A primary genetic map of the pericentromeric region of the human X chromosome

We report a genetic linkage map of the pericentromeric region of the human X chromosome, extending from Xp11 to Xq13. Genetic analysis with five polymorphic markers, including centromeric alpha satellite DNA, spanned a distance of approximately 38 cM. Significant lod scores were obtained with linkage analysis in 26 families from the Centre d'Etude du Polymorphisme Humain, establishing estimates of genetic distances between these markers and across the centromere. Physical mapping experiments, using a panel of somatic cell hybrids segregating portions of the X chromosome due to translocations or deletions, are in agreement with the multilocus linkage analysis and indicate the order Xp11 . . . DXS7(L1.28)-TIMP- DXZ1(alpha satellite, cen)- DXS159(cpX73)-PGK1 . . . Xq13. The frequency of recombination in the two approximately 20-cM intervals flanking alpha satellite on either chromosome arm was roughly proportional to the estimated physical distance between markers; no evidence for a reduced crossover frequency was found in the intervals adjacent to the centromere. However, significant interfamilial variations in recombination rates were noted in this region. This primary map should be useful both as a foundation for a higher resolution centromere-based linkage map of the X chromosome and in the localization of genes to the pericentromeric region.     

A refined linkage map for DNA markers around the pericentromeric region of chromosome 10

A refined genetic linkage map for the pericentromeric region of human chromosome 10 has been constructed from data on 12 distinct polymorphic DNA loci as well as the locus for multiple endocrine neoplasia type 2A (MEN 2A), a dominantly inherited cancer syndrome. The map extends from D10S24 (at 10p13-p12.2) to D10S3 (at 10q21-q23) and is about 70 cM long. Overall, higher female than male recombination frequencies were observed for this region, with the most remarkable female excess in the immediate vicinity of the centromere, as previously reported. Most of the DNA markers in this map are highly informative for linkage and the majority of the interlocus intervals are no more than 6 cM apart. Thus this map should provide a fine framework for future efforts in more detailed mapping studies around the centromeric area. A set of ordered cross-overs identified in this work is a valuable resource for rapidly and accurately localizing new DNA clones isolated from the pericentromeric region.     

Ordering of markers in the pericentromeric region of chromosome 10

Seven polymorphic cosmids previously assigned to 10cen-q11.2 were mapped between D10S34 and RBP3, and ordered by interphase in situ hybridization and yeast artificial chromosome analysis. Some of the presumed unique sequences from the centromeric region have homologies either within the same region or within the centromeric region of other chromosomes.     

Molecular evolution of the human chromosome 15 pericentromeric region

We present a detailed molecular evolutionary analysis of 1.2 Mb from the pericentromeric region of human 15q11. Sequence analysis indicates the region has been subject to extensive interchromosomal and intrachromosomal duplications during primate evolution. Comparative FISH analyses among non-human primates show remarkable quantitative and qualitative differences in the organization and duplication history of this region - including lineage-specific deletions and duplication expansions. Phylogenetic and comparative analyses reveal that the region is composed of at least 24 distinct segmental duplications or duplicons that have populated the pericentromeric regions of the human genome over the last 40 million years of human evolution. The value of combining both cytogenetic and experimental data in understanding the complex forces which have shaped these regions is discussed.     

The organisation of repetitive sequences in the pericentromeric region of human chromosome 10.

Three satellite DNA families are present in the pericentromeric region of chromosome 10; the alpha satellite and two 5 bp satellite families defined here as satellites 2 and 3. Pulsed field gel electrophoresis (PFGE) demonstrates that these sequences are organised into five discrete arrays which are linked within a region of approximately 5.3 Megabases (Mb) of DNA. The alpha satellite is largely confined to a 2.2 Mb array which is flanked on its p arm side by two 100-150 kb satellite 3 arrays and on its q arm side by a 900 kb satellite 2 array and a further 320 kb satellite 3 array. This linear order is corroborated by fluorescent in situ hybridisation analyses. In total, these arrays account for 3.6 Mb of DNA in the pericentromeric region of chromosome 10. These data provide both physical information on sequences which may be involved in centromere function and a map across the centromere which has the potential to link yeast artificial chromosome (YAC) contigs currently being developed on both arms of this chromosome.     

