Localization of Jacobsen syndrome breakpoints on a 40-Mb physical map of distal chromosome 11q

Abstract

Jacobsen syndrome is a haploinsufficiency disorder caused, most frequently by terminal deletion of part of the long arm of chromosome 11, with breakpoints in 11q23.3-11q24.2. Inheritance of an expanded p(CCG)n trinucleotide repeat at the folate-sensitive fragile site FRA11B has been implicated in the generation of the chromosome breakpoint in several Jacobsen syndrome patients. The majority of such breakpoints, however, map distal to this fragile site and are not linked with its expression. To characterize these distal breakpoints and ultimately to further investigate the mechanisms of chromosome breakage, a 40-Mb YAC contig covering the distal long arm of chromosome 11 was assembled. The utility of the YAC contig was demonstrated in three ways: (1) by rapidly mapping the breakpoints from two new Jacobsen syndrome patients using FISH; (2) by demonstrating conversion to high resolution PAC contigs after direct screening of PAC library filters with a YAC clone containing a Jacobsen syndrome breakpoint; and (3) by placing 23 Jacobsen syndrome breakpoints on the physical map. This analysis has suggested the existence of at least two new Jacobsen syndrome breakpoint cluster regions in distal chromosome 11.

Figure 1

A 40-Mb YAC contig covering the distal long arm of chromosome 11. At top are the 169 resolved positions defined by the associated STSs. The prefix S in the name of STSs is an abbreviation of D11S. Alternate YACs are shaded for clarity. + and ? indicate a positive or uncertain PCR result for the STS at that position, respectively. Hatched segments indicate possible physical deletions or regions of instability in the YACs, consistently observed in different preparations of the same YAC. A discontinuity in the contig between positions 143 and 144 is indicated by a gap. Numbers of positions linked by a single YAC are boxed. Positions 106 and 107 (asterisks) had the reverse order in the PAC contig of Fig. 2.

Figure 1

A 40-Mb YAC contig covering the distal long arm of chromosome 11. At top are the 169 resolved positions defined by the associated STSs. The prefix S in the name of STSs is an abbreviation of D11S. Alternate YACs are shaded for clarity. + and ? indicate a positive or uncertain PCR result for the STS at that position, respectively. Hatched segments indicate possible physical deletions or regions of instability in the YACs, consistently observed in different preparations of the same YAC. A discontinuity in the contig between positions 143 and 144 is indicated by a gap. Numbers of positions linked by a single YAC are boxed. Positions 106 and 107 (asterisks) had the reverse order in the PAC contig of Fig. 2.

Figure 1

A 40-Mb YAC contig covering the distal long arm of chromosome 11. At top are the 169 resolved positions defined by the associated STSs. The prefix S in the name of STSs is an abbreviation of D11S. Alternate YACs are shaded for clarity. + and ? indicate a positive or uncertain PCR result for the STS at that position, respectively. Hatched segments indicate possible physical deletions or regions of instability in the YACs, consistently observed in different preparations of the same YAC. A discontinuity in the contig between positions 143 and 144 is indicated by a gap. Numbers of positions linked by a single YAC are boxed. Positions 106 and 107 (asterisks) had the reverse order in the PAC contig of Fig. 2.

Figure 1

A 40-Mb YAC contig covering the distal long arm of chromosome 11. At top are the 169 resolved positions defined by the associated STSs. The prefix S in the name of STSs is an abbreviation of D11S. Alternate YACs are shaded for clarity. + and ? indicate a positive or uncertain PCR result for the STS at that position, respectively. Hatched segments indicate possible physical deletions or regions of instability in the YACs, consistently observed in different preparations of the same YAC. A discontinuity in the contig between positions 143 and 144 is indicated by a gap. Numbers of positions linked by a single YAC are boxed. Positions 106 and 107 (asterisks) had the reverse order in the PAC contig of Fig. 2.

Figure 2

A PAC contig corresponding to YAC clone y939H03 covering the chromosome breakpoint of Jacobsen syndrome patient RB. STS markers within the contig are listed without the D11 prefix for clarity; e.g., D11S982E is shown as S982E; the prefix dJ is omitted from PAC names. Alternate PACs are shaded. YAC contig position numbers are in parentheses. STSs were demonstrated within PACs by PCR. PAC end clones are given the prefix ec, together with the clone name and end from which they are derived; they were screened against PACs by hybridization. (+) Positive results for PCR of STSs or hybridization with PAC end clones. Overlap of PAC clones in the contig was also determined by cross-hybridization of PACs against each other. (?) An unclear hybridization.

Figure 3

Localization of 23 Jacobsen syndrome chromosome breakpoints on the YAC contig of distal chromosome 11q. (Solid bar) The intact region of the deleted chromosome with the most distal marker known to be retained (+). (Shaded bar) The maximum extent of the region in which the breakpoint must be located with the most proximal deleted marker (usually bounded by −). (X) A breakpoint is defined with the resolution of a single position on the YAC contig, i.e., to FRA11B for patients 3 and 8, and close to D11S1336 for patient RB. Patients numbered 1–17 are from Penny et al. (1995), of which patients 3 and 8 were shown to have breakpoints at fragile site FRA11B (Jones et al. 1995); patients VH and AD are from Michaelis et al. (1998); patient C is from Breton-Gorius et al. (1995); patient GS is from T. Mattina, C. Jones, and A. Tunnacliffe (in prep.); and patients RB and MC are described in this paper.