Whole‐genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome

Abstract

Clinical laboratory diagnostic evaluation of the genomes of children with suspected genetic disorders, including chromosomal microarray and exome sequencing, cannot detect copy number neutral genomic rearrangements such as inversions, balanced translocations, and complex chromosomal rearrangements (CCRs). We describe an infant with a clinical diagnosis of Cornelia de Lange syndrome (CdLS) in whom chromosome analysis revealed a de novo complex balanced translocation, 46,XY,t(5;7;6) (q11.2;q32;q13)dn. Subsequent molecular characterization by whole-genome sequencing (WGS) identified 23 breakpoints, delineating segments derived from four chromosomes (5;6;7;21) in ancestral or inverted orientation. One of the breakpoints disrupted a known CdLS gene, NIPBL. Further investigation revealed paternal origin of the CCR allele, clustering of the breakpoint junctions, and molecular repair signatures suggestive of a single catastrophic event. Notably, very short DNA segments (25 and 41 bp) were included in the reassembled chromosomes, lending additional support that the DNA repair machinery can detect and repair such segments. Interestingly, there was an independent paternally derived miniscule complex rearrangement, possibly predisposing to subsequent genomic instability. In conclusion, we report a CCR causing a monogenic Mendelian disorder, urging WGS analysis of similar unsolved cases with suspected Mendelian disorders. Breakpoint analysis allowed for identification of the underlying molecular diagnosis and implicated chromoanagenesis in CCR formation.

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

“…Although this type of aberration complies with some aspects of chromothripsis, including the involvement of one chromosome and six breakpoints with genomic fragment shuffling in a balanced manner (Kloosterman et al, 2011(Kloosterman et al, , 2012Maher and Wilson, 2012), the fact that the breakpoints are not clustered and appear to occur within transcriptionally active areas (four out of six breakpoints occur within genes) is also in line with a chromoplexy-type event (Shen, 2013;Redin et al, 2017). Although chromothripsis and chromoplexy were first characterized in cancer genomes, the same "mutagenic phenomenon" has been shown to underlie Mendelian diseases and genomic disorders by disruption of genes through truncating breakpoints (haploinsufficiency), by the generation of fusion genes (ectopic expression), or other position effects (Maher and Wilson, 2012;Baca et al, 2013;Redin et al, 2017;Plesser Duvdevani et al, 2020). This process may occur in a random order of DNA fusion but interestingly in this present case, almost all the inversion events happen sequentially from one another in a potential "chained" fashion rather than a single "pulverizing" event which is more suggestive of chromoplexy (chained rearrangements) over chromothripsis (a single catastrophic event occurring).…”

“…Moreover, the identification of several de novo inversions on a single chromosome, generated through a chromothriptic-like mutational event, suggests that such mutational process may lead to hidden complexities in seemingly "simple" structural variants. As we continue to refine and improve our ability to resolve inversions and other complex structural variants, "unsolved" Mendelian diseases should be investigated by applying new and developing genomic methodologies that allow phasing multiple breakpoint junctions in cis (Liu et al, 2019;Plesser Duvdevani et al, 2020).…”

“…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.…”

RNA-seq in DMD urinary stem cells recognized muscle-related transcription signatures and addressed the identification of atypical mutations by whole-genome sequencing

“…In patients DI and SE, we found two large and never-before-reported inversions in the DMD gene, further supporting the value of WGS in detecting novel complex rearrangements. 53 , 54 , 55 …”

Fine Breakpoint Mapping by Genome Sequencing Reveals the First Large X Inversion Disrupting the NHS Gene in a Patient with Syndromic Cataracts

“…With the advent of WGS approaches, there is increasing evidence that some SVs can cause disease phenotypes due to gene disruption, cryptic copy-number imbalance, or gene dysregulation by positional effects [ 3 , 16 , 26 ]. Paired-end WGS mapping of SVs using the algorithm of read-pair orientation has been efficiently used in detecting breakpoints in highly repetitive regions such as centromeric regions, segmental duplications, and short arms [ 15 , 18 , 19 , 27 , 28 , 29 , 30 , 31 ]. Using this strategy, we successfully identified breakpoints at a base-pair resolution of a large balanced inversion, first characterised as inv(X)(p22q27) in a male patient suffering from a syndromic form of congenital cataracts; thus, providing a more precise clinical interpretation for this SVs.…”