Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation

Abstract

Copy-number variants (CNVs) have been the predominant focus of genetic studies of structural variation, and chromosomal microarray (CMA) for genome-wide CNV detection is the recommended first-tier genetic diagnostic screen in neurodevelopmental disorders. We compared CNVs observed by CMA to the structural variation detected by whole-genome large-insert sequencing in 259 individuals diagnosed with autism spectrum disorder (ASD) from the Simons Simplex Collection. These analyses revealed a diverse landscape of complex duplications in the human genome. One remarkably common class of complex rearrangement, which we term dupINVdup, involves two closely located duplications ("paired duplications") that flank the breakpoints of an inversion. This complex variant class is cryptic to CMA, but we observed it in 8.1% of all subjects. We also detected other paired-duplication signatures and duplication-mediated complex rearrangements in 15.8% of all ASD subjects. Breakpoint analysis showed that the predominant mechanism of formation of these complex duplication-associated variants was microhomology-mediated repair. On the basis of the striking prevalence of dupINVdups in this cohort, we explored the landscape of all inversion variation among the 235 highest-quality libraries and found abundant complexity among these variants: only 39.3% of inversions were canonical, or simple, inversions without additional rearrangement. Collectively, these findings indicate that dupINVdups, as well as other complex duplication-associated rearrangements, represent relatively common sources of genomic variation that is cryptic to population-based microarray and low-depth whole-genome sequencing. They also suggest that paired-duplication signatures detected by CMA warrant further scrutiny in genetic diagnostic testing given that they might mark complex rearrangements of potential clinical relevance.

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

“…9, 10). Statistically significant CNV segments were integrated with predicted balanced SVs using a series of breakpoint linking methods to identify signatures of 20 canonical, balanced, and complex SV classes (Supplementary Table 8) 27,30 .…”

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

“…All computational analyses have been previously described 74,83 . In brief, reads were reverse-complemented and aligned using BWA 84 .…”

“…Anomalous read-pairs in terms of insert size, mate mapping, or mate orientation were extracted using Sambamba and clustered using ReadPairCluster, our single-linkage clustering algorithm 11,85 . Anomalous read-pair clusters meeting our established thresholds of structural variation were subsequently classified based on their read-pair orientation signature into the following categories: deletions, insertions, inversions, and translocations 83 . When no clusters were found that matched the proposed karyotype, BAM files were agnostically analyzed and manually inspected for anomalous pairs or split reads.…”

An open resource of structural variation for medical and population genetics

“…The spectrum of SVs present in gnomAD-SV was diverse: we completely resolved 5,295 complex SVs across 11 mutational subclasses, of which 3,901 (73.7%) involved inverted segments (Figure 2), confirming prior predictions that most inversion variation accessible to short-read WGS comprises complex SVs rather than canonical inversions. 1,30 Across all SV classes, most SVs were small (median SV size = 331 bp; Figure 1f) and rare (AF < 1%; 92% of SVs; Figure 1g), with nearly half of all SVs (49.8%) appearing as "singletons" (i.e., only one allele observed across all samples). While singleton proportion varied by SV class, it was strongly dependent on SV size across all classes, suggesting that the amount of genetic material rearranged is a principal determinant of selection against most SVs (Figure 1h and Extended Data Figure 5a).…”