Sequencing of human genomes with nanopore technology

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 gen...

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Bibliographic Details
Published in:	Nature communications Vol. 10; no. 1; pp. 1869 - 9
Main Authors:	Bowden, Rory, Davies, Robert W., Heger, Andreas, Pagnamenta, Alistair T., de Cesare, Mariateresa, Oikkonen, Laura E., Parkes, Duncan, Freeman, Colin, Dhalla, Fatima, Patel, Smita Y., Popitsch, Niko, Ip, Camilla L. C., Roberts, Hannah E., Salatino, Silvia, Lockstone, Helen, Lunter, Gerton, Taylor, Jenny C., Buck, David, Simpson, Michael A., Donnelly, Peter
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 23-04-2019 Nature Publishing Group Nature Portfolio
Subjects:	45/23 631/114/2785 631/208/212/2301 692/308/2056 Adult Ataxia Cerebellar Ataxia - diagnosis Cerebellar Ataxia - genetics Clinical medicine Diagnostic systems Female Gene sequencing Genetic Testing - methods Genome, Human - genetics Genomes Genomics Genomics - instrumentation Genomics - methods Haplotypes High-Throughput Nucleotide Sequencing - instrumentation High-Throughput Nucleotide Sequencing - methods Humanities and Social Sciences Humans Infant Male Mathematical analysis multidisciplinary Nanopores Nanotechnology Nucleotides Pancytopenia Pancytopenia - diagnosis Pancytopenia - genetics Polymorphism, Single Nucleotide - genetics Porosity Science Science (multidisciplinary) Technology Tumor Suppressor Proteins - genetics Whole genome sequencing Whole Genome Sequencing - instrumentation Whole Genome Sequencing - methods
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Summary:	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. Nanopore sequencing technology generates longer reads than current technologies, but with more errors. Here, the authors develop new analytical tools to improve accuracy and evaluate the potential of nanopore sequencing for clinical human genomics.
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-019-09637-5