Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Contig Mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources
PubMed1996

Delineation of 7q11.2 deletions associated with Williams-Beuren syndrome and mapping of a repetitive sequence to within and to either side of the common deletion.

The majority of Williams-Beuren syndrome (WBS) patients have been shown to have a microdeletion within 7q11.2 including the elastin gene locus. The extent of these deletions has, however, not been well characterized. Thirty-five deletion patients were tested for all polymorphic markers in the 7q11.2 region bounding ELN to define the extent of deletions associated with WBS. With only one exception, ELN, D7S1870, and one copy of the D7S489 locus (D7S489U) were always included in the deletions. One patient showed lack of maternal inheritance at D7S1870 and not at ELN or D7S489U. A product corresponding to D7S489U was amplified from YAC 743G6 and from the P1 clone RMC07P008, thereby localizing both to within the common deletion. The boundary of the deleted region on the proximal (centromeric) side is D7S653 and on the distal side is D7S675, neither of which were ever included in the deletion. One locus, D7S489L, was variably deleted in patients, indicating a minimum of two common breakpoints on the proximal side. At least one additional repeat amplified by D7S489 (D7S489M) was localized to a YAC contig mapping distal to the common deletion. The D7S489 sequence is highly homologous to several cDNA clones in the GenBank database and contains an Alu sequence. It is possible that this andsolidusor other repetitive sequences in this region could play a role in the mechanism of deletion.

Base Sequence↗
PubMed1997

Clone-contig and STS maps of the hereditary hemochromatosis region on human chromosome 6p21.3-p22.

YAC-based and bacterial-clone based STS-content maps were constructed that served as the framework physical maps for the positional cloning of a candidate gene for hereditary hemochromatosis. The YAC-based map comprises 43 YACs and 86 STS and spans approximately 8 Mb of DNA between the class I region of the major histocompatibility complex on human chromosome 6p21.3 and D6S276 in 6p22. Comparison with published maps revealed a hole in the MIT/Whitehead and CEPH YAC maps that includes the immediate region around the hemochromatosis gene itself. Approximately 3 Mb of DNA was covered by a bacterial clone contig that consists of 38 BACs, 45 PACs, 26 PI clones and one lambda phage. The bacterial clone-based STS map comprises 153 STSs. A contiguous block of 8 STSs could be amplified from both human chromosome 6 and 5. Further characterization of selected STSs and bacterial clones by radiation hybrid mapping and fluorescence in situ hybridization, respectively, revealed the presence of a multicopy DNA segment, more than one bacterial clone length in size, which is duplicated near the chromosome-6 centromere and part of which is present in multiple copies on chromosome 5. Possible implications of the incomplete public YAC-contig map and of the multicopy segment for physical mapping and linkage disequilibrium studies of the hemochromatosis candidate region are discussed.

Bacteria↗
PubMed1996

A 4.5-megabase YAC contig and physical map over the hemochromatosis gene region.

We have constructed a yeast artificial chromosome (YAC) contig over the candidate hemochromatosis gene region. This contig comprises 16 YACs from the CEPH, Washington University, and ICI YAC libraries and covers 4.5 Mb at 6p21.3-6p22. The complete contig has been restriction mapped, enabling the precise relationship between the YACs to be determined and the mapping of a total of 12 STSs. Nine of these are highly polymorphic STSs that are closely linked to hemochromatosis; this series includes D6S265 and D6S1260, which comprise the most proximal and distal markers linked to HC. This is the first YAC contig that spans the hemochromatosis candidate region, and it provides valuable resource material for the cloning of this and other genes in the region distal to the MHC class I complex.

Base Sequence↗
PubMed2001

A transgenic insertion causing cryptorchidism in mice.

A distinctive feature of gonadal maturation in mammals is the movement to an extraabdominal location. Testicular descent is a complex, multistage process whereby the embryonic gonads migrate from their initial abdominal position to the scrotum. Failure in this process results in cryptorchidism, a frequent congenital birth defect in humans. We report here a new mouse transgenic insertional mutation, cryptorchidism with white spotting (crsp). Males homozygous for crsp exhibit a high intraabdominal position of the testes, associated with complete sterility. Heterozygous males have a wild-type phenotype, and homozygous females are fertile. Surgically descended testes in crsp/crsp males show normal spermatogenesis. Using FISH and genetic analyses, the transgenic insert causing the crsp mutation has been mapped to the distal part of mouse chromosome 5. Transgene integration resulted in a 550-kb deletion located upstream of the Brca2 gene. A candidate gene encoding a novel G protein-coupled receptor (Great) with an expression pattern suggesting involvement in testicular descent has been identified.

