Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier

Abstract

Chromoanagenesis is a genomic event responsible for the formation of complex structural chromosomal rearrangements (CCRs). Germline chromoanagenesis is rare and the majority of reported cases are associated with an affected phenotype. Here, we report a healthy female carrying two de novo CCRs involving chromosomes 4, 19, 21 and X and chromosomes 7 and 11, respectively, with a total of 137 breakpoint junctions (BPJs). We characterized the CCRs using a hybrid-sequencing approach, combining short-read sequencing, nanopore sequencing, and optical mapping. The results were validated using multiple cytogenetic methods, including fluorescence in situ hybridization, spectral karyotyping, and Sanger sequencing. We identified 137 BPJs, which to our knowledge is the highest number of reported breakpoint junctions in germline chromoanagenesis. We also performed a statistical assessment of the positioning of the breakpoints, revealing a significant enrichment of BPJ-affecting genes (96 intragenic BPJs, 26 genes, p < 0.0001), indicating that the CCRs formed during active transcription of these genes. In addition, we find that the DNA fragments are unevenly and non-randomly distributed across the derivative chromosomes indicating a multistep process of scattering and re-joining of DNA fragments. In summary, we report a new maximum number of BPJs (137) in germline chromoanagenesis. We also show that a hybrid sequencing approach is necessary for the correct characterization of complex CCRs. Through in-depth statistical assessment, it was found that the CCRs most likely was formed through an event resembling chromoplexy—a catastrophic event caused by erroneous transcription factor binding.

High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance

“…This insertion was missed by CMA, WES, and WGS [ 55 ]. Therefore, it is important to be cognizant of the complementary nature of different genomic technologies [ 56 ].…”

Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin–Siris Syndrome

“…Herein, we present a patient with Coffin-Siris syndrome 1 (CSS1) and multiple inversions affecting a single chromosome. Complex structural variants have been shown to present a challenge for detection as well as molecular and genomic characterization partly due to the inability to properly phase detected variants, as well as subsequent clinical interpretation of potential contribution of variant effects to observed clinical phenotype(s) (Grochowski et al, 2018;Eisfeldt et al, 2020;Plesser Duvdevani et al, 2020). To experimentally dissect the genomic architecture of the rearranged chromosome 6 of this patient, and to explore whether genes involved in the rearrangement contributed to the observed clinical traits, we employed several technologies including karyotyping (Gbanding), fluorescence in situ hybridization (FISH), quantitative PCR (qPCR), aCGH, WGS, and genomic optical mapping in this study.…”

Complex genomic rearrangements: an underestimated cause of rare diseases

“…The fourth case (case 2 in [ 8 ]) is a complex translocation between chromosomes 1, 5, and 10, whereas chromosome 10 carries an additional deletion (green). (E) Chromoplexy: the last case [ 9 ] is a highly complex rearrangement with 137 breakpoints affecting chromosomes 4, 7, 11,19, 21, and X. Abbreviations: aCGH, array comparative genomic hybridization; der, derivative chromosome; chr, chromosome; GS, genome sequencing; Jct, junction; SINE, short interspersed nuclear element.…”

“…Historically, CGR breakpoints were inferred using fluorescence in situ hybridization (FISH), multi-color banding, as well as karyotyping and chromosomal microarray (CMA) [6]. Because genome sequencing (GS) methodologies have increased our ability to detect and interpret complex genomic events, a growing number of reports of clinically relevant CGRs with an unexpected level of complexity have been published in the scientific literature [7][8][9][10][11][12]. Hence, CGRs, that were once presumed to be 'ultra-rare' occurrences may be more common than originally thought.…”