Introduction

Several disease genes of medical importance have been assigned to the region 13q14-q21 of chromosome 13. Deletions in the region, occurring in a proportion of retinoblastoma patients, provided a clue to the identification and isolation of the RB1 gene [1]. Other chromosomal rearrangements in the region found in association with chronic B-cell leukaemia, indicate that it may be the location of a gene involved in the development of this form of leukaemia [2]. Linkage analysis has shown that the locus for Wilson disease (WND), an autosomal recessive disorder of copper metabolism, is tightly linked to the chromosomal marker D13S31 [3, 4] positioned at the junction of chromosomal bands 13q14.3-q21.1 [5]. Recent abstracts suggest that the gene has been cloned [6, 7].

In order to identify microsatellite markers in the 13q14 region, two CA-repeats were isolated from clones from a lambda phage library from hybrid cell line ICD, containing 13pter-q14.3 as its sole human material [8], that also hybridized to cell line E8 (13q14.1-qter) as detected by fluorescent in situ hybridization (FISH) [9].

These CA-repeats were mapped on a panel of 13 cell lines with breakpoints in the chromosomal region 13q 14–21. In addition, we mapped 6 restriction fragment length polymorphism (RFLP) [3, 4, 10, 13], and 11 microsatellites from three different genetic maps [10–12] on this hybrid panel. The three genetic maps provide only approximate locations of the loci, the map of Bowcock et al. [10] being the only one which also includes the RFLP markers previously analyzed. Unfortunately, these three maps have no markers in common except for two loci at 13q32-q34, D13S64 and D13S71, which appear on the maps of Bowcock et al. [10] and Petrukhin et al. [11].

In the present study, we present a deletion hybrid breakpoint map of the chromosomal region 13q14–21, divided in 10 distinct intervals, which integrates the relative positions of the markers from the three genetic maps [10–12], and from the earlier RFLP map [13], and of 2 newly isolated microsatellites.

Materials and Methods

Hybrid Cell Lines

Hybrid cell lines GF7 (human chromosome 13 only [8]), ICD (13pter-13q14.3 [8]), WC-H38B3B6 (13pter-q13::13q21.1 -qter [14]), WC-H12D12 (13pter-q14::13q22-qter [14]), NM-87-26XT (13q12-q14:: 13q22-qter [15]), PKII-90-P5b (= PK88-25, 13pter-q12::13q21.2-qter [15]), KSF39 (13pter-q14.1 [16]), KBF11 (13pter-q12::13q14-qter [16]), E8 (13q14.1-qter[17]), D1 (13pter-q14.1 [17]), RHF 407 (13q14.3–13qter [2]), RHF 2324 (13pter-13q14.3 [2]), GS89a (13pter-q14::13q32–34 [D. Warburton, unpubl.]), and CF27 (13pter-q14.1::13q22-qter [T.K. Mohandas, unpubl.] were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum in the presence of antibiotics. All hybrid cell lines except GF7 and ICD contain other human chromosomes in addition to the der(13). DNA was isolated after treatment of the cells with SDS and proteinase K by phenol extraction according to standard procedures.

Plasmid Cloning, Sequencing and Primer Design

(CA)n-containing EMBL3 clones λ42.6 and λ42.7 were isolated from a phage lambda library from cell line ICD [8]. Phage λ42.6 was cut with Sau3A and ligated in the BamHI site of pBluescriptKS(−). Phage λ42.1 was cut with RsaI, HaeIII, and AluI and ligated in the EcoRV site of pBluescriptKS(−). The ligation mix was transformed into Escherichia coli JM83 or DH5α competent cells, respectively. (CA)n-containing subclones were identified by colony hybridization with an end-labelled (GT)12 oligonucleotide. The clones were sequenced from both ends using the T7 sequenase kit (Pharmacia LKB, Uppsala, Sweden) and standard primers. Primers on both sides of the CA-repeats were selected with the aid of the computer program ‘primer designer’ (Scientific & Educational Software, Need City, Pa., USA).