Amino Acid Sequence↗
PubMed1993

Microdissection and microcloning of genomic DNA markers from human chromosomal region 11q23.

A human genomic DNA library was constructed by using a microdissection-microcloning procedure with polymerase chain reaction (PCR) techniques on DNA from the chromosome 11q23 region. A total of 450 recombinant pUC clones were isolated from the library. Their insert sizes ranged from 150 to 850 bp with a mean of 320 bp. Fifty pUC clones were randomly selected and analyzed in detail. Southern blot analyses showed that 21 (42%) clones were unique DNA sequences, 20 (40%) clones were repetitive sequences, and 9 (18%) clones had no detectable hybridization. The unique sequences were used further in a secondary screening of a partially digested human genomic DNA library constructed in phage vector, and 4 clones were isolated. The chromosomal locations of these phage clones were confirmed to be in the q23 region of chromosome 11 by fluorescence in situ suppression hybridization. These pUC microclones isolated from the chromosomal region-specific genomic DNA library will be useful in the construction of physical contig maps with yeast artificial chromosome and/or cosmid clones and in the positional cloning of disease-associated genes localized to the q23 region of chromosome 11.

Chromosome Mapping↗
PubMed1993

Organization of the multiple polymorphic sites of the D19S11 locus within a 650-kb cosmid contig.

The D19S11 locus has been previously described as consisting of a complex set of six nonallelic polymorphic sites detected with a combination of four restriction enzymes and three probes that were subcloned from a single cosmid. These probes also hybridized to additional nonvariant fragments on Southern blots of human genomic DNA. In the course of establishing a contig map of human chromosome 19, a set of cosmids that were positive for at least one of the probes defining this locus was identified. These cosmids, along with additional cosmids, were assembled using a combination of strategies, including fluorescence in situ hybridization studies using G1 interphase nuclei and sperm pronuclei as chromatin targets, into a single overlapping set of cosmids that spans approximately 650 kb. Cosmids that are positive for the MEL gene probe are localized at the centromeric end of the spanning path, with some cosmids being positive for both the MEL gene probe and one of the D19S11 probes. The EcoRI fragments with homology to the various probes have been identified; some cosmids have homology to all three D19S11 probes. The positions for five of the six polymorphic sites were localized within a 40-kb region, with four sites within 15 kb.

Blotting, Southern↗
PubMed1994

A YAC contig spanning the hypophosphatemic rickets disease gene (HYP) candidate region.

Dominant X-linked hypophosphatemic rickets (HYP) is the most common form of familial rickets. Linkage studies have localized the gene for this disorder to Xp22.1 between the markers DXS365 and DXS274, a region estimated to be approximately 3.5 cM. We have constructed a 1.5-Mb YAC contig encompassing this region by hybridization screening of high-density YAC clone filters. Rapid chromosome walking was achieved by direct hybridization of a pool of Alu-PCR products derived from a YAC containing DXS365 to the filter grids. Overlaps between YACs in the contig were estimated by hybridization of end probes to YAC digest blots and by analysis of cosmid fingerprints obtained by hybridization of YAC inserts to a flow-sorted chromosome X cosmid library. All YACs in the contig have been verified by fluorescence in situ hybridization. Several YACs spanning the HYP gene candidate region were selected for further analysis by rare-cutter enzyme digestion and pulsed-field gel electrophoresis. We estimate that the markers flanking the disease region, DXS365 and DXS274, are less than 1 Mb apart. This clone contig map provides an essential resource for the isolation of the HYP gene.

Animals↗
PubMed1993

Mhc-DRB genes of platyrrhine primates.

The two infraorders of anthropoid primates, Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys and the hominoids) are estimated to have diverged from a common ancestor 37 million years ago. The major histocompatibility complex class II DRB gene and haplotype polymorphism of the Catarrhini has been characterized in several recent studies. The present study was undertaken to obtain information on the DRB polymorphism of the Platyrrhini. Fifty-five complete exon 2 DRB sequences were obtained from six species of Platyrrhini representing both the Callitrichidae and the Cebidae families. Combined with the results of a parallel contig mapping study, our data indicate that at least three loci (DRB1*03, DRB3, and DRB5) are shared by the Catarrhini and the Platyrrhini. However, the three loci are occupied by functional genes in the former infraorder and mostly by pseudogenes in the latter. Instead of the pseudogenes, the Platyrrhini have evolved a new set of apparently functional genes-DRB11 and DRB*W12 through DRB*W19, which have thus far not been found in the Catarrhini. The DRB*W13, *W14, *W15, *W17, *W18, and *W19 genes seem to be restricted to the Cebidae family, whereas the DRB*W16 locus has so far been documented in the Callitrichidae family only. The DRB alleles of the cotton-top tamarin, and perhaps also those of the common marmoset (both members of the family Callitrichidae), are characterized by low nucleotide diversity, possibly indicating that they diverged from a common ancestral gene relatively recently.

