Localization of 616 human chromosome 3-specific cosmids using a somatic cell hybrid deletion mapping panel.

A total of 5700 human chromosome 3-specific cosmid clones was isolated from a series of cosmid libraries constructed from somatic cell hybrids whose only human component was an entire chromosome 3 or a chromosome 3 containing an interstitial deletion removing 50% of long arm sequences. Several unique sequence chromosome 3-specific hybridization probes were isolated from each of 616 of these cosmids. These probes were then used to localize the cosmids by hybridization to a somatic cell hybrid deletion mapping panel capable of resolving chromosome 3 into nine distinct subregions. All 616 of the cosmids were localized to either the long or short arm of chromosome 3 and 63% of the short arm cosmids were more precisely localized. We have identified a total of 87 cosmids that contain fragments that are evolutionarily conserved. Fragments from these cosmids should prove useful in the identification of new chromosome 3-specific genes as well as in comparative mapping studies. The localized cosmids should provide excellent saturation of human chromosome 3 and facilitate the construction of physical and genetic linkage maps to identify various disease loci including Von Hippel Lindau disease and renal and small cell lung carcinoma.     

Regional assignment of 41 human DNA fragments on chromosome 7 by means of a somatic cell hybrid panel

Summary To detect new restriction fragment length polymorphisms that would cover human chromosome 7 with a network of genetic landmarks, a chromosome 7-specific phage gene library was screened for human single-copy fragments. With use of a somatic cell hybrid panel containing defined regions of human chromosome 7, 41 cloned human single-copy sequences were assigned to five regions of this chromosome. Of special importance are the cell hybrid clones GM1059Rag5 and 7851Rag10-1, derived from human cells with interstitial deletions spanning the bands 7q22-q32, within which the cystic fibrosis gene is located. Twelve new probes are described in 7q22-q32, five of which detect a total of six RFLPs.     

A hybrid cell mapping panel for regional localization of probes to human chromosome 8

We have characterized a panel of somatic cell hybrids that carry fragments of human chromosome 8 and used this panel for the regional localization of anonymous clones derived from a chromosome 8 library. The hybrid panel includes 11 cell lines, which were characterized by Southern blot hybridization with chromosome 8-specific probes of known map location and by fluorescent in situ hybridization with a probe derived from a chromosome 8 library. The chromosome fragments in the hybrid cell lines divide the chromosome into 10 intervals. Using this mapping panel, we have mapped 56 newly derived anonymous clones to regions of chromosome 8. We have also obtained physical map locations for 7 loci from the genetic map of chromosome 8, thus aligning the genetic and physical maps of the chromosome.     

Alu-PCR: characterization of a chromosome 6-specific hybrid mapping panel and cloning of chromosome-specific markers.

The Alu-polymerase chain reaction (Alu-PCR) was applied to selectively amplify DNA sequences from human chromosome 6 using a single primer (A1) directed to the human Alu consensus sequence. A specific amplification pattern was demonstrated for a panel of eight somatic cell hybrids containing different portions of chromosome 6. This PCR pattern permits the identification of submicroscopic DNA alterations and can be utilized as a reference for additional chromosome 6-specific hybrids. To obtain new chromosome 6-specific markers we established two libraries from PCR-amplified sequences using two somatic cell hybrids (MCH381.2D and 640-5A). Out of a total of 109 clones that were found to be chromosome 6 specific, 13 clones were regionally assigned. We also included a procedure that allows the isolation of chromosome 6-specific markers from hybrids that contain human chromosomes other than 6. Our results will contribute to the molecular characterization of chromosome 6 by fostering characterization of somatic cell hybrids and by the generation of new regionally assigned DNA markers.     

