De novo assembly and phasing of a Korean human genome

• Published in: Nature (London) Vol. 538; no. 7624; pp. 243 - 247
• Main Authors: Seo, Jeong-Sun, Rhie, Arang, Kim, Junsoo, Lee, Sangjin, Sohn, Min-Hwan, Kim, Chang-Uk, Hastie, Alex, Cao, Han, Yun, Ji-Young, Kim, Jihye, Kuk, Junho, Park, Gun Hwa, Kim, Juhyeok, Ryu, Hanna, Kim, Jongbum, Roh, Mira, Baek, Jeonghun, Hunkapiller, Michael W., Korlach, Jonas, Shin, Jong-Yeon, Kim, Changhoon
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13-10-2016; Nature Publishing Group
• Subjects: 38; 45/23; 45/91; 631/208/726; 631/208/728; Alleles; Asian Continental Ancestry Group - genetics; Chromosomes, Artificial, Bacterial - genetics; Cloning; Contig Mapping; Cytochrome P-450 CYP2D6 - genetics; Diploidy; DNA sequencing; Genes; Genetic Variation - genetics; Genome, Human - genetics; Genomes; Genomics; Haplotypes; Haplotypes - genetics; Histocompatibility Antigens Class II - genetics; Humanities and Social Sciences; Humans; letter; Methods; multidisciplinary; Precision Medicine; Reference Standards; Republic of Korea; Science; Sequence Analysis, DNA; South Korea
• DOI: 10.1038/nature20098
• EISSN: 1476-4687
• ISSN: 0028-0836

De novo
assembly and phasing of the genome of an individual from Korea using a combination of different sequencing approaches provides a useful population-specific reference genome and represents the most contiguous human genome assembly so far.
A Korean human genome
Jeong-Sun Seo and colleagues report
de novo
assembly and phasing of the genome of an individual from Korea using a combination of PacBio long-read sequencing, Illumina short-read sequencing, 10X Genomics linked reads, bacterial artificial chromosome (BAC) sequencing and BioNano Genomics optical mapping. This provides a useful population-specific reference genome and represents the most contiguous human genome assembly to date. The authors use this to close gaps in the human reference genome and map structural variation.
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
2
, next-generation mapping
3
, microfluidics-based linked reads
4
, 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.