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Population-scale nanopore sequencing provides new insight into role of SVs in human disease

Thu 21st November 2019

PromethION

1,817 human genomes sequenced using nanopore, up to 10x more structural variants per individual genome than generated with short-read sequencing methods.

deCODE genetics have used nanopore technology to generate long-read whole human sequencing data on 1,817 Icelanders, identifying a median of 23,111 autosomal structural variants (SVs) per individual, spanning cumulatively a median of 9.9 Mbp.

In the publication, authors from deCODE genetics commented:

"We present the first application of Oxford Nanopore Technologies sequencing at a population scale. We sequenced 1,817 Icelanders, including 369 trios, recruited as part of various phenotyping efforts at deCODE genetics.

“SVs impacting protein function are disproportionately rare; as a result, we believe that large scale SV studies will be essential to understand their role in disease.”

Long reads simplify the resolution of large and complex SVs as it’s possible to map them to a reference much more accurately than shorter sequencing reads. To date, the size limit of short reads has made the discovery, genotyping and characterisation of SVs difficult.

This study highlights the role of long reads in SV resolution, finding 23,111 SVs per individual using GridION and PromethION, which compares to 2,000-8,000 in large scale studies using short read sequencing and 23,000-31,000 found in comprehensive studies.

With known causative effects in an extensive range of both normal and aberrant phenotypes, the need to comprehensively characterise SVs is becoming increasingly clear. The results of the study suggest that SVs account for more variant bases than single nucleotide polymorphisms (SNPs) in the human genome.

The team found that rare SVs are larger in size than common ones, and also more likely to impact protein function. They also discovered an association with a rare deletion of the first exon of PCSK9, finding that carriers of this deletion have 1.36 sd lower LDL cholesterol levels than the population average.

Gordon Sanghera, CEO Oxford Nanopore commented:

“Nanopore sequencing offers a simpler solution for the resolution of structural variations; it uniquely provides rich, long-read sequencing data in sufficient volume for population sequencing. We look forward to seeing what’s next for deCODE as they look to further understand the role of SVs in health and disease.”

The PromethION enables the same real-time, long-read, direct DNA and RNA sequencing as MinION and GridION, at a population scale. Each flow cell can product in excess of 150Gb and flow cells can be run independently or simultaneously. Run at full capacity, the PromethION 48 has produced 7Tb in 72 hours — that’s the equivalent of 50 human genomes to 30X coverage depth in three days.

Read the full publication.

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