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

Autor: Levy-Sakin M; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA., Pastor S; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA., Mostovoy Y; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA., Li L; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China., Leung AKY; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China., McCaffrey J; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA., Young E; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA., Lam ET; Bionano Genomics, San Diego, CA, 92121, USA., Hastie AR; Bionano Genomics, San Diego, CA, 92121, USA., Wong KHY; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA., Chung CYL; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China., Ma W; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA., Sibert J; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA., Rajagopalan R; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA., Jin N; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China., Chow EYC; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China., Chu C; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA., Poon A; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA., Lin C; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA., Naguib A; Bionano Genomics, San Diego, CA, 92121, USA., Wang WP; Bionano Genomics, San Diego, CA, 92121, USA., Cao H; Bionano Genomics, San Diego, CA, 92121, USA., Chan TF; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China.; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China., Yip KY; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.; Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China., Xiao M; School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.; Institute of Molecular Medicine and Infectious Disease in the School of Medicine, Drexel University, Philadelphia, PA, 19104, USA., Kwok PY; Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94143, USA. pui.kwok@ucsf.edu.; Department of Dermatology, University of California-San Francisco, San Francisco, CA, 94143, USA. pui.kwok@ucsf.edu.; Institute for Human Genetics, University of California-San Francisco, San Francisco, CA, 94143, USA. pui.kwok@ucsf.edu.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2019 Mar 04; Vol. 10 (1), pp. 1025. Date of Electronic Publication: 2019 Mar 04.
DOI: 10.1038/s41467-019-08992-7
Abstrakt: Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome.
Databáze: MEDLINE