A first step towards clinical routine long-read sequencing in Sweden, a national pilot study on chromosomal rearrangements

Here, the Genomic Medicine Sweden Rare Diseases (GMS-RD) consortium validated HiFi Revio long-read whole genome sequencing (lrGS) for clinical digital karyotyping of SVs nationwide. The first 16 samples included in this study were collected from all health care regions in Sweden. We established a national pipeline and a shared variant database for variant calling and filtering. The included validation samples cover a spectrum of simple and complex SVs including inversions, translocations and copy number variants.

Type: Whole Genome Sequencing
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000000676	PacBio HiFi Revio WGS data from 16 individuals sequenced in the Genomic Medicine Sweden (GMS) Long read project. Each individual was sequenced on one PacBio Revio SMRT cell. The DNA was extracted from blood. The HiFi data was aligned to GRCh38 using minimap2 or the SMRT-link software.	unspecified	16

Publications	Citations
A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities. Eisfeldt J, Ameur A, Lenner F, Ten Berk de Boer E, Ek M, Wincent J, Vaz R, Ottosson J, Jonson T, Ivarsson S, Thunström S, Topa A, Stenberg S, Rohlin A, Sandestig A, Nordling M, Palmebäck P, Burstedt M, Nordin F, Stattin EL, Sobol M, Baliakas P, Bondeson ML, Höijer I, Saether KB, Lovmar L, Ehrencrona H, Melin M, Feuk L, Lindstrand A. Genome Res 34: 2024 1774-1784	0

Publications

Citations

A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities.
Eisfeldt J, Ameur A, Lenner F, Ten Berk de Boer E, Ek M, Wincent J, Vaz R, Ottosson J, Jonson T, Ivarsson S, Thunström S, Topa A, Stenberg S, Rohlin A, Sandestig A, Nordling M, Palmebäck P, Burstedt M, Nordin F, Stattin EL, Sobol M, Baliakas P, Bondeson ML, Höijer I, Saether KB, Lovmar L, Ehrencrona H, Melin M, Feuk L, Lindstrand A. Genome Res 34: 2024 1774-1784