Nanopore sequencing and assembly of a human genome with ultra-long reads

被引：1187

作者：

Jain, Miten ^{[1
]}

Koren, Sergey ^{[2
]}

Miga, Karen H. ^{[1
]}

Quick, Josh ^{[3
]}

Rand, Arthur C. ^{[1
]}

Sasani, Thomas A. ^{[4
,5
]}

Tyson, John R. ^{[6
,7
]}

Beggs, Andrew D. ^{[8
]}

Dilthey, Alexander T. ^{[2
]}

Fiddes, Ian T. ^{[1
]}

Malla, Sunir ^{[9
]}

Marriott, Hannah ^{[9
]}

Nieto, Tom ^{[8
]}

O'Grady, Justin ^{[10
]}

Olsen, Hugh E. ^{[1
]}

Pedersen, Brent S. ^{[5
]}

Rhie, Arang

Richardson, Hollian ^{[10
]}

Quinlan, Aaron R. ^{[4
,5
,11
]}

Snutch, Terrance P. ^{[6
,7
]}

Tee, Louise ^{[8
]}

Paten, Benedict ^{[1
]}

Phillippy, Adam M. ^{[2
]}

Simpson, Jared T. ^{[12
,13
]}

Loman, Nicholas J. ^{[3
]}

Loose, Matthew ^{[9
]}

机构：

[1] Univ Calif Santa Cruz, Genom Inst, Santa Cruz, CA 95064 USA

[2] NHGRI, Computat & Stat Genom Branch, Genorne Informat Sect, Bethesda, MD 20892 USA

[3] Univ Birmingham, Inst Microbiol & Infect, Birmingham, W Midlands, England

[4] Univ Utah, Dept Human Genet, Salt Lake City, UT USA

[5] Univ Utah, USTAR Ctr Genet Discovery, Salt Lake City, UT USA

[6] Univ British Columbia, Michael Smith Labs, Vancouver, BC, Canada

[7] Univ British Columbia, Djavad Mowafaghian Ctr Brain Hlth, Vancouver, BC, Canada

[8] Univ Birmingham, Inst Canc & Genom Sci, Surg Res Lab, Birmingham, W Midlands, England

[9] Univ Nottingham, Sch Life Sci, DeepSeq, Nottingham, England

[10] Univ East Anglia, Norwich Med Sch, Norwich, Norfolk, England

[11] Univ Utah, Dept Biomed Informat, Salt Lake City, UT USA

[12] Inst Canc Res, Toronto, ON, Canada

[13] Univ Toronto, Dept Comp Sci, Toronto, ON, Canada

来源：

NATURE BIOTECHNOLOGY | 2018年 / 36卷 / 04期

基金：

美国国家卫生研究院; 英国生物技术与生命科学研究理事会; 英国惠康基金; 加拿大健康研究院;

关键词：

DNA; VARIANTS; METHYLATION; LENGTH; GENES; GAPS; TIME;

D O I：

10.1038/nbt.4060

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing similar to 30x theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 similar to 3 Mb). We developed a protocol to generate ultra-long reads (N50 > 100 kb, read lengths up to 882 kb). Incorporating an additional 5x coverage of these ultra-long reads more than doubled the assembly contiguity (NG50 similar to 6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4-Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length, and closure of gaps in the reference human genome assembly GRCh38.

引用

页码：338 / +

页数：13

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