A high-resolution meiotic mapping panel for the pericentromeric region of chromosome 10.

Familial multiple endocrine neoplasia type 2A (MEN 2A) is a dominantly inherited cancer syndrome characterized by tumors in tissues derived from the neural crest. The disease manifests as medullary carcinoma of the thyroid, pheochromocytoma, and hyperparathyroidism. The MEN2A locus has been mapped near the centromere of chromosome 10 by linkage analysis. Statistical analyses have not resolved the location of MEN2A among several close markers. We have used our family material to refine the positions of 36 identified and confirmed crossovers among the markers most closely linked to MEN2A. This high-resolution meiotic mapping panel will help order loci in this pericentromeric region and narrow the region in which MEN2A maps.     

A cluster of expressed zinc finger protein genes in the pericentromeric region of human chromosome 10.

Three members of the human zinc finger Krüppel family, ZNF11/KOX2, ZNF22/KOX15, and ZNF25/KOX19, have been regionally localized to the pericentromeric region of chromosome 10 by in situ chromosomal hybridization and somatic cell hybrid analysis. ZNF25/KOX19 is located centromeric to a breakpoint in chromosome band 10q11.2 in the chromosome region 10p11.2-q11.2, whereas ZNF22/KOX15 maps distal to it in band 10q11.2. Sequences hybridizing to the KOX2 probe are found at two loci, ZNF11A and ZNF11B, that map proximal and distal to the 10q11.2 breakpoint, respectively. The two ZNF11 loci probably represent two related sequences in 10p11.2-q11.2. This cluster of ZNF/KOX genes is of particular interest since the loci for multiple endocrine neoplasia type 2A and 2B (MEN2A and MEN2B) syndromes have been assigned to this region by linkage analysis.     

A physical map of human chromosome 10 and a comparison with an existing genetic map.

A physical map for 13 loci on chromosome 10 was developed by determining the dosage of the corresponding DNA sequences in cell lines with unbalanced chromosome 10 rearrangements. Nine of the sequences were assigned to a smaller segment of the chromosome than previously and four sublocalizations were confirmed. The physical map covers most of chromosome 10, from 10p13 to 10q23. The linear order of loci within the physical map agrees with existing linkage maps of chromosome 10. A comparison between the physical map and existing genetic maps indicate an uneven distribution of recombination for chromosome 10. There appear to be hot spots of recombination in the regions defined by q21.1 and q22-q23. In addition, there is a suppression of recombination in the pericentromeric region in males which is not evident in females.     

A physical map of the human pseudoautosomal region.

A physical map of the human pseudoautosomal region has been constructed using pulsed field gel electrophoresis and the infrequently cutting restriction enzymes BssHIII, EagI, SstII, NotI, MluI and NruI. This map extends 2.3 Mbp from the telomere to sex-chromosome-specific DNA, includes at least seven CpG islands and locates four genetically mapped loci. Five of the CpG islands are organized into two clusters. One cluster is adjacent to the telomere, the other extends into sex-chromosome-specific DNA. There is congruence between the genetic and physical maps which implies that the frequency of recombination is approximately uniform throughout the DNA.     

Linkage relationships of the Wiskott-Aldrich syndrome to 10 loci in the pericentromeric region of the human X chromosome

Twelve families with Wiskott-Aldrich syndrome (WAS) were studied by linkage analysis using 10 polymorphic marker loci from the X-chromosome pericentromeric region. The results confirm close linkage of WAS to the DXS14, DXS7, TIMP, and DXZ1 loci and are consistent with previous data suggesting that WAS maps to the proximal Xp and is flanked by the DXS14 and DXS7 loci. The strongest linkage (Z = 10.19 at theta = 0.00) was found to be between WAS and the hypervariable DXS255 locus, a marker locus already mapped between DXS7 and DXS14 and which was informative for all meioses included in this analysis. Linkage of the WAS to two pericentromeric Xq loci, DXS1 and PGK1, was also established. On the basis of these results, accurate predictive testing should now be feasible in the majority of WAS families.     

