Ring chromosomes uncovered by optical genome mapping: impact of telomeric-associated regions and reference genome selection on structural variant interpretation.

Ring chromosomes (RCs) are rare structural variants usually formed by fusion of both chromosome arm extremities, frequently associated with terminal deletions. RCs are investigated through karyotype, fluorescence in situ hybridization, chromosomal microarray analysis, and, more recently, optical genome mapping (OGM), which enables genome-wide structural variant detection; however, its accuracy depends on alignment to a reference genome and proper filtering of SVs. Here, two patients with previously characterized ring chromosomes 3 and 18, each with a terminal deletion in only one chromosome arm (3p and 18q), were analyzed by OGM after aligning the data against two reference genomes (GRCh38/hg38 and T2T-CHM13) and compared with long-read sequencing (LRS) results stemming from a parallel study that included both patients. Patient 1's RC3 was misinterpreted as a translocation between chromosomes 3 and 19 when analyzed with GRCh38/hg38. Reanalysis with T2T-CHM13 correctly identified the RC3 and demonstrated retention of the full 3q arm, including telomeric-associated regions, which was confirmed by LRS. Patient 2's ring chromosome 18 was identified with GRCh38/hg38 only after lowering the confidence score filter, whereas T2T-CHM13 detected the RC18 immediately without involvement of 18p telomeric-associated regions. LRS diverged from this analysis by showing the presence of these regions in the RC18 due to its nucleotide-level resolution. Only eight out of ~ 3,000 RCs have been reported in the literature as resolved using OGM, and here we add two more cases analyzed with different reference genomes and highlight the techniques' advantages and limitations for RC characterization. Since the T2T-CHM13 analysis outperformed GRCh38/hg38 because it resolves previously inaccessible telomeric regions, we included an investigation into which other chromosomes could also benefit more from this approach.