講演情報
[PE2-4]Mapping and characterization of structural variants in 9,363 Japanese individuals
○Ashouri Saeideh1, Yosuke Kawai1, Yosuke Omae1,2, Reiko Miyahara2,3, Seik-Soon Khor1, Eisei Noiri2, Katsushi Tokunaga1, National Center Biobank Network (1.Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan, 2.Central Biobank, National Center Biobank Network, Tokyo, Japan, 3.Center for Surveillance, Immunization and Epidemiologic Research, National Institute of Infectious Diseases, Tokyo, Japan)
Structural variants (SVs) rearrange large segments of DNA (≥50bp) in the genome. Here, we generate a catalogue of SVs identified from whole genome sequencing data of 9,850 Japanese individuals from the biobanks of National Center Biobank Network (NCBN) sequenced at high coverage (median depth 30x) using NovaSeq6000 (Illumina Inc., San Diego, CA, USA). High coverage whole-genome sequencing data of 2,504 individuals of the 1000 Genomes Project phase 3 (median depth 36x) were used as population references for the current study. Samples with non-uniform genome-wide coverage, chromosome aneuploidies or structural abnormalities, and abnormal insert size distribution were excluded before SV calling. We analyzed the data using five different SV detection tools, including Manta, DELLY, LUMPY, CNVnator, and xTea, representing all algorithmic approaches (discordant-pair, split-read, local assembly, and read-depth) to detect a broad range of SVs including deletions, insertions, duplications, inversions, breakends (BNDs), copy number variations (CNVs), and non-reference mobile element insertions (MEIs). As expected from larger effective population size, individuals with African ancestry harbored the greatest number of genetic variants compared to others. We discovered a rich landscape of SVs corresponded to a median of 3,317 deletions, 1,592 insertions, 86 inversions, 595 duplications, 646 BNDs, 261 CNVs, and 1,488 non-reference MEIs per genome. Here we present a comprehensive catalogue of SVs from the Japanese population which will be used to enhance population genetics studies.