PCR Reactions

Reactions were carried out in 20-µl volumes of ‘Supertaq reaction buffer’ (Sphearo Q HT Biotechnology, Leiden, The Netherlands) with final concentrations of 10mM Tris-HCl (pH = 9.0), 50 mM KCl, 1.5 mM Mg2+, 0.1% Triton X-100, 0.01% gelatin, and including 0.2 mM of each dNTP (dATP, dCTP, dGTP, dTTP), 0.125 U Taq polymerase (Supertaq, Sphearo Q HT Biotechnology), 100 ng of each primer and 100–300 ng template DNA. After an initial denaturation step of 93° C for 2 min, thermal cycling was carried out for 27 cycles consisting of denaturation at 93°C for 1 min, annealing at 5–10°C below Td for 1 min, and extension at 72° C for 1 min, followed by a final extension step at 72 °C for 5 min. For some primer sets, it was necessary to increase the annealing temperature of the first cycles to increase specificity. PCR products were visualized on agarose gels, stained with ethidium bromide.

Radioactive PCR was carried out by substituting 1/10 of the dCTP by [α-32P]dCTP. Products were size separated on 4–6% Polyacrylamide gels and analyzed after exposure to an X-ray-sensitive film.

Results

Development of New Microsatellite Markers

Two human insert-containing phages from an EMBL3 library from cell line ICD [9], shown by FISH to lie distal to the translocation breakpoint of the der(13) involved in alveolar rhabdomyosarcoma in cell lines E8 and D1, contained a CA-repeat as determined by hybridization with a (GT)12 oligonucleotide. (CA)n-containing fragments of these phages, designated λ42.6 and λ 42.7, were sub-cloned and sequenced (see Materials and Methods). The designed primers flanking the CA-repeat are presented in table 1. Both CA-repeats were polymorphic with heterozygosities of 41 and 82%, respectively.

Table 1 (CA)n sequences D13S319 and D13S320
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Order of Markers

The 13 der(13) hybrid cell lines (see Materials and Methods) were analyzed by PCR for the presence or absence of the RFLP markers RB1, D13S25, D13S26, D13S31, D13S55, D13S59, and the microsatellite sequences D13S118, D13S119, D13S131, D13S133, D13S134, D13S135, D13S137, D13S144, D13S152, D13S153, D13S163, D13S319, D13S320. Primer source and sequences are indicated in table 2. The cell lines divide the region 13q14-q21 into 10 distinct intervals (fig. 1). The order of markers was: CEN — D13S320 — (D13S118, D13S153) — RB1 — D13S319 — D13S25 — (D13S31, D13S59, D13S133, D13S137) — D13S163 — D13S119 — (D13S26, D13S55) — (D13S131, D13S134, D13S135, D13S144, D13S152) — TEL. All hybrids were tested for all markers. No gaps were identified in the deletion hybrids. All markers were present on the monochromosomal cell line GF7.

Fig. 1
figure 1

a A deletion hybrid breakpoint map of the region 13q14–q21. The der(13) are indicated by horizontal bars. Equal length has arbitrarily been attributed to all intervals. The putative position of the WND gene is indicated by a black arrow, that of the BCLL gene by the spotted arrow, b Breakpoints in 13q14–q21 from the der(13) of the cell lines used in this study. Modified after Bowcock and Taggart [23].

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Table 2 Chromosome 13 markers used as STS
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Discussion

The relative order of the microsatellite markers is in agreement with the order that the subsets have on each of the genetic maps [10–12]. This also applies to the relative order of the RFLP markers [3, 13]. The order along the chromosome as determined by linkage analysis is thus confirmed using physical mapping.

The cell hybrids used define 10 distinct intervals in the PCR-based hybrid breakpoint map of the chromosomal region 13q14-q21. The map stretches from the translocation breakpoint of the der(13) of cell lines E8 and D1 in 13q14.1 to the proximal breakpoint of the distal segment of the der(13) of cell line PKII-90-P5b at 13q21.2, an estimated distance of 20 Mb [derived from 18].

The smallest deletion seen in BCLL is determined by the cell lines RHF 407 and RHF 2324, which contain the different translocation products from a translocation involving 13q14 in a B-cell chronic lymphocytic leukaemia patient [2]. Therefore, BCLL potentially maps in interval 4 or 5 of the map. WND is closely linked to the marker D13S31 [3, 4], and between the markers D13S31 and D13S59 [3]. As D13S31 and D13S59 are situated in interval 6, WND will also be situated in this interval, which must be in proximal 13q21.1 [5].