental duplications (SDs) are among the last regions of the human reference genome (GRCh38) to be fully sequenced. Using a complete telomere-to-telomere human genome (T2T-CHM13), we present a comprehensive view of human SD organization. SDs account for nearly one-third of the additional sequence, increasing the genome-wide estimate from 5.4 to 7.0% [218 million base pairs (Mbp)]. An analysis of 268 human genomes shows that 91% of the previously unresolved T2T-CHM13 SD sequence (68.3 Mbp) better represents human copy number variation. Comparing long-read assemblies from human ( n = 12) and nonhuman primate ( n = 5) genomes, we systematically…

• ON
  Oxford Nanopore Technologies
• NI
  National Institutes of Health

  Awards: 1U01HG010973, 5R01HG002385, U41HG007234, 5U01HG010971