Characterization of Rare Genomic Structural Variants Across 2,981 Genomes Reveals Significant Involvements in Recessive Conditions

Background Genomic structural variants (SV) underlie genomic diversity and human diseases, encompassing various types of deletions/duplications and genomic rearrangements. Current methods experience challenges in precisely identifying and determining SV composition which often lead to incorrect interpretation and/or missing detection of clinically significant variants. Here, we introduce SCARD (Split-read, Chimeric read-pAirs, and Read-depth Difference), an integrated approach optimized for detection and characterization of rare SVs using genome sequencing data, applied to investigate the SV spectrum across 2,504 individuals and 477 trios/probands from the 1000 Genomes Project. Methods We evaluated the rare SV (with minor allele frequency < 1%) detection performance using 16 clinical cases with 18 previously ascertained exonic deletions/duplications in dominant/recessive conditions. In addition, SCARD characterized the spectrum, inheritance rate, and clinical implications of rare SVs identified from 2,981 genomes. We described clinically significant, loss-of-function (LoF) SVs involving genes associated with autosomal recessive disorders, defined by OMIM and/or ClinGen Dosage Sensitivity Map. Finally, to evaluate the specificity of rare SV calling, we compared our SVs in 15 cases to that of long-read sequencing datasets, and those results from 13 SV detection methods (13callers). Results SCARD accurately detected all 18 exonic deletions/duplications, ranging from 490bp to 24.5kb, confirmed by gap-PCR and/or Sanger sequencing, outperforming other methods that only achieved 15/18 at best. Among 2,504 genomes analyzed, we identified 429,259 rare simple deletions/duplications and 7,795 structural rearrangements, with 10.7% of deletions/duplications (46,032/429,259) and 40.1% of structural rearrangements (3,126/7,795) being novel to that from 13callers. Notably, 45.2% (1,133/2,504) of the subjects carried LoF SVs involving autosomal recessive disorders related genes. In 477 trios, the overall de novo rate for rare SVs was 0.5% (383/77,349). Lastly, among the 15 cases with long-read sequencing datasets, the specificities of detecting deletions/duplications, structural rearrangements, and all SVs by SCARD were 98.0% (2,858/2,917), 94% (47/50), and 97.9% (2,905/2,967), respectively. In comparison, 13callers missed or misinterpreted 325 of the 2,905 validated rare SVs (11.2%) reported by SCARD. Conclusions Our study demonstrates that SCARD enables comprehensive, genome-wide identification and precise delineation of rare SVs, particularly for those affecting exons, revealing a high carrier rate of AR disorders contributed by rare SVs.