Development of a somatic cell hybrid mapping panel and molecular probes for human chromosome 3

A somatic cell hybrid mapping panel and molecular probes have been developed for human chromosome 3. This panel defines 11 regions for the short and long arms of the chromosome. Four hundred thirty-two probes have been mapped using these hybrids. One hundred thirty-one of these probes were derived from EcoRI and HindIII flow-sorted libraries. The remaining 301 probes were isolated from NotI boundary and random (partial MboI) libraries constructed from a hybrid that provided a relative enrichment in 3p DNA sequences. For some regions of the chromosome, significant differences in the distribution of probes were noted. This was observed for both the unique sequence flow-sorted and NotI probes. These differences are in agreement with previous suggestions that Giemsa light bands are GC-rich, and therefore gene-rich (especially housekeeping genes), and that the Giemsa dark bands may contain DNA that is more highly condensed. The isolation of probes from different types of libraries, or by different screening strategies, appears to reduce deficiencies that might arise from the use of probes derived with a more limited approach. These hybrids and probes should facilitate the construction of physical and genetic linkage maps to identify various disease loci involving chromosome 3.     

Regional localization of DNA sequences on chromosome 21 using somatic cell hybrids.

We have used a panel of Chinese hamster X human somatic cell hybrids, each containing various portions of chromosome 21 as the only detectable human chromosome component, for regional mapping of cloned, chromosome 21-derived DNA sequences. Thirty unique and very low-repeat sequences were mapped to the short arm and three sections of the long arm. Three unique sequences map to the proximal part of the terminal band 21q22.3, and five to the distal part of this band. Some of these may represent parts of gene sequences that may be relevant to the pathogenesis of Down syndrome, as 21q22 is the area required to be present in triplicate for the full clinical picture.     

A somatic cell hybrid panel and DNA probes for physical mapping of human chromosome 7p.

To identify by reverse genetics genes on the short arm of human chromosome 7 expected to be involved in the regulation of human craniofacial and limb development, we have set up a human mouse somatic cell hybrid panel that divides 7p into 9 fragments. The breakpoints are defined by deletions or translocations involving one chromosome 7 in the cells of the human cell fusion partners. Particularly densely covered with these cytogenetic anchor points is the proximal area of 7p within and around 7p13. The number of cytogenetic mapping points within proximal 7p could be increased by four, using two diploid human cell lines with small interstitial deletions in this region for dosage studies. We used Southern blots of this panel to assign to 7q or subregions of 7p more than 300 arbitrary DNA probes or genes that provide reference points for physical mapping of 7p. Three reciprocal translocations with one of the breakpoints in 7p13 mark the location of a gene involved in Greig cephalopolysyndactyly syndrome. To define an area in which we could identify candidates for this developmental gene, we established a macrorestriction map using probes flanking the putative gene region. The Greig translocations were found to be located within a 630-kb NotI restriction fragment.     

A mouse-human hybrid cell panel for mapping human chromosome 16

A mouse-human hybrid cell panel for human chromosome 16 was constructed from human cell lines with breakpoints on chromosome 16 at p13.11, q13, q22 and q24. Fusions with the human fibroblast line GM3884, t(X;16)(q26;q24) allowed the isolation of clones with either the derivative X or the derivative 16 as the only human chromosome. This was a consequence of both the genes APRT and HPRT being involved in the translocation. The breakpoints of the line GM3884 were confirmed by aphidicolin induction of the common fragile site at 16q23. The results of the fusions with this line suggest a localisation of the APRT gene at 16q24 and confirm the localisation of HPRT to Xq26 to Xq27.3. These hybrid cell lines enable the localisation of genes and DNA fragments to six clearly defined regions. Further localisation within three of these regions is possible by use of the three fragile sites on chromosome 16. In situ hybridisation with the probe pBLUR confirmed that of three lines tested all contained a single human chromosome.     

A somatic cell hybrid mapping panel for regional assignment of human chromosome 13 DNA sequences

We have constructed somatic cell hybrids containing different overlapping deletions involving human chromosome 13. Cytogenetic characterisation of the breakpoints allowed division of the chromosome into six distinct regions. Molecular characterisation of these hybrids allowed regional assignment of anonymous DNA sequences, cDNAs, and isoenzyme variants and these hybrids should prove valuable in the analysis and isolation of genes and disease loci on chromosome 13.     