An 18-locus linkage map of the pericentromeric region of the human X chromosome: Genetic framework for mapping X-linked disorders

We report a high-resolution genetic linkage map of the region Xp11.4 to Xq13.3, spanning the centromere of the X chromosome and encompassing approximately 30 cM. This 18-locus map is composed of 11 intervals that are spaced on average about 3 cM apart. Markers incorporated into the map together detect 19 distinct polymorphisms and include five genes (TIMP, SYP, AR, CCG1, PGK1), the OATL1 cluster, the hypervariable locus DXS255, the centromeric locus DXZ1, and 10 other anonymous DNA segments. Given that this map spans roughly one-fifth of the length of the X chromosome and includes many loci currently used in both diagnosis and mapping of X-linked disorders, it should be useful for genetic counseling and for guiding efforts to clone disease genes in this region.     

A physical map of the Q region of B10.P

The murine class I MHC Q region is part of a large complex multigene family whose members have various peptide-binding functions. The structure of the Q region is complex, varying extensively in the b, d, k, and q haplotypes so far examined. To better understand the structural heterogeneity, we examined the Q region of B10.P, a strain whose immunological characteristics are distinct from other haplotypes. A total of 89 cosmids were isolated from genomic DNA. The B10.P Q region was found to contain seven genes in a 190-kb cluster linked to D^p and two additional Q genes in a separate 55-kb cluster. The gene arrangement in this haplotype was unique and did not correspond to any other haplotype; this underscores the complexity of chromosomal structure in this region. In addition to the Q region clusters, Tla region was tentatively aligned in five clusters spanning approximately 300 kb. One 37-kb M region cosmid was also identified. Received: 24 February 1995 / Accepted: 10 October 1995     

A refined physical map of the long arm of human chromosome 16

Mapping of 33 anonymous DNA probes and 12 genes to the long arm of chromosome 16 was achieved by the use of 14 mouse/human hybrid cell lines and the fragile site FRA16B. Two of the hybrid cell lines contained overlapping interstitial deletions in bands q21 and q22.1. The localization of the 12 genes has been refined. The breakpoints present in the hybrids, in conjunction with the fragile site, can potentially divide the long arm of chromosome 16 into 16 regions. However, this was reduced to 14 regions because in two instances there were no probes or genes that mapped between pairs of breakpoints.     

A primary genetic map of markers of human chromosome 10

We have constructed a primary genetic map for human chromosome 10 from 13 polymorphic marker systems defining 11 loci, using a new gene mapping algorithm implemented in the computer program GMS. The loci form a continuous genetic map that spans approximately 116 cM in males and 170 cM in females. These loci provide regularly spaced anchor points for linkage studies, except for one interval that is 28 cM in males and 64 cM in females.     

Genetic linkage mapping of multiple epiphyseal dysplasia to the pericentromeric region of chromosome 19.

Multiple epiphyseal dysplasia (MED) is an inherited chondrodystrophy that results in deformity of articular surfaces and in subsequent degenerative joint disease. The disease is inherited as an autosomal dominant trait with high penetrance. An MED mutation has been mapped by genetic linkage analysis of DNA polymorphisms in a single large pedigree. Close linkage of MED to 130 tested chromosomal markers was ruled out by discordant inheritance patterns. However, strong evidence for linkage of MED to markers in the pericentromeric region of chromosome 19 was obtained. The most closely linked marker was D19S215, with a maximum LOD score of 6.37 at theta = .05. Multipoint linkage analysis indicated that MED is located between D19S212 and D19S215, a map interval of 1.7 cM. Discovery of the map location of MED in this family will facilitate identification of the mutant gene. The closely linked DNA polymorphisms will also provide the means to determine whether other inherited chondrodystrophies have underlying defects in the same gene.     

