Sequencing of human genomes with nanopore technology

被引：136

作者：

Bowden, Rory ^{[1
]}

Davies, Robert W. ^{[2
,3
,4
]}

Heger, Andreas ^{[2
]}

Pagnamenta, Alistair T. ^{[1
]}

de Cesare, Mariateresa ^{[1
]}

Oikkonen, Laura E. ^{[1
]}

Parkes, Duncan ^{[1
]}

Freeman, Colin ^{[1
]}

Dhalla, Fatima ^{[6
,7
]}

Patel, Smita Y. ^{[6
,8
]}

Popitsch, Niko ^{[1
,5
,9
]}

Ip, Camilla L. C. ^{[1
]}

Roberts, Hannah E. ^{[1
]}

Salatino, Silvia ^{[1
]}

Lockstone, Helen ^{[1
]}

Lunter, Gerton ^{[1
,2
]}

Taylor, Jenny C. ^{[1
,5
]}

Buck, David ^{[1
]}

Simpson, Michael A. ^{[2
]}

Donnelly, Peter ^{[1
,2
,10
]}

机构：

[1] Univ Oxford, Wellcome Ctr Human Genet, Oxford OX3 7BN, England

[2] Genomics Plc, Oxford OX1 1JD, England

[3] Hosp Sick Children, Program Genet & Genom Biol, Toronto, ON M5G 0A4, Canada

[4] Hosp Sick Children, Ctr Appl Genom, Toronto, ON M5G 0A4, Canada

[5] Biomed Res Ctr, Natl Inst Hlth Res, Oxford OX4 2PG, England

[6] Oxford Univ Hosp, Dept Clin Immunol, Oxford OX3 9DU, England

[7] Univ Oxford, MRC Weatherall Inst Mol Med, Dev Immunol Grp, Oxford OX3 9DS, England

[8] Oxford Biomed Res Ctr, Natl Inst Hlth Res, Clin Immunol Grp, Oxford OX4 2PG, England

[9] St Anna Kinderkrebsforsch, Childrens Canc Res Inst, A-1090 Vienna, Austria

[10] Univ Oxford, Dept Stat, Oxford OX1 3LB, England

来源：

NATURE COMMUNICATIONS | 2019年 / 10卷 / 1期

基金：

英国惠康基金;

关键词：

GENETIC-VARIATION; MUTATIONS; RESOURCE; LEUKEMIA; SPECTRUM;

D O I：

10.1038/s41467-019-09637-5

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Whole-genome sequencing (WGS) is becoming widely used in clinical medicine in diagnostic contexts and to inform treatment choice. Here we evaluate the potential of the Oxford Nanopore Technologies (ONT) MinION long-read sequencer for routine WGS by sequencing the reference sample NA12878 and the genome of an individual with ataxia-pancytopenia syndrome and severe immune dysregulation. We develop and apply a novel reference panel-free analytical method to infer and then exploit phase information which improves single-nucleotide variant (SNV) calling performance from otherwise modest levels. In the clinical sample, we identify and directly phase two non-synonymous de novo variants in SAMD9L, (OMIM #159550) inferring that they lie on the same paternal haplotype. Whilst consensus SNV-calling error rates from ONT data remain substantially higher than those from short-read methods, we demonstrate the substantial benefits of analytical innovation. Ongoing improvements to base-calling and SNV-calling methodology must continue for nanopore sequencing to establish itself as a primary method for clinical WGS.

引用

页数：9

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