Complex genomic rearrangements: an underestimated cause of rare diseases

Abstract

Complex genomic rearrangements (CGRs) are known contributors to disease but are often missed during routine genetic screening. Identifying CGRs requires (i) identifying copy number variants (CNVs) concurrently with inversions, (ii) phasing multiple breakpoint junctions incis, as well as (iii) detecting and resolving structural variants (SVs) within repeats. We demonstrate how combining cytogenetics and new sequencing methodologies is being successfully applied to gain insights into the genomic architecture of CGRs. In addition, we review CGR patterns and molecular features revealed by studying constitutional genomic disorders. These data offer invaluable lessons to individuals interested in investigating CGRs, evaluating their clinical relevance and frequency, as well as assessing their impact(s) on rare genetic diseases.

Keywords: chromosomal abnormalities; clinical diagnostics; constitutional diseases; genomic disorders; structural variation; whole-genome sequencing.

Figure 1.. Recurrent patterns of complex genomic rearrangements (CGRs) in constitutional and cancer genomes.

(A) Pie charts showing the proportion and absolute numbers of duplications (left) [,,–95] and deletions (right) [96] causing Pelizaeus–Merzbacher disease. (B) Deletions and duplications in complex genomic events causing Yuan–Harel–Lupski syndrome [97], MECP2 duplication syndrome [41,51,98], and 17p13.3 duplication syndrome [49]. (C) Copy number signature of DUP–NML–DUP (interspersed duplications). One of four predicted DUP–NML–DUP genomic structures [49] is displayed at the bottom; this specific type was experimentally observed in pericentric inversions [10,99]. (D) Copy number signature of the DUP–TRP/INV–DUP CGR [inverted triplication (blue) flanked by duplications (red)]. The derivative structure displayed in the bottom was proposed from aCGH, Sanger sequencing, and FISH experiments. It is the first structure identified in probands affected with MECP2 duplication syndrome or Pelizaeus–Merzbacher disease [41]. Recently, three alternative structures were proposed based on experimental observations in cancer genomes [55]. (E) Copy number signature of a recombinant DEL–NML–DUP (telomeric deletion followed by a copy number neutral chromosome with a telomeric duplication). The duplicated sequence (red) is inverted and inserted at the location of the deletion (green). This rearrangement results from a meiotic recombination in a parent carrying a heterozygous copy number neutral pericentric INV [10] which will be resolved as a recombinant chromosome with a DEL–NML–DUP structure. (F) Copy number signature of DUP/INV–DEL (inverted duplication adjacent to terminal deletion). This structure results from chromosomes with terminal deletions further repaired by a fold-back mechanism mediated by short segments of homology creating a spacer [B] between the inverted duplications [A]. This type of structure can also be resolved as a translocation (inverted duplication translocation) or as a ring chromosome, both of which can be generated through a breakage–fusion–bridge cycle [100]. Purple and orange arrows represent the location of junctions in the reference genome. Abbreviations: aCGH, array comparative genomic hybridization; der, derivative chromosome; DUP, duplication; FISH, fluorescence-in-situ-hybridization; INV, inversion; MIM, Mendelian Inheritance in Man; NML, normal; pter, end of the short arm (p) of the chromosome; qter, end of the long arm (q) of the chromosome; TRP, triplication.

Figure 2.. Resolving genomic aberrations through multiple methodologies.

Four cases from the literature are presented in which the complete genomic architecture could be resolved through a combination of aCGH, short-read GS, breakpoint sequence alignment, and finally Sanger validation of one of the exemplified breakpoint junctions. These cases include (A) a supernumerary marker chromosome [53], (B) an individual with multiple de novo inversions affecting a single chromosome [12], (C) a complex pericentric inversion accompanied by CNVs at the junctions DUP–NML–INV/DUP [10], and (D) a DUP–TRP/INV–DUP at the MECP2 locus [41]. The relative positions and orientations of primers used to amplify each junction are shown as green and purple arrows in the CNV view. Abbreviations: aCGH, array comparative genomic hybridization; CNV, copy number variation; DUP, duplication; GS, genome sequencing; INV, inversion; Jct, junction; NML, normal; TRP, triplication.

Figure 3.. Nonrecurrent patterns of highly complex genomic rearrangements (CGRs) can be classified as intrachromosomal or interchromosomal events.

(A) Chromoanasynthesis: an intrachromosomal rearrangement on chromosome 1 first analyzed with aCGH and resolved by GS (patient P2109_162 [7]). The CGR contained multiple deletions (green) and one duplication (red) as well as a hidden inversion (blue) and a deletion which was later revealed by GS. (B) Chromothripsis: an intrachromosomal chromosome 7 rearrangement first analyzed with aCGH. Linked-read GS uncovered five additional inversions and three deletions (patient 00 [7]). (C) Inserted translocation: one individual carried (Cplex9 [101]) an altered chromosome 13 with an inserted segment (blue) from chromosome 9 at the location of the deletion (green). (D) Complex translocation. 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.