Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes.

Nazeefa Fatima,Anna Petri,Ulf Gyllensten,Adam Ameur,Lars Feuk

doi:10.3390/genes11121444

Nazeefa Fatima, Anna Petri + Show 3 more

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https://doi.org/10.3390/genes11121444

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Abstract

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies.

Highlights

All human genomes are different, and to a large extent the genetic variation between individuals can be explained as insertions, deletions, duplications, or translocations [1,2]
This study reports findings from the first PromethION sequencing runs of Swedish human genomes, as well as the analysis of structural variations (SVs) in the same human individuals sequenced on two different long-read platforms
It should be noted that we obtained a high coverage in the RSII Pacific Biosciences (PacBio) data (>65×), sufficient even for creating high quality de novo genome assemblies [29]

Summary

Introduction

All human genomes are different, and to a large extent the genetic variation between individuals can be explained as insertions, deletions, duplications, or translocations [1,2]. Taken together, such structural variation (SV) events affect a large portion of the genomic sequence when comparing any given individual to the existing reference genome, and our knowledge about SVs is still incomplete, they have been shown to contribute to a number of human diseases and conditions [3,4,5,6,7]. As of today, most human WGS projects are performed using short-read sequencing, and while this offers sequencing at a low cost per sample, the alignments of short reads to a reference genome can cause ambiguity and pose challenges for SV detection [16,17,18]

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