An expanded mouse-human hybrid cell panel for mapping human chromosome 16

A mouse/human hybrid cell panel of human chromosome 16 has been extended to a total of 31 hybrids. These hybrids were derived from constitutional translocations and deletions ascertained during clinical cytogenetic studies. This panel of hybrids, together with four fragile sites, have the potential to divide chromosome 16 into 38 regions. Rapid detailed physical mapping of gene probes or anonymous DNA probes is possible using this hybrid panel. This hybrid cell panel also allows the physical mapping of other chromosomes with three breakpoints on chromosomes 1, 4, 11 and 13 and two on chromosomes 3, 10 and 18.     

Isolation and regional localization of 25 anonymous DNA probes on a chromosome 13 hybrid panel

Clones were isolated from two flow-sorted chromosome 13 libraries. Twenty-five clones were localized to various regions of chromosome 13, using a well-characterized panel of rodent x human hybrid cell lines. Eight DNA markers were localized to 13q14.2----q22, where the gene for Wilson disease, a recessive disorder of copper metabolism, was previously assigned. The new markers will be useful for the diagnosis of presymptomatic sibs of Wilson disease patients. We isolated six DNA clones proximal to the retinoblastoma gene, a region in which a translocation associated with rhabdomyosarcoma has been observed. Probes for both of these regions will be useful for the cloning of the genes involved in these diseases.     

Isolation and comparative mapping of a human chromosome 20-specific alpha-satellite DNA clone.

We have isolated and characterized a human genomic DNA clone (PZ20, locus D20Z2) that identifies, under high-stringency hybridization conditions, an alphoid DNA subset specific for chromosome 20. The specificity was determined using fluorescence in situ hybridization. Sequence analysis confirmed our previously reported data on the great similarity between the chromosome 20 and chromosome 2 alphoid subsets. Comparative mapping of pZ20 on chimpanzee and gorilla chromosomes, also performed under high-stringency conditions, indicates that the alphoid subset has ancestral sequences on chimpanzee chromosome 11 and gorilla chromosome 19. However, no hybridization was observed to chromosomes 21 in the great apes, the homolog of human chromosome 20.     

Somatic cell hybrid deletion map of human chromosome 18.

The creation of a physical map of chromosome 18 will be useful for the eventual identification of specific chromosomal regions that are critical in the occurrence of Edwards syndrome, the 18q- syndrome, and the 18p- syndrome. To begin the investigation of these syndromes, a physical map has been constructed to order random DNA fragments to specific portions of chromosome 18. A set of somatic cell hybrids that retain deletions or translocations involving chromosome 18 has been isolated and characterized. Over 200 lambda phage from a chromosome 18-specific library have been localized to 11 distinct regions of chromosome 18 using the chromosomal breakpoints present in the somatic cell hybrids.     

Regional mapping of unique DNA sequences from human chromosome 3 derived from a flow-sorted chromosome library

Eight single-copy DNA probes specific for human chromosome 3 were isolated by screening a human chromosome 3-derived genomic library. Southern blot analyses of DNAs isolated from a panel of somatic cell hybrids allowed us to regionally assign all probes to subregions on chromosome 3. Three clones were localized to the short arm of chromosome 3 (3p21----pter), two to the long arm (3q21----qter), and three to the 3q21----3p21 subregion. Six of these DNA sequences map to regions overlapping a segment of chromosome 3 (3p14----p23) frequently deleted in small cell lung cancer cells. Restriction fragment length polymorphism analyses indicate that at least three of the eight single-copy probes studies show MspI or BglII polymorphisms. This library is a useful source of chromosome 3-specific probes.     

Ordering of human chromosome 3p markers by radiation hybrid mapping.

