Mapping and phasing of structural variation in patient genomes using nanopore sequencing

Mircea Cretu Stancu,Ewart De Bruijn,Marleen M Nieboer,Daniela Giachino,Sjors Middelkamp,Jeroen De Ridder,Giorgia Mandrile,Wigard P Kloosterman,Jerome Korzelius,Edwin Cuppen,Giulia Pregno,Ivo Renkens,Jose Espejo Valle-Inclan,Michael E Talkowski,Markus J Van Roosmalen,Tobias Marschall,Joep De Ligt

doi:10.1038/s41467-017-01343-4

Abstract

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline—NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.

Highlights

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, for complex variation
As a first step toward real-time clinical genome sequencing, we evaluated the use of the MinION device to sequence the genomes of two patients with multiple congenital abnormalities[16], denoted as Patient 1 and Patient 2, respectively
For all subsequent analyses of the NA12878 sample, we considered all the SVs preset in the 1KG or PB data sets as true positive SV calls (TPs) and any additional SV calls made by NanoSV as false positive calls (FPs)

Summary

Introduction

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, for complex variation. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of longread sequencing in mapping and phasing of SVs for both clinical and research applications. The first success has been achieved using the Pacific BioSciences SMRT long-read sequencing platform[12,13], and alternative methods to capture long-range information have been introduced, such as BioNano optical mapping[14] and 10× Genomics linked-read technology[15]. While short-read next-generation sequencing data rely on multiple (often) indirect sources of information in order to accurately identify SVs, structural changes can be directly reflected in longread data

Methods

Results

Conclusion