Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.

TitleScalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Publication TypeJournal Article
Year of Publication2023
AuthorsKolmogorov, M, Billingsley, KJ, Mastoras, M, Meredith, M, Monlong, J, Lorig-Roach, R, Asri, M, Jerez, PAlvarez, Malik, L, Dewan, R, Reed, X, Genner, RM, Daida, K, Behera, S, Shafin, K, Pesout, T, Prabakaran, J, Carnevali, P, Yang, J, Rhie, A, Scholz, SW, Traynor, BJ, Miga, KH, Jain, M, Timp, W, Phillippy, AM, Chaisson, M, Sedlazeck, FJ, Blauwendraat, C, Paten, B
JournalNat Methods
Volume20
Issue10
Pagination1483-1492
Date Published2023 Oct
ISSN1548-7105
KeywordsGenome, Human, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Methylation, Nanopore Sequencing, Pilot Projects, Sequence Analysis, DNA
Abstract

Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer's and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.

DOI10.1038/s41592-023-01993-x
Alternate JournalNat Methods
PubMed ID37710018
PubMed Central ID3083463
Grant ListU24 HG010262 / HG / NHGRI NIH HHS / United States
U24 HG011853 / HG / NHGRI NIH HHS / United States
U01 HG010961 / HG / NHGRI NIH HHS / United States
R01 HG010485 / HG / NHGRI NIH HHS / United States
OT2 OD026682 / OD / NIH HHS / United States
T32 HG012344 / HG / NHGRI NIH HHS / United States
ZIA NS003154 / ImNIH / Intramural NIH HHS / United States
ZIA AG000538 / ImNIH / Intramural NIH HHS / United States
U24 NS072026 / NS / NINDS NIH HHS / United States
P30 AG019610 / AG / NIA NIH HHS / United States
P30 AG072980 / AG / NIA NIH HHS / United States
OT3 HL142481 / HL / NHLBI NIH HHS / United States
OT2 OD033761 / OD / NIH HHS / United States

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