Amino Acid Sequence↗
PubMed1995

Analysis of pericentromeric chromosome 21 specific YAC clones by FISH: identification of new markers for molecular-cytogenetic application.

Fluorescence in situ hybridization (FISH) of chromosome 21 specific yeast artificial chromosome (YAC) clones after Alu-PCR (polymerase chain reaction) amplification has been used to find new region-specific DNA probes for the heterochromatic region of chromosome 21. Six overlapping YAC clones from a pericentromeric contig map (region 21cen-21q11) were analyzed. Four YAC clones were characterized as hybridizing to several chromosomal locations. They are, therefore, either chimeric or shared by different chromosomes. Two of them containing alphoid satellite DNA, are localized at the centromeric regions of chromosomes 13 and 21 (clone 243A11), and on 13cen, 21cen and 1q3 (clone 781G5); the two others are localized at both 21q11 and 13q2 (clone 759D3), and at 18p (clone 770B3). Two YACs were strongly specific for chromosome 21q11 only (clones 124A7 and 881D2). These YACs were used effectively as probes for identifications of chromosome 21 during metaphase and interphase analysis of 12 individuals, including three families with Down syndrome offspring, and 6 aminocyte samples. The location of YAC clones on 21q11 close to the centromeric region allows the application of these clones as molecular probes for the analysis of marker chromosomes with partial deletions of the long arm as well as for pre- and postnatal diagnosis of trisomy 21 when alphoid or more distal region-specific DNA probes are uninformative. Overlapping YAC clones covering human chromosome 21q may be systematically used to detect a set of band-specific DNA probes for molecular-cytogenetic application.

Base Sequence↗
PubMed1993

Multiplication of Mhc-DRB5 loci in the orangutan: implications for the evolution of DRB haplotypes.

The beta chain-encoding (B) class II genes of the primate major histocompatibility complex belong to several families. The DRB family of class II genes is distinguished by the occurrence of haplotype polymorphism--the existence of multiple chromosomal forms differing in length, gene number, and gene combinations, each form occurring at an appreciable frequency in the population. Some of the haplotypes, or fragments thereof, are shared by humans, chimpanzees, and gorillas. In an effort to follow the DRB haplotype polymorphism further back in time, we constructed DRB contig maps of the two chromosomes present in the orangutan cell line CP81. Two types of genes were found in the two haplotypes, Popy-DRB5 and Popy-DRB1*03, the former occurring in two copies and one gene fragment in each haplotype, so that the CP81 cell line contains four complete DRB5 genes and two DRB5 fragments altogether. Since the four genes are more closely related to one another than they are to other DRB5 genes, they must have arisen from a single ancestral copy by multiple duplications. At the same time, however, the two CP81 haplotypes differ considerably in their restriction enzyme sites and in the presence of Alu elements at different positions, indicating that they have been separated for a length of time that exceeds the lifespan of a primate species. Moreover, a segment of about 100 kilobase pairs is shared between the orangutan CP81-1 and the human HLA-DR2 haplotype. These findings indicate that part of the haplotype polymorphism may have persisted for more than 13 million years, which is the estimated time of human-orangutan divergence.

Amino Acid Sequence↗
PubMed1997

A yeast artificial chromosome (YAC) library containing 10 haploid chicken genome equivalents.

We report the construction of a YAC library that provides 10-fold redundant coverage of the chicken genome. The library was made by transforming S. cerevisiae AB1380 with YAC constructs consisting of partially digested and size fractionated (>465 kb) EcoRI genomic fragments ligated to pCGS966 YAC vector arms. The primary library provides 8.5-fold redundant coverage and consists of 16,000 clones arrayed in duplicate 96-well microtiter plates and gridded on nylon membranes at high density (18,000 clones/484cm2). The average insert size, 634 kb, was derived from size fractionation of a random sample of 218 YACs. Hybridization of five unlinked chicken genes to colony blots revealed six or more positive clones. This is consistent with the theoretical expectation from average insert sizes and number of clones. A second collection of clones consists of a further 20,000 colonies, of which 20% contain inserts larger than 450 kb and 80% contain only coligated vector arms. We estimate that these clones provide a further 1.5-fold redundant coverage of the chicken genome; thus, the total collection of 36,000 clones provides 10-fold redundant coverage of the chicken genome. The library is intended as a resource for fine-scale analysis of the organization of the chicken genome and is presently being used to construct a contig map of chicken Chromosome (Chr) 16, which contains the MHC and nucleolar organizer.

Animals↗
PubMed2002

A novel gene is disrupted at a 14q13 breakpoint of t(2;14) in a patient with mirror-image polydactyly of hands and feet.

Mirror-image polydactyly of hands and feet (MIP) is a very rare congenital anomaly characterized by mirror-image duplication of digits. To isolate the gene responsible for MIP, we performed translocation breakpoint cloning from an MIP patient with t(2;14)(p23.3;q13). We isolated a good candidate gene for MIP that was disrupted by the translocation of the patient. We had previously con structed a 1.2-megabase bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) contig covering the 14q13 breakpoint of t(2;14)(p23.3;q13). From a 500-kb segment consisting of seven BAC/PAC clones in the contig, we isolated a novel gene (the mirror-image polydactyly 1 gene, designated as MIPOL1, GenBank Accession No. AY059470), in addition to the hepatocyte nuclear factor 3 alpha gene (HNF3A, GenBank Accession No. XM 007360). MIPOL1 spans about 350kb, comprises 15 exons, and encodes 442 amino acids. Northern blot analysis revealed that MIPOL1 expression is definite but very weak in adult heart, liver, skeletal muscle, kidney, and pancreas, and in fetal kidney. In view of the genome sequence and the contig map constructed, the 14q13 breakpoint of the patient was identified as located in intron 11 of MIPOL1, indicating that the gene was disrupted by the translocation, and that the breakage resulted in MIPOL1 protein truncation. Whole-mount in situ hybridization in mouse resulted in mouse Mipol1 signals all over E10.5-E13.5 mouse embryos. Two other unrelated patients with limb anomalies similar to MIP were subjected to mutation analysis of MIPOL1, but none had any mutations. We then isolated BAC clones from the other breakpoint, 2p23.3. A search for genes and expressed sequence tags in a more than 300-kb region around the 2p23.3 breakpoint found only the neuroblastoma-amplified protein gene (NAG, GenBank Accession No. NM 015909), which is located at least 50kb centromeric to the breakpoint and is not likely to be related to MIP. MIPOL1 is a good candidate gene for the MIP type of anomaly.

Chromosomes, Human, Pair 14↗
PubMed1993

Conservative evolution of the Mbc-DP region in anthropoid primates.

To determine the organization of the DP region in the Mbc of anthropoid primates, we constructed contig maps from cosmid clones of the chimpanzee and orangutan, representatives of the infraorder Catarrhini, as well as of the cotton-top tamarin, a representative of the infraorder Platyrrhini. We found the maps to be remarkably similar to each other and to the previously published map of the human DP region. In each of the four species, the DP region consists of four loci arranged in the same order (DPB2 . . . DPA2 . . . DPB1 . . . DPA1) and in the same transcriptional orientation (tail-to-tail). The regions in the four species are of approximately the same length and many of the restriction sites are shared between species. The inserts of most Alu elements, of a ribosomal protein pseudogene, and of an IgC epsilon-like pseudogene are found in corresponding positions in all four species. The data indicate that the human-type organization of the DP region was established before the divergence of the Catarrhini and Platyrrhini lines more than 37 million years ago and that it has remained principally intact since that time. This conservation of the DP region is in striking contrast to the evolutionary instability of certain other Mbc regions, in particular those occupied by the DRB or C4 and CYP21 loci. We interpret the stability of the DP region as an indication that the region is being phased out functionally.

Animals↗
PubMed1995

Construction and utility of a human chromosome 22-specific Fosmid library.

We have previously demonstrated the capability of the Fosmid vector based on Escherichia coli F-factor replicon to stably propagate cosmid-sized human genomic DNA fragments. Using the Fosmid vector, we have constructed and arrayed a 10 x human chromosome 22-specific library, partly by picking human positive clones from a total Fosmid library constructed using DNA from human-hamster hybrid cell line containing human chromosome 22, and partly by using flow-sorted chromosomal DNA. The clones and physical contig maps of the clones in the library will serve as a valuable resource for detailed analysis of the chromosome by providing reliable materials for high resolution mapping and sequencing. In order to efficiently build physical maps for the chromosomal regions of interest spanning several hundred kilobases to a megabase, it is necessary to rapidly identify subsets of the Fosmid clones from the library that cover such regions. In this report, we describe a method of using random amplification products derived from YAC clones to rapidly identify a subset of Fosmid clones that cover a specific genomic subregion.

Animals↗
PubMed1999

Elucidation of the mechanism of homozygous deletion of 3p12-13 in the U2020 cell line reveals the unexpected involvement of other chromosomes.

Homozygous deletions in tumor cells have been useful in the localization and validation of tumor suppressor genes. We have described a homozygous deletion in a lung cancer cell line (U2020) which is located within the most proximal of the three regions on the short arm of chromosome 3 believed to be lost in lung cancer development. Construction of a YAC contig map indicates that the deletion spans around 8 Mb, but no large deletion was apparent on conventional cytogenetic analysis of the cell line. To investigate this paradox, whole chromosome, arm-specific, and regional paints have been used. This analysis has revealed that genetic loss has occurred by complex rearrangements of chromosomes 3, rather than simple interstitial deletion. These studies emphasize the power of molecular cytogenetics to disclose unsuspected tumor-specific translocations within the extremely complex karyotypes characteristic of solid tumors.

Carcinoma, Small Cell↗
PubMed1999

A diagnostic fluorescent marker kit for six limb girdle muscular dystrophies.

The autosomal progressive muscular dystrophies which are grouped together under the term limb girdle muscular dystrophies (LGMD) are diseases characterized by a progressive impairment of the proximal limb muscles and myopathic changes on electromyogram and muscle biopsy. Eight independent purely recessive genetic entities have been recognized in this group of diseases by genetic localization or causative gene identification. We have developed fluorescent genetic markers bracketing six of these loci (LGMD2A-LGMD2F). The marker loci were genotyped in 96 LGMD2 families leading to genetic definition of 25 of them either with a high likelihood or with a suggested localization (7 LGMD2A, 5 LGMD2B, 4 LGMD2C, 4 LGMD2D, 2 LGMD2E and 3 LGMD2F). In addition, 18 families were excluded for all six tested loci; for 45 of the 53 remaining families at least one exclusion could be demonstrated. This kit, which makes the rapid genetic testing of LGMD2 families possible, may be useful in a diagnostic process.

Chromosome Mapping↗
PubMed2000

Recent developments from the Leishmania genome project.

A first generation cosmid contig map of the Leishmania major Friedlin genome has been constructed, and genomic sequencing is well underway. Chromosome 1 (Chr1) and Chr3 have been completely sequenced, and Chr4 is virtually complete. Sequencing of several other chromosomes is in progress and the complete genome sequence may be available as soon as 2003. More than 600 completely sequenced new genes have been identified, representing approximately 8% of the total gene complement (approximately 8,600 genes) of Leishmania. Notably, a large proportion (approximately 69%) of the genes remain unclassified, with 40% of these being potentially Leishmania- (or kinetoplastid-) specific. Most interestingly, the genes are organized into large (>100-300 kb) polycistronic clusters of adjacent genes on the same DNA strand. Chr1 contains two such clusters organized in a 'divergent' manner, whereas Chr3 contains two 'convergent' clusters, with a single 'divergent' gene at one telomere, with the two large clusters separated by a tRNA gene. Statistical analyses of Chr1 show that the 'divergent junction' region between the two polycistronic gene clusters may be a candidate for an origin of DNA replication.

Animals↗
PubMed2002

Microsynteny between pea and Medicago truncatula in the SYM2 region.

The crop legume pea (Pisum sativum) is genetically well characterized. However, due to its large genome it is not amenable to efficient positional cloning strategies. The purpose of this study was to determine if the model legume Medicago truncatula, which is a close relative of pea, could be used as a reference genome to facilitate the cloning of genes identified based on phenotypic and genetic criteria in pea. To this end, we studied the level of microsynteny between the SYM2 region of pea and the orthologous region in M. truncatula. Initially, a marker tightly linked to SYM2 was isolated by performing differential RNA display on near-isogenic pea lines. This marker served as the starting point for construction of a BAC physical map in M. truncatula. A fine-structure genetic map, based on eight markers from the M. truncatula physical map, indicates that the two genomes in this region share a conserved gene content. Importantly, this fine structure genetic map clearly delimits the SYM2-containing region in pea and the SYM2-orthologous region in M. truncatula, and should provide the basis for cloning SYM2. The utility of the physical and genetic tools in M. truncatula to dissect the SYM2 region of pea should have important implications for other gene cloning experiments in pea, in particular where the two genomes are highly syntenic within the region of interest.

Chromosome Mapping↗