11. Evaluation of Hi-C versus optical genome mapping for diagnosing constitutional genomic structural variants

He Fang



He Fanga, Yajuan Liub, Steve Eackerc, Whitney Neufeld-Kaiserb

aUniversity of Washington, Lynnwood, WA, United States; bUniversity of Washington, Seattle, WA, United States; cPhaseGenomics, Seattle, WA, United States

Accurate diagnosis, prognosis, and management of genetic diseases require precise characterization of genomic structural variants (GSVs). However, current methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray analysis (CMA), have limitations that preventing a comprehensive understanding of GSVs and are often ordered reflexively in the clinical setting. To overcome these limitations, we implemented proximity ligation sequencing (Hi-C), which can capture ultra-long-range genome contiguity information, and compares it to optical genome mapping (OGM).

We performed Hi-C on ~100 clinical samples previously characterized by karyotyping, FISH and/or CMA, representing various types of GSVs and samples (blood, amniotic fluid, chorionic villi, cultured cells, tissues). We performed both OGM and Hi-C on 16 samples. Our results indicate that Hi-C effectively detects both balanced and unbalanced chromosomal rearrangements, such as translocations (including Robertsonian translocations), insertions, and inversions, with 100% concordance with standard of care methods. Hi-C is highly accurate in detecting copy number alterations (91% sensitivity and 100% specificity). The sensitivity of detecting smaller CNVs increased with increasing sequencing depth. Furthermore, deeper sequencing allows Hi-C to detect long stretches of homozygosity and low-level mosaicisms. Hi-C and OGM showed complete concordance in 12 of 16 samples.  OGM failed to detect Robertsonian translocations in 2 samples and failed for 2 cultured amniocytes samples. Our study demonstrates that Hi-C and OGM are promising new methods that provides a comprehensive understanding of GSVs and has the potential to greatly enhance the diagnosis, prognosis, and therapeutic management of genetic disorders.