A mapped set of DNA markers for human chromosome 17

We have developed and mapped by genetic linkage a primary set of markers for chromosome 17. The map consists of 21 loci derived from 27 probe/enzyme systems, including eight highly informative markers at loci containing a variable number of tandemly repeated DNA sequences (VNTRs). The map is continuous from the telomeric region of the short arm to the telomeric region of the long arm, covering estimated genetic distances of 218 cM in males and 279 cM in females. The average heterozygosity among all 21 loci in the population sample analyzed is 58%; 77% heterozygosity was observed among the eight VNTR markers that were highly informative. This map will make it possible to detect by linkage the location of genetic defects associated with chromosome 17 and will also provide anchor points for a high-resolution map of this chromosome.     

A mapped set of genetic markers for human chromosome 9

A genetic map of markers for human chromosome 9, spanning a genetic distance of 147 cM in males and 231 cM in females, has been constructed from linkage studies with 19 loci in a large panel of reference families. The markers included four classical systems previously assigned to chromosome 9, and restriction fragment length polymorphisms of two cloned genes, ABL oncogene and argininosuccinase synthetase pseudogene 3 (ASSP3). The remaining 13 marker loci, with an average heterozygosity of 42%, were defined by arbitrary DNA probes newly ascertained from genomic libraries; seven of them were variable number of tandem repeat (VNTR) loci. A subset of 7 of the 19 linked markers is proposed for a primary map that could detect linkage with a genetic defect within the covered region of chromosome 9, provided that at least 45 phase-known meioses were available for study in an affected family.     

Sequence-tagged sites (STSs) for a set of mapped markers on chromosome 21.

Sequence tagged sites (STSs) have been proposed as a "common language" for comparing physical and genetic maps of the human genome produced by a variety of techniques. We have produced 44 STSs from 38 mapped loci on human chromosome 21. The STSs represent most of the loci designated as genetic reference or ordered physical framework markers, along with a number of others chosen to span all regions of 21q. Of the STSs, 12 are from gene segments, including 4 from exons of the APP gene encoding the amyloid beta protein precursor, and 32 mark anonymous DNA loci. These STSs make each of the corresponding loci readily accessible to the research community without the need for exchange of clones. These sites also represent multiple start points for the isolation of YAC clones that should permit overlapping the entire chromosome 21 long arm as cloned DNA.     

Isolation and analysis of DNA markers specific to human chromosome 15.

Chromosome-specific DNA markers provide a powerful approach for studying complex problems in human genetics and offer an opportunity to begin understanding the human genome at the molecular level. The approach described here for isolating and characterizing DNA markers specific to human chromosome 15 involved construction of a partial chromosome-15 phage library from a human/Chinese hamster cell hybrid with a single human chromosome 15. Restriction fragments that identified unique- and low-copy loci on chromosome 15 were isolated from the phage inserts. These fragments were regionally mapped to the chromosome by three methods, including Southern analysis with a mapping panel of cell hybrids, in situ hybridization to metaphase chromosomes, and quantitative hybridization or dosage analysis. A total of 42 restriction fragments of unique- and low-copy sequences were identified in 14 phage. The majority of the fragments that have been characterized so far exhibited the hybridization pattern of a unique locus on chromosome 15. Regional mapping assigned these markers to specific locations on chromosome 15, including q24-25, q21-23, q13-14, q11-12, and q11. RFLP analysis revealed that several markers displayed polymorphisms at frequencies useful for genetic linkage analysis. The markers mapped to the proximal long arm of chromosome 15 are particularly valuable for the molecular analysis of Prader-Willi syndrome, which maps to this region. Polymorphic markers in this region may also be useful for definitively establishing linkage with one form of dyslexia. DNA probes in this chromosomal region should facilitate molecular structural analysis for elucidation of the nature of instability in this region, which is frequently associated with chromosomal aberrations.     

A primary map of ten DNA markers and two serological markers for human chromosome 19

We have constructed a primary map of 10 DNA and 2 protein markers for chromosome 19. Three of the markers define loci with a variable number of tandem repeats (VNTRs); 3 define genes--insulin receptor, low-density lipoprotein (LDL) receptor, and apolipoprotein CII; and 2 are classical markers for blood group antigens (Lewis and Secretor). The estimated genetic distance covered by the map is 137 cM in males and 189 cM in females. In some regions of the chromosome we found significant differences in recombination frequencies according to sex. This set of markers will be efficient for linkage studies in families segregating genetic defects and will provide anchor points for a high-resolution map of chromosome 19.     

A new locus for coeliac disease mapped to chromosome 15 in a population isolate

Coeliac disease is a common multifactorial disease with a strong genetic component, which is not entirely explained by the HLA association. Four previous whole-genome screens have produced somewhat inconsistent results suggesting genetic heterogeneity. We attempted to overcome this problem by performing a genome-wide scan in a Finnish sub-population, expected to be more homogeneous than the general population of Finland. The families in our study originate from the northeastern part of Finland, the Koilliskaira region, which has been relatively isolated since its founding in the 16th century. Genealogical studies have confirmed that the families share a common ancestor in the 16th century. Nine families with altogether 23 patients were genotyped for 399 microsatellite markers and the data were analysed with parametric linkage analysis using two dominant and one recessive model. A region on chromosome 15q11-q13 was implicated with a LOD score of 3.14 using a highly penetrant dominant model. Addition of more markers and one more sib-pair increased the LOD score to 3.74. This result gives preliminary evidence for existence of a susceptibility factor in this chromosomal region.     