To construct a panel of radiation hybrids (RHs) for human chromosome 3p mapping, mouse microcell hybrid cells, A9(neo3/t)-5, containing a single copy of human chromosome 3p with pSV2neo plasmid DNA integrated at 3p21-p22 were irradiated and fused to mouse A9 cells. A panel of 96 RHs that retain several sizes and portions of human chromosome 3p segments was used to map 25 DNA markers for chromosome 3p. Eight of them, H28, H29, H32, H33, H35, H38, H48, and H64, were cloned from Alu-primed PCR products using A9(neo3/t)-5 cell DNA as a template. The most likely order of the 24 markers, except for H28, based on the statistical ordering method proposed by Falk, was cen-D3S4-D3S3-D3S30-H29-D3S13-D3S2-+ ++H48-D3F15S2-D3S32-D3S23-CCK-H35-H33- D3S11-D3S12-RARB-THRB(ERBA2-pBH302)- H64-H38-RAF1-D3S18-H32-D3S22-pter. The order and location of these markers were in good agreement with those previously determined by other mapping methods, suggesting that a panel of these 96 RHs is a valuable source for a rapid mapping of human chromosome 3p markers.     

A deletion panel of the long arm of the X chromosome: subregional localization of 22 DNA probes

Summary Two males and two females with different but overlapping deletions on the proximal long arm of the X chromosomes have been investigated. Their karyotypes, which have been well characterized by high resolution banding techniques, are 46,Y,del(X)(pterq21.1:: q21.33qter); 46,Y,del(X) (pterq21.2::q21.31qter); 46,X,del(X) (pterq21.31::q24.3qter) and 46,X,del (X)(pterq21.1:). A deletion panel, which makes it possible to subdivide the long arm of the X chromosome into seven subregions, has been established using the genomic DNA from the four families, and applied to the fine subregional localization of the loci for 22 DNA probes. Based on the results obtained, the possible location of the loci in question has been narrowed down considerably, in some cases to an area of only 5% of the previously assigned region; hybridization to Southern blots of a panel with well-characterized chromosome deletions is thus a powerful means of localizing DNA probes, especially with respect to the X probes.Part of the results from this investigation were published at Human Gene Mapping 9 as abstracts     

Chromosomal assignment of porcine microsatellites by use of a somatic cell hybrid mapping panel

A well-established and characterized somatic cell hybrid panel was used to map three polymorphic microsatellites. Microsatellite S0072, representing the linkage group S0007-S0072, was assigned to porcine chromosome 14. Micro-satellite S0009, representing the unassigned linkage group EAM-S0009-S0071, was assigned tentatively to porcine chromosome 11. Finally, S0062 was tentatively mapped to chromosome 18. S0062 may represent the first marker for porcine chromosome 18.     

Regional mapping of the gene for human lysosomal acid phosphatase (ACP2) using a hybrid clone panel containing segments of human chromosome 11

Summary A clone panel containing various segments of human chromosome 11 has been selected and used for regional assignment of the gene for human lysosomal acid phosphatase (ACP₂) to the short arm of chromosome 11, in the region 11p11 11p12. Further evidence has also been presented to update the regional assignment of the gene for lactate dehydrogenase A (LDH_A) to 11p12 11p13, and to support a previous assignment of the genes for the two components of the human cell-surface antigens of the SA11 (previously designated A_L) group, SA11-1 and SA11-3 (previously designated A_L-a₁ and A_L-a₃), to 11pter 11p13. This regional clone panel will be useful for rapid regional mapping of other genes assigned to chromosome 11.     

Method for localization of cloned DNA fragments on the Escherichia coli chromosome.

In exponentially growing cultures of Escherichia coli strains carrying the dnaC28 mutation, DNA replication can be synchronized by temperature changes (R. L. Rodriguez, M. S. Dalbey, and C. I. Davern, J. Mol. Biol. 74:599-604, 1973). We used this synchronization procedure and DNA-DNA hybridization to develop a technique for the localization of cloned chromosomal fragments on the genetic map. Because of the bidirectional nature of replication in E. coli, our method gave two possible positions (one on each replication arm). However because of the precision obtained for each position (+/- 1 map unit), the final mapping with various genetic techniques was greatly facilitated. Using this technique and a simple chromosomal mobilization test, we located at 93.2 +/- 1 min a cloned DNA fragment carrying an extragenic suppressor of dnaA46, a thermosensitive mutation in the dnaA initiation gene. Further analysis showed that the groES (mopA) and groEL (mopB) genes, both located at 94.2 min on the standard map, were indeed carried by the cloned suppressor fragment.