Please use this identifier to cite or link to this item: doi:10.22028/D291-28717
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Title: Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Author(s): Cretu Stancu, Mircea
van Roosmalen, Markus J.
Renkens, Ivo
Nieboer, Marleen M.
Middelkamp, Sjors
de Ligt, Joep
Pregno, Giulia
Giachino, Daniela
Mandrile, Giorgia
Espejo Valle-Inclan, Jose
Korzelius, Jerome
de Bruijn, Ewart
Cuppen, Edwin
Talkowski, Michael E.
Marschall, Tobias
de Ridder, Jeroen
Kloosterman, Wigard P.
Language: English
Title: Nature Communications
Volume: 8
Issue: 1
Startpage: 1326
Publisher/Platform: Nature Publishing Group UK
Year of Publication: 2017
Publikation type: Journal Article
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.
DOI of the first publication: 10.1038/s41467-017-01343-4
URL of the first publication:
Link to this record: hdl:20.500.11880/27714
ISSN: 2041-1723
Date of registration: 7-Sep-2019
Faculty: MI - Fakultät für Mathematik und Informatik
Department: MI - Informatik
Professorship: MI - Prof. Dr. Tobias Marschall
Collections:SciDok - Der Wissenschaftsserver der Universität des Saarlandes

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