A linkage group of five DNA markers on human chromosome 10

Five chromosome 10 DNA markers (D10S1, D10S3, D10S4, D10S5, and RBP3) were typed in five large pedigrees with multiple endocrine neoplasia type 2A (MEN-2A) and in five non-MEN-2A pedigrees. Linkage analyses showed that these loci and the locus for MEN-2A (MEN2A) are in one linkage group spanning at least 70 cM. The order of the marker loci is RBP3-D10S5-D10S3-D10S1-D10S4, with interlocus recombination frequencies of 7, 13-19, 19, and 19%, respectively, all on the same side of MEN2A. Analyses of sex-specific recombination frequencies indicated no significant differences between males and females for any of the map intervals studied. Previous localization of D10S5 and RBP3 to the proximal region of the long arm and the pericentric region, respectively, comparison of results with other studies, and our preliminary results with other chromosome 10 markers suggest that the D10S4 end of the map extends into the long arm. Our linkage map has been constructed using only two- and three-locus analyses. It will be possible to combine our results with those of other groups to construct a more detailed and accurate genetic map of chromosome 10.     

A high-resolution cytogenetic map of 168 cosmid DNA markers for human chromosome 11.

We have constructed a high-resolution cytogenetic map with 168 DNA markers, including 90 RFLP markers for human chromosome 11. The cosmid clones were mapped by fluorescence in situ suppression hybridization, in which discrete fluorescent signals can be detected directly on prometaphase R-banded chromosomes. Although these cosmid clones were distributed throughout the chromosome, they had some tendency to localize in the regions of R-positive band, such as 11p15, 11p11.2, 11q13, 11q23, and 11q25. Since these regions of chromosome 11 are considered to contain genes responsible for certain genetic diseases, cancer breakpoints involved in chromosome rearrangements, and tumor-suppressor genes, this high-resolution cytogenetic map will contribute to the molecular characterization of such genes. This map will also provide many landmarks essential for construction of the complete physical map with contigs of cosmid and YAC clones.     

A genetic linkage map of markers for human chromosome 20

A continuous genetic linkage map with five polymorphic DNA markers, including one that defines a locus containing a variable number of tandem repeats (VNTR), has been constructed from genotypic analysis of 59 large reference families. The map spans a genetic distance of 105 cM in males and 115 cM in females and provides initial anchor points for a high-resolution map of human chromosome 20.     

NotI-STS markers for human chromosome 3 are gene markers

Ninety four NotI-STS markers to seventy two individual NotI clones were developed basing on DNA nucleotide sequences from NotI-"jumping" and "linking" NotI-libraries of human chromosome 3. The localization of NotI-STS markers and their ordering on chromosome was established by combined data of RH-mapping (our data), contig-mapping, cytogenetic mapping and in silico mapping. Performed comparison of NotI-STS DNAs with human genome sequences revealed two gaps in the regions, 3p21.33 (marker NLI-256) and 3p21.31 (NL3-005), and segmental duplication. Identical DNA fragments are localized in the regions 12q and 3p22-21.33 (marker NL3-007). In the region 3q28-q29 (marker NLM-084) a fragment was detected with its identical copies present also on chromosomes 1, 2, 15 and 19. For 69 NotI-STSs, significant homologies with nucleotide sequences of 70 genes and two cDNAs were detected taking in consideration homologies to NotI-STS 5'- and 3'-terminal sequences. Association of NotI-STSs with genes is confirmed by high correlation of gene density distribution with the density of NotI-STS markers on the map of human chromosome 3. Obtained data evidence possibility of NotI-STS marker application as gene markers and allow considering constructed NotI-map as gene map of human chromosome 3.     

A reordering of human chromosome 19 long-arm DNA markers and identification of markers flanking the myotonic dystrophy locus

The gene for myotonic dystrophy (DM), the most common form of adult muscular dystrophy, has previously been mapped to the proximal long arm of chromosome 19. We have conducted linkage analysis on 53 DM families (comprising 421 individuals) using seven DM-linked DNA markers. This analysis, combined with our somatic cell hybrid mapping panel data, places the DM locus more distal on the chromosome 19 long arm than previously thought. Further, we have been able to unequivocally identify DNA markers that flank the disease locus. The definition of a 10-cM region of chromosome 19 that contains the DM locus should prove useful in both the search for the causative gene and the molecular diagnosis of DM.     

