Mind the gap: the relevance of the genome reference to resolve rare and pathogenic inversions

Chromosomal inversions (INV) are particularly challenging to detect due to their copy-number neutral state and association with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage sensitive genes in cis. Short-read genome sequencing (srGS) can only resolve ~70% of cytogenetically visible inversions referred to clinical diagnostic laboratories, likely due to breakpoints in repetitive regions. Here we study twelve inversions by srGS (n=3) or long read genome sequencing (lrGS) (n=9)

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
EGAD50000000635	Pacbio Hifi whole genome sequencing data from six individuals carrying cytogenetically visible inversions. The HiFi data was produced on the PacBio Revio machine, using 1 flowcell per sample. The resulting data was aligned to hg19 using minimap2, and converted into bam using samtools.	unspecified	6

Publications	Citations
Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps. Bilgrav Saether K, Eisfeldt J, Bengtsson JD, Lun MY, Grochowski CM, Mahmoud M, Chao HT, Rosenfeld JA, Liu P, Ek M, Schuy J, Ameur A, Dai H, Undiagnosed Diseases Network, Hwang JP, Sedlazeck FJ, Bi W, Marom R, Wincent J, Nordgren A, Carvalho CMB, Lindstrand A. Genome Res 34: 2024 1785-1797	0