RT Journal Article
SR Electronic
T1 Mapping and phasing of structural variation in patient genomes using nanopore sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 129379
DO 10.1101/129379
A1 Mircea Cretu Stancu
A1 Markus J. van Roosmalen
A1 Ivo Renkens
A1 Marleen Nieboer
A1 Sjors Middelkamp
A1 Joep de Ligt
A1 Giulia Pregno
A1 Daniela Giachino
A1 Giorgia Mandrile
A1 Jose Espejo Valle-Inclan
A1 Jerome Korzelius
A1 Ewart de Bruijn
A1 Edwin Cuppen
A1 Michael E. Talkowski
A1 Tobias Marschall
A1 Jeroen de Ridder
A1 Wigard P. Kloosterman
YR 2017
UL http://biorxiv.org/content/early/2017/04/24/129379.abstract
AB Structural genomic variants form a common type of genetic alteration underlying human genetic disease and phenotypic variation. Despite major improvements in genome sequencing technology and data analysis, the detection of structural variants still poses challenges, particularly when variants are of high complexity. Emerging long-read single-molecule sequencing technologies provide new opportunities for detection of structural variants. Here, we demonstrate sequencing of the genomes of two patients with congenital abnormalities using the ONT MinION at 11x and 16x mean coverage, respectively. We developed a bioinformatic pipeline - NanoSV - to efficiently map genomic structural variants (SVs) from the long-read data. We demonstrate that the nanopore data are superior to corresponding short-read data with regard to detection of de novo rearrangements originating from complex chromothripsis events in the patients. Additionally, genome-wide surveillance of SVs, revealed 3,253 (33%) novel variants that were missed in short-read data of the same sample, the majority of which are duplications < 200bp in size. Long sequencing reads enabled efficient phasing of genetic variations, allowing the construction of genome-wide maps of phased SVs and SNVs. We employed read-based phasing to show that all de novo chromothripsis breakpoints occurred on paternal chromosomes and we resolved the long-range structure of the chromothripsis. This work demonstrates the value of long-read sequencing for screening whole genomes of patients for complex structural variants.