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. 2003 Nov;73(5):1061-72.
doi: 10.1086/379155. Epub 2003 Oct 14.

Molecular and fluorescence in situ hybridization characterization of the breakpoints in 46 large supernumerary marker 15 chromosomes reveals an unexpected level of complexity

S E Roberts  1 , F Maggouta, N S Thomas, P A Jacobs, J A Crolla
Affiliations

Molecular and fluorescence in situ hybridization characterization of the breakpoints in 46 large supernumerary marker 15 chromosomes reveals an unexpected level of complexity

S E Roberts et al. Am J Hum Genet. 2003 Nov.

Abstract

Supernumerary marker chromosomes (SMCs) of chromosome 15, designated "SMC(15)s," are the most common SMC in humans, accounting for as much as 60% of all those observed. We report the characterization of 46 large SMC(15)s, using both fluorescence in situ hybridization and polymerase chain reaction analysis within and distal to the Prader-Willi/Angelman syndrome critical region (PWACR). Our aim was to establish detailed information on origin, content, and breakpoints, to address the formation of SMC(15)s, and to facilitate genotype-phenotype correlations. For all patients in whom we were able to establish the parental origin, the SMC(15)s were maternally derived. Two patients were observed who had familial SMC(15)s, both inherited from the mother; however, in all remaining patients for whom parental samples were available, the SMC(15)s were shown to have arisen de novo. With one exception, all the SMC(15)s were shown to include the entire PWACR. Detailed investigations of the distal breakpoints categorized the SMC(15)s into two groups. Group A, representing approximately two-thirds of the SMC(15)s, had a breakpoint beyond the standard distal PWS/AS deletion breakpoint BP3, at a position close to the microsatellite marker D15S1010 and the bacterial artificial chromosome 10I10. The group B SMC(15)s were shorter, with more variable breakpoints located around BP3. The majority of the SMC(15)s were shown to have asymmetrical breakpoints, with the two inverted arms of the SMC being unequal in length. Our study revealed an unexpected level of complexity and heterogeneity among SMC(15)s that is not seen in other chromosome 15 rearrangements, such as deletions and duplications. This suggests that multiple mechanisms are involved in the formation of large SMC(15)s.

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Figures

Figure 1
Figure 1
BAC and microsatellite positions. A, Schematic map of chromosome 15q, showing the relative positions of the BAC probes (shown beneath the line) and microsatellite markers used in the FISH and PCR analysis. The numbers shown above the line are the microsatellite markers, which, for brevity, are listed without the preceding “D15S.” The exact orders of both the BACs and microsatellite markers are not known, because information is unavailable for several of those used. Genes are boxed (UBE3A [MIM 601623] and GABRB3 [MIM 137192]). B, More detailed BAC and microsatellite marker positions, as given in Ensembl release 11.31.1 (February 27, 2003). The distance (expressed as Mb from pter) is shown at the top. The BACs shown at the bottom (dark lines) are those that have exact positions defined in Ensembl. Electronic information on the position of 399P21 is not available, because this BAC has become “buried,” but it contains the STS Y00757. BACs that are PCR positive for the respective microsatellite markers are indicated (gray downward arrows).
Figure 2
Figure 2
PCR results for 44 SMC(15)s (DNA was unavailable for B4, and A18 has been omitted because PCR analysis was completely uninformative). The microsatellite markers are shown in order from the centromere to telomere, with the double lines showing the positions of the common proximal (BP1 and BP2) and distal (BP3) breakpoints seen in patients with deletion/duplication. The positions of some of the BACs are shown on the left of the microsatellite markers. Those shown in boldface are known to contain the adjacent microsatellite marker, whereas the exact positions of those shown in italics are not known. For some individuals (gray hatched bar), we cannot differentiate between one or two breakpoints within this region, because microsatellite markers were uninformative. Proximal to the bar, the copy number is four (except in patients A10, A14, and A17), and, distal to the bar, the copy number is two. For SMCs with two breakpoints the black bar represents the region where the first breakpoint occurs (i.e., the copy number is reduced from four to three), and the white bar represents the second breakpoint (i.e., the copy number is reduced from three to two). The patient numbers are shown at the bottom, with the boxes showing the patients that were also analyzed using FISH. A, Group A patients. B, group B patients. The breakpoints of some of the group B patients appear to be similar to those in group A, but this is because uninformative microsatellite markers make it impossible to define the breakpoints.
Figure 3
Figure 3
Representative examples of FISH on peripheral blood metaphase chromosomes of patient A1, reflecting the asymmetry observed in most of the SMC(15)s analyzed. BACs are labeled with digoxigenin (red), and the plasmid probe pTRA-25 (chromosome 15 centromere) is labeled with biotin (green). Enlargements of the SMC(15)s are shown in the insets. Arrows indicate the SMC(15)s. BAC 322N14 reveals two signals on the SMC (a), and a single signal results from BAC 18H24 (b). No signal is observed with BAC 10I10 (c).
Figure 4
Figure 4
Representative examples of FISH on peripheral blood metaphase chromosomes of patient B3, reflecting the symmetry in some of the SMC(15)s analyzed. BACs are labeled with biotin (green), and the plasmid probe pTRA-25 (chromosome 15 centromere) is labeled with digoxigenin (red). Enlargements of the SMC(15)s are shown in the insets. Arrows indicate the SMC(15)s. BAC 322N14 shows two signals (merged) on the SMC(15) (a). No signal is visible on the SMC(15) with BAC 18H24 (b).
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References

Electronic-Database Information

    1. Ensembl Genome Browser, http://www.ensembl.org (for BACs and microsatellite markers)
    1. Entrez, http://www.ncbi.nlm.nih.gov/entrez (for microsatellite markers)
    1. Genome Database, http://www.gdb.org (for microsatellite marker primer sequences)
    1. Online Mendelian Inheritance in Man (OMIM), http://www.ncbi.nlm.nih.gov/Omim/ (for AS, ATP10, HERC2, and PWS
    1. Unique—Rare Chromosome Disorder Support Group, http://www.rarechromo.org - PubMed

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