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Nature. 2016 Oct 13;538(7624):243-247. doi: 10.1038/nature20098. Epub 2016 Oct 5.

De novo assembly and phasing of a Korean human genome.

Seo JS1,2,3,4,5, Rhie A1,2,3, Kim J1,4, Lee S1,5, Sohn MH1,2,3, Kim CU1,2,3, Hastie A6, Cao H6, Yun JY1,5, Kim J1,5, Kuk J1,5, Park GH1,5, Kim J1,5, Ryu H4, Kim J4, Roh M4, Baek J4, Hunkapiller MW7, Korlach J7, Shin JY1,5, Kim C4.

Author information

1
Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul 110-799, South Korea.
2
Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799, South Korea.
3
Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 110-799, South Korea.
4
Bioinformatics Institute, Macrogen Inc., Seoul 153-023, South Korea.
5
Genome Institute, Macrogen Inc., Seoul 153-023, South Korea.
6
BioNano Genomics, San Diego, California 92121, USA.
7
Pacific Biosciences of California, Inc., Menlo Park, California 94025, USA.

Abstract

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

PMID:
27706134
DOI:
10.1038/nature20098
[Indexed for MEDLINE]

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