Oxford Nanopore sequencing selected to generate comprehensive insights by characterising a more complete genome using samples from the 1000 Genomes Project
Oxford Nanopore technology will enable the 1000 Genomes Project, spearheaded by researchers at the University of Washington and Seattle Children’s Hospital, to gain greater genomic insights into clinically relevant variants by providing accurate, affordable, scalable and comprehensive information
Uncovering new discoveries across the genome
Oxford Nanopore sequencing technology is to be used by a group of researchers led by Evan Eichler, University of Washington and Danny Miller, University of Washington and Seattle Children’s Hospital, to initially sequence 500 of the 1000 Genomes Project samples. Their goal is to gain more scientific insights from the comprehensive genomic dataset and to create a catalogue of structural variation (SV) from a diverse set of individuals. Building on the established 1000 Genomes Project, which produced a broad catalogue of human genomic variation, this project is expected to further our understanding of variation.
Through nanopore sequencing of 500 specifically selected genomes in the first instance, the data will provide crucial information through sequencing long fragments of DNA, on an already well studied cohort of samples. The aim is to make new discoveries by uncovering SVs across the sample set and in doing so, further insights will be gained in forming links between genotype and phenotype when SVs have been implicated. In addition to studying the canonical four bases, sequencing with nanopore will aim to allow the investigation to reach beyond traditional approaches, with methylation and other epigenetic modifications routinely produced without additional sample preparation techniques.
The recent ‘Telomere-to-Telomere’ sequence of a complete human genome demonstrates the need to sequence more exemplar datasets to uncover the incidence of SVs and make associations between SVs and human disease. Traditional short-read technologies have typically struggled to resolve complex SVs, however Oxford Nanopore’s any-length fragment capabilities overcome these barriers.
In addition to spanning complex genomic regions, nanopore sequencing technology also provides real-time information about base modifications; differences in DNA methylation are increasingly linked to diseases, including cancer. Oxford Nanopore sequencing is the only approach to enable direct detection of a full class of methylation changes across the whole genome, and the sequencing of long fragments makes phasing of modifications simpler.
Gordon Sanghera, CEO Oxford Nanopore Technologies, commented:
“As we know through Evan Eichler’s earlier research, a significant fraction of all disease-causing variation is made up of variants that are larger than a single base-pair substitution, meaning that nanopore sequencing can reveal new insights throughout the genome. So we are delighted that Oxford Nanopore has been selected for this important study and we look forward to it delivering accurate, affordable, scalable and comprehensive long read insight.
We are also pleased to be contributing to ongoing democratisation of DNA sequencing as this is an open data project, which we hope will enable even more discoveries.”
Evan Eichler, Professor of Genome Sciences, University of Washington, commented:
"Long-read sequencing is discovering potential disease-causing structural variations that were previously missed by short reads. The challenge is interpreting these variants of unknown significance. Having a database of structural variants from unaffected diverse controls is key to pinpointing to the disease-causing events."
Data from this Nanopore-only study will be open access, with the results being made available immediately; the aim is to complete the sequencing of this subset within a year. This is the first step towards the characterisation of the full 1000 Genomes Project data set.
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More information on the 1000 Genomes Project can be found here.
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