A genetic,physical, and comparative map of rat chromosome 10

A map of rat Chromosome (Chr) 10 was generated from 21 markers, mostly of conserved structural genes, by linkage analysis and fluorescence in situ hybridization. The study emphasizes the proximal third of the chromosome which, until now, has been relatively devoid of markers. Based on comparative analysis, our data suggest that genes on rat Chr 10 are conserved on mouse Chr 11, 16, 17 and human Chr 16, 5, and 17. Received: 22 November 1995 / Accepted: 29 January 1996     

High-resolution cytogenetic-based physical map of human chromosome 16

A panel of 54 mouse/human somatic cell hybrids, each possessing various portions of chromosome 16, was constructed; 46 were constructed from naturally occurring rearrangements of this chromosome, which were ascertained in clinical cytogenetics laboratories, and a further 8 from rearrangements spontaneously arising during tissue culture. By mapping 235 DNA markers to this panel of hybrids, and in relation to four fragile sites and the centromere, a cytogenetic-based physical map of chromosome 16 with an average resolution of 1.6 Mb was generated. Included are 66 DNA markers that have been typed in the CEPH pedigrees, and these will allow the construction of a detailed correlation of the cytogenetic-based physical map and the genetic map of this chromosome. Cosmids from chromosome 16 that have been assembled into contigs by use of repetitive sequence fingerprinting have been mapped to the hybrid panel. Approximately 11% of the euchromatin is now both represented in such contigs and located on the cytogenetic-based physical map. This high-resolution cytogenetic-based physical map of chromosome 16 will provide the basis for the cloning of genetically mapped disease genes, genes disrupted in cytogenetic rearrangements that have produced abnormal phenotypes, and cancer breakpoints.     

Analysis of the monomeric alphoid sequences in the pericentromeric region of human chromosome 7

To further define the structure of the pericentromeric region of human chromosome 7, we have identified and characterized a YAC clone (YAC 311.H5) containing the D7S1480 locus, which maps to the short arm near the centromere of this chromosome, by linkage in CEPH families and radiation hybrid analysis. This YAC contains two new blocks of alphoid DNA (named Z5 and Z6). Both Z5 and Z6 show monomeric structures and a lack of higher-order repeats, and, therefore, belong to suprachromosomal family type 4 (M1). The orientation of the two blocks and the physical distances over the region were defined by pulsed-field gel electrophoresis (PFGE) and fluorescence in situ hybridization on chromatin fibers (FiberFISH). A YAC contig spanning the centromeric region has been developed by STS content.     

A physical map of the apolipoprotein gene cluster on human chromosome 19

Summary We have generated a restriction map around the cloned genes for human apolipoproteins CI, CII, and E by pulsed-field gel analysis. We show that the genes are clustered within an area of about 50 kb on chromosome 19. The genes are all oriented in the same direction, head to tail.     

A compositional map of the cen-q21 region of human chromosome 21

A compositional map of the centromere and of the subcentromeric region of the long arm of human chromosome 21 was established by determining the GC levels (GC is the molar fraction of guanine+cytosine in DNA) of 11 YACs (yeast artificial chromosomes) covering this 13–14 Mb region which extends from the α-satellite sequences of the C(entromeric) band qll.1, through R(everse) band q11.2, to the proximal part of G(iemsa) band q21. The entire region is made up of GC-poor, or L, isochores with only one GC-rich H1 isochore, at least 2 Mb in size, located in band q21. The almost identical GC levels of the centromeric α-satellite repeats (38.5%), of R band q11.2 (39%), and of G bands (38–40%) provide a direct demonstration that base composition cannot be the only cause of the cytogenetic differences between C, G, and the majority of R bands, namely the H3^- R bands (which do not contain the GC-richest H3 isochores). The results obtained also show that isochores may be as long as 6 Mb, at least in the GC-poor regions of the genome, and support previous observations suggesting that YACs from isochore borders are unstable and/or difficult to clone. Genes and CpG islands are very rare in the GC-poor region investigated, as expected from the fact that their concentration is proportional to the GC levels of the isochores in which they are contained.