RT Journal
A1 Eisfeldt, Jesper
A1 Ameur, Adam
A1 Lenner, Felix
A1 Ten Berk de Boer, Esmee
A1 Ek, Marlene
A1 Wincent, Josephine
A1 Vaz, Raquel
A1 Ottosson, Jesper
A1 Jonson, Tord
A1 Ivarsson, Sofie
A1 Thunström, Sofia
A1 Topa, Alexandra
A1 Stenberg, Simon
A1 Rohlin, Anna
A1 Sandestig, Anna
A1 Nordling, Margareta
A1 Palmebäck, Pia
A1 Burstedt, Magnus
A1 Nordin, Frida
A1 Stattin, Eva-Lena
A1 Sobol, Maria
A1 Baliakas, Panagiotis
A1 Bondeson, Marie-Louise
A1 Höijer, Ida
A1 Saether, Kristine Bilgrav
A1 Lovmar, Lovisa
A1 Ehrencrona, Hans
A1 Melin, Malin
A1 Feuk, Lars
A1 Lindstrand, Anna
T1 A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities
JF Genome Research 
JO Genome Research 
YR 2024 
FD November 01 
VO 34 
IS 11 
SP 1774 
OP 1784 
DO 10.1101/gr.279510.124 
UL http://genome.cshlp.org/content/34/11/1774.abstract 
AB Clinical genetic laboratories often require a comprehensive analysis of chromosomal rearrangements/structural variants (SVs), from large events like translocations and inversions to supernumerary ring/marker chromosomes and small deletions or duplications. Understanding the complexity of these events and their clinical consequences requires pinpointing breakpoint junctions and resolving the derivative chromosome structure. This task often surpasses the capabilities of short-read sequencing technologies. In contrast, long-read sequencing techniques present a compelling alternative for clinical diagnostics. Here, Genomic Medicine Sweden—Rare Diseases has explored the utility of HiFi Revio long-read genome sequencing (lrGS) for digital karyotyping of SVs nationwide. The 16 samples from 13 families were collected from all Swedish healthcare regions. Prior investigations had identified 16 SVs, ranging from simple to complex rearrangements, including inversions, translocations, and copy number variants. We have established a national pipeline and a shared variant database for variant calling and filtering. Using lrGS, 14 of the 16 known SVs are detected. Of these, 13 are mapped at nucleotide resolution, and one complex rearrangement is only visible by read depth. Two Chromosome 21 rearrangements, one mosaic, remain undetected. Average read lengths are 8.3–18.8 kb with coverage exceeding 20× for all samples. De novo assembly results in a limited number of phased contigs per individual (N50 6–86 Mb), enabling direct characterization of the chromosomal rearrangements. In a national pilot study, we demonstrate the utility of HiFi Revio lrGS for analyzing chromosomal rearrangements. Based on our results, we propose a 5-year plan to expand lrGS use for rare disease diagnostics in Sweden.