Low copy repeats mediate distal chromosome 22q11.2 deletions: Sequence analysis predicts breakpoint mechanisms

Abstract

Genomic disorders contribute significantly to genetic disease and, as detection methods improve, greater numbers are being defined. Paralogous low copy repeats (LCRs) mediate many of the chromosomal rearrangements that underlie these disorders, predisposing chromosomes to recombination errors. Deletions of proximal 22q11.2 comprise the most frequently occurring microdeletion syndrome, DiGeorge/Velocardiofacial syndrome (DGS/VCFS), in which most breakpoints have been localized to a 3 Mb region containing four large LCRs. Immediately distal to this region, there are another four related but smaller LCRs that have not been characterized extensively. We used paralog-specific primers and long-range PCR to clone, sequence, and examine the distal deletion breakpoints from two patients with de novo deletions mapping to these distal LCRs. Our results present definitive evidence of the direct involvement of LCRs in 22q11 deletions and map both breakpoints to the BCRL module, common to most 22q11 LCRs, suggesting a potential region for LCR-mediated rearrangement both in the distal LCRs and in the DGS interval. These are the first reported cases of distal 22q11 deletions in which breakpoints have been characterized at the nucleotide level within LCRs, confirming that distal 22q11 LCRs can and do mediate rearrangements leading to genomic disorders.[Supplemental material is available online at www.genome.org. The sequence data have been submitted to GenBank under accession nos. EF025176-EF025177.]Chromosome 22q11 shows a high frequency of de novo genomic rearrangement. This instability is attributed to the presence of several large paralogous low copy repeats (LCRs) or segmental duplications (SDs), each containing a complex modular structure and a high degree of sequence identity (>96%) over large stretches of the repeat . The LCRs apparently mediate aberrant interchromosomal exchanges during meiosis (Saitta et al. 2004), and 22q11 deletions, which occur in up to 1:4000 live births (Burn and Goodship 1996), are among the most frequent constitutional rearrangements. Other chromosomes are also known to contain similar "rearrangementpromoting" low copy repeats that are implicated in mediating genomic disorders. Examples of such well-known genetic disorders include Prader-Willi and Angelman syndromes, Williams syndrome, NF1 microdeletions, Sotos syndrome, Smith-Magenis syndrome, and the reciprocal deletions and duplications of Charcot Marie Tooth and HNPP (for reviews, see Emanuel and Shaikh 2001;.There are a total of eight LCRs within 22q11. The four proximal LCRs have been extensively characterized, given their involvement in recurrent rearrangements of 22q11 that lead to DGS/VCFS (Edelmann et al. 1999;Shaikh et al. 2001) and Cat eye syndrome (CES) (McTaggart et al. 1998). We have previously referred to the four proximal LCRs as LCR-A through LCR-D based on their chromosomal order, with LCR-A being closest to the centromere . These proximal LCRs are larger than the distal ones and have a complex modular structure. LCR-A and LCR...

The recurrent distal 22q11.2 microdeletions are often de novo and do not represent a single clinical entity: a proposed categorization system

“…DD and/or ID have been reported in more than 80% of distal 22q11.2 microdeletion patients described in the literature to date and tend to be relatively mild to moderate in severity. [7][8][9][10][11][12][13][14][15][16][17][18] Taken together, global DD and ID seem to be key components of the distal 22q11.2 microdeletions phenotype irrespective of the size and position of the deletion. Behavioral and neurological problems were also quite common in our patients in all deletion types.…”

“…[7][8][9][10][11][12][13][14][15][16][17][18] These deletions are mediated by nonallelic homologous recombination between the five telomeric LCR22s (LCR22-D to -H) in the distal portion of the 22q11.2 region (Figure 2). 10 Distal 22q11.2 microdeletions that span the LCR22-F to -G interval encompassing the tumor suppressor SMARCB1 gene (also called INI1) have been reported to manifest many of the presenting features mentioned above but also have high incidence of malignant rhabdoid tumors in infancy and early childhood, predominantly in the kidneys and central nervous system, which necessitates tumor surveillance in these patients. [19][20][21][22][23][24] Depending on the mediating LCR22s, the distal 22q11.2 microdeletions can vary in size between ~700 kb and ~3.0 Mb.…”

“…[7][8][9][10][11][12][13][14][15][16][17][18] Moreover, some patients present with cleft lip and/or cleft palate. Although some of our patients manifested some of these features, the majority of them presented with nonspecific, nondiagnostic features that were quite variable, as shown in the Results section.…”

“…6 Recently, others and we demonstrated that the five telomeric LCR22s, namely LCR22-D to H, at the distal portion of 22q11.2 are causally implicated in the recurrent distal 22q11.2 microdeletion-associated phenotype(s) (OMIM 611867), and their reciprocal microduplications in the region immediately distal to the DG/VCFs typically deleted region (Figure 2). [7][8][9][10][11][12][13][14][15][16][17][18] The structure of the LCR22-D, -E, and -F has been studied and was shown to contain the BCRL module in each LCR22, suggesting that the distal 22q11.2 microdeletions/microduplications are mediated by nonallelic homologous recombination. 10 To date, the distal 22q11.2 microdeletions have been grouped together as a single clinical entity despite the fact that these deletions are variable in size and position depending on the Purpose: The five segmental duplications (LCR22-D to -H) at the distal region of chromosome 22 band q11.2 in the region immediately distal to the DiGeorge/velocardiofacial syndrome deleted region have been implicated in the recurrent distal 22q11.2 microdeletions.…”

Caracterização fenotípica em indivíduos com microarranjos na região cromossômica 22q11

“…Três classes de deleções foram identificadas: 3 Mb em 90% dos indivíduos com síndrome VCF, conhecida como a região tipicamente deletada (typically deleted region, TDR); 1,5 Mb em 7% a 8% dos indivíduos, identificada como região crítica DiGeorge (DGRC); rearranjos menores dentro da região crítica de 3 Mb, presentes em 2 a 3% dos casos (AUGUSSEAU et al, 1986;LINDSAY et al, 1995;CARLSON et al, 1997;EDELMANN et al, 1999;REISH et al, 2003;RUITER et al, 2003;D'ANTONI et al, 2004;SHAIKH et al, 2007;STACHON et al, 2007;BASHIR et al, 2008;BLENNOW et al, 2008;EMANUEL, 2008;ROSA et al, 2009;DRAAKEN et al, 2010). …”