Isolation and regional localization of 35 unique anonymous DNA markers for human chromosome 22

Thirty-five new, unique, DNA probes have been isolated and each has been assigned to one of five regions on chromosome 22. The distribution of probes along the chromosome is what would be expected based on the estimated size of each region with the exception of the short arm (22p). RFLP analysis was performed using 13 different restriction enzymes and over 50% of the probes were found to have useful polymorphisms. Probes mapping to 22q11 were further characterized by pulsed-field gel analysis and it has been possible to link several on large restriction fragments. These 35 new probes will be useful reagents for producing genetic and physical maps of chromosome 22.     

Restriction fragment length polymorphisms detected by anonymous DNA probes mapped to defined intervals of human chromosome 16

Summary Three anonymous DNA probes ACH207, ACH224, and ACH202, isolated from a flow-purified chromosome 16 library and mapped to defined intervals of human chromosome 16, detected restriction fragment length polymorphisms (RFLPs). The RFLPs were of simple two allele types. The ACH207 (D16S4) probe detected a TaqI and an MspI RFLP with polymorphism information content (PIC) values of 0.30 and 0.27; the ACH224 (D16S5) probe detected and RsaI RFLP, PIC value of 0.34; and the ACH202 (D16S14) probe detected an XbaI RFLP, PIC value of 0.22.     

A locus for hereditary capillary malformations mapped on chromosome 5q

Capillary malformations (port-wine stains) are the most common vascular malformations occurring in 0.3% of live births. Most capillary malformations occur sporadically and present as a solitary lesion. Capillary malformations can also occur as a component of well-described syndromes. Familial occurrence of multiple capillary malformations has been described in the literature, suggesting autosomal dominant inheritance with variable expression in this subgroup. A hereditary basis underlying the development of solitary capillary malformations has not been found, but may well be possible. We have mapped a locus for an autosomal dominant disorder in a three-generation family that manifested itself with multiple cutaneous capillary malformations to chromosome 5q13-22. This locus spans 48 cM between the markers D5S647 and D5S659 and harbours several candidate genes. By defining the gene(s) responsible for capillary malformations, we will gain more insight in the pathogenesis of this disorder. It is likely that genes implicated in these familial cases may be involved in the more sporadic cases.     

A major locus for submergence tolerance mapped on rice chromosome 9

Submergence stress is a widespread problem in rice-growing environments where drainage is impeded. A few cultivars can tolerate more than 10 days of submergence, but the genes conferring this tolerance have not been identified. We used randon-amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers to map submergence tolerance in 169 F₂ plants and the resulting F₃ families of a cross between a tolerant indica rice line, IR40931-26, and a susceptible japonica line, PI543851. IR40931-26 inherited strong submergence tolerance from the unimproved cultivar FR13A. Eight-day old F₃ seedlings were submerged for 14–16 days in 55-cm deep tanks, and tolerance was scored after 7 days recovery on a scale of 1 (tolerant) to 9 (susceptible). The tolerant and susceptible parents scored 1.5 and 8.4, respectively, and the F₃ means ranged from 1.6 to 8.9. Two bulks were formed with DNA from F₂ plants corresponding to the nine most tolerant and the nine most susceptible F₃ families. Of 624 RAPD primers used to screen the bulks, five produced bands associated with either tolerance or susceptibility. These markers were mapped to a region of chromosome 9 by linkage to RFLP markers. A submergence tolerance quantitative trait locus (QTL), here designatedSub1, was located ca. 4 cM from the RFLP marker C1232 and accounted for 69% of the phenotypic variance for the trait.     

A prostate-derived cDNA that is mapped to human chromosome 19 encodes a novel protein

The epithelial cells of prostate gland secrete various secretory products that play an important role in the growth and differentiation of prostate gland. These secretory products have also been implicated in neuroendocrine differentiation of benign prostatic hyperplasia and prostate malignancy. We have cloned a prostate-derived cDNA encoding a novel protein with a predicted molecular weight of 78 kDa (P(78)), and precisely mapped the cDNA sequence to chromosome 19. The P(78) gene has a complex genomic structure with 18 exons and 17 introns. The P(78) contains two conserved structural domains with limited similarity to domain D of synapsin I. The P(78) mRNA was expressed in various human cell lines. Western blot analysis using antibody specific for the P(78) revealed the presence of the P(78) protein in the prostate cancer cell lines with much lower level in metastatic prostate cancer cell lines compared to that in a primary prostate cancer cell line.     

Isolation and mapping of 75 new DNA markers on human chromosome 3.

We have isolated and mapped 75 new DNA markers including 52 restriction fragment length polymorphism (RFLP) markers on human chromosome 3. Clones were mapped by nonisotopic in situ hybridization, in which discrete fluorescent signals can be detected on prometaphase R-banded chromosomes. Thirty-seven markers were mapped to each arm of chromosome 3, and one was localized to the centromere. Five markers defined variable number of tandem repeat (VNTR) loci. Although the 75 clones were scattered throughout the chromosome, they were concentrated in the R-positive bands. This physical map of chromosome 3 will contribute to the characterization of the chromosomal and molecular aberrations involved in renal cell carcinoma, small-cell lung cancer, and other malignancies and in single-gene disorders such as von Hippel-Lindau disease and autosomal dominant retinitis pigmentosa.