Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)

Abstract

Approximately one in 500 individuals carries a reciprocal translocation. Balanced translocations are usually associated with a normal phenotype unless the translocation breakpoints disrupt a gene(s) or cause a position effect. We investigated breakpoint junctions at the sequence level in phenotypically normal balanced translocation carriers. Eight breakpoint junctions derived from four nonrelated subjects with apparently balanced translocation t(1;22)(p36;q13) were examined. Additions of nucleotides, deletions, duplications, and a triplication identified at the breakpoints demonstrate high complexity at the breakpoint junctions and indicate involvement of multiple mechanisms in the DNA breakage and repair process during translocation formation. Possible detailed nonhomologous end-joining scenarios for t(1;22) cases are presented. We propose that cryptic imbalances in phenotypically normal, balanced translocation carriers may be more common than currently appreciated.[Supplemental material is available online at www.genome.org.]With the exception of benign copy number variation, it is generally assumed that a normal phenotype is associated only with a balanced genotype. However, a balanced translocation may produce an abnormal phenotype by disruption of a gene at the translocation breakpoint, through the formation of a novel fusion gene product, or by a position effect. Moreover, in apparently balanced translocations with abnormal phenotypes, duplications and deletions at the breakpoints have been identified that impact the phenotype. Baptista et al. (2005) hypothesized that breakpoints of normal individuals with apparently balanced chromosome rearrangements are relatively simple. However, their study was based on molecular cytogenetic methods (fluorescence in situ hybridization [FISH] and microarray-based comparative genomic hybridization [array CGH]) only. Breakpoints in only a few constitutional rearrangements in individuals with normal phenotypes have been examined at the DNA sequence level. These include translocations t(11;22) (Kurahashi et al. 2000(Kurahashi et al. , 2007, the most common constitutional translocation in humans, in which junction fragments were identified, and other translocation events including t(1;22)(p21.2;q11.2) (Gotter et al. 2004), t(4;22)(q35.1;q11.2) (Nimmakayalu et al. 2003), and t(8;22)(q24.13;q11.21) (Gotter et al. 2007). We have previously examined apparently balanced translocations in phenotypically normal individuals and found evidence that translocation junctions may show sequence inconsistency at the breakpoints created by addition of nucleotides and duplications (Gajecka et al. 2006b).The resolution of DNA double-strand breaks (DSBs) can result in translocation formation through a variety of different pathways. In homologous recombination repair, the DNA ends can be aligned and joined using sequence homology. Alternatively, the broken ends can be brought together and rejoined in the absence of long tracks of sequence homology through nonhomologous end-joining (NHEJ). Two ...

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

“…However, the remainder appear to entail complex rearrangements; six are insertions of DNA from <10 kb away, 14 are insertions from distant loci, and five are small-scale rearrangements that appear as insertions because they perturb alignment of the breakpoint region. Similar small-scale insertions and rearrangements have recently been reported at breakpoints in a tumor genome (Hampton et al 2009), and at several large-scale rearrangement breakpoints identified among human individuals (Gajecka et al 2008) and in the gibbon lineage ).…”

Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations

“…NAHR between LINEs has, indeed, been instrumental in shaping the structure of the human genome (Han et al 2008). However, thus far, NAHR between LINEs has rarely been detected in large-scale studies analyzing the breakpoints of pathogenic CNVs and balanced translocations (Burwinkel and Kilimann 1998;Segal et al 1999;Gribble et al 2005Gribble et al , 2007Higgins et al 2008;Chiang et al 2012), nor have they been observed in the many case reports mapping balanced translocation breakpoints (McMullan et al 2002;Gajecka et al 2008). In a recent systematic mapping study of chromosomal subtelomeric rearrangements, the breakpoints of four unbalanced translocation breakpoints were sequenced (Luo et al 2011).…”

Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles

“…Smaller duplications at reciprocal breakpoints have been noted previously, but much smaller than the tens of kilobases found here. For example, in four cases of MALT lymphoma, duplications ranging from 105 bp to 3.3 kb were observed at reciprocal breakpoints (Liu et al 2004); duplications of ;250 bp have been found in chronic myeloid leukemia (Litz et al 1993), and a 337-bp duplication of chromosome 22 was seen at a balanced t(1;22) breakpoint in a phenotypically normal individual (Gajecka et al 2008). Microduplication of a few base pairs has also been described (Gajecka et al 2006), which is presumably just a signature of the joining mechanism.…”

“…In breast cancers, Stephens et al (2009) found that 15% of rearrangements showed non-templated sequence and a further 4% contained genomic shards. Microhomology is usual at the junctions of rearrangements in leukemia translocations (Nickoloff et al 2008), constitutional rearrangements (Gajecka et al 2008), and at many non-recurrent CNV (copy number variant) breakpoint junctions, including tandem duplications (Hastings et al 2009b;Vissers et al 2009). …”

“…This applies both to neoplastic and constitutional translocations. While some additional rearrangements involve only a few base pairs to a few hundred base pairs (Shimizu et al 1992;Gajecka et al 2008), many of them involve tens to thousands of kilobases. Most familiar are deletions at the breakpoints, illustrated in Figure 1B.…”