Long‐read sequencing and optical genome mapping identify causative gene disruptions in noncoding sequence in two patients with neurologic disease and known chromosome abnormalities

• Published in: American journal of medical genetics. Part A 2024-12, Vol.194 (12), p.e63818-n/a
• Main Authors: Sund, Kristen L., Liu, Jie, Lee, Joyce, Garbe, John, Abdelhamed, Zakia, Maag, Chelsey, Hallinan, Barbara, Wu, Steven W., Sperry, Ethan, Deshpande, Archana, Stottmann, Rolf, Smolarek, Teresa A., Dyer, Lisa M., Hestand, Matthew S.
• Format: Article
• Language: English
• Subjects: Child; Child, Preschool; Chromosome Aberrations; chromosome analysis; Chromosome Mapping; Chromosome rearrangements; Chromosomes; Developmental Disabilities - genetics; Developmental Disabilities - pathology; DNA damage; Epilepsy; Female; Gene mapping; Genomes; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Inversion; long read; Male; Nervous System Diseases - diagnosis; Nervous System Diseases - genetics; Nervous System Diseases - pathology; neurologic disease; Neurological diseases; Next-generation sequencing; noncoding; Nucleotide sequence; optical genome mapping; Patients; Phenotype; Phenotypes; structural variation; Translocation, Genetic - genetics
• ISSN: 1552-4825; 1552-4833; 1552-4833
• DOI: 10.1002/ajmg.a.63818

Despite advances in next generation sequencing (NGS), genetic diagnoses remain elusive for many patients with neurologic syndromes. Long‐read sequencing (LRS) and optical genome mapping (OGM) technologies improve upon existing capabilities in the detection and interpretation of structural variation in repetitive DNA, on a single haplotype, while also providing enhanced breakpoint resolution. We performed LRS and OGM on two patients with known chromosomal rearrangements and inconclusive Sanger or NGS. The first patient, who had epilepsy and developmental delay, had a complex translocation between two chromosomes that included insertion and inversion events. The second patient, who had a movement disorder, had an inversion on a single chromosome disrupted by multiple smaller inversions and insertions. Sequence level resolution of the rearrangements identified pathogenic breaks in noncoding sequence in or near known disease‐causing genes with relevant neurologic phenotypes (MBD5, NKX2‐1). These specific variants have not been reported previously, but expected molecular consequences are consistent with previously reported cases. As the use of LRS and OGM technologies for clinical testing increases and data analyses become more standardized, these methods along with multiomic data to validate noncoding variation effects will improve diagnostic yield and increase the proportion of probands with detectable pathogenic variants for known genes implicated in neurogenetic disease.