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PubMed1995

Cosmid contigs from the tuberous sclerosis candidate region on chromosome 9q34.

Tuberous sclerosis (TSC) is a heterogeneous multisystem disorder with loci on 9q34 (TSC1) and 16p13.3 (TSC2). The TSC2 gene has recently been isolated, while the TSC1 gene has been mapped to a 5-cM region between the markers D9S149 and D9S114. In our effort to localise and clone TSC1, we have obtained three adjacent cosmid contigs that cover the core of the candidate region. The three contigs comprise approximately 600 kb and include 80 cosmids, 2 P1 clones, 1 YAC, 5 anonymous markers and 4 sequence-tagged sites. The ABO blood group locus, the Surfeit gene cluster, the dopamine beta-hydroxylase gene (DBH) and VAV2, a homologue of the vav oncogene, have all been mapped within the contigs. Exon trapping and mutation screening experiments, aimed at identifying the TSC1 gene, are currently in progress.

Bacteriophage P1↗
PubMed2000

Sample sequencing of the human major histocompatibility complex class I region identifies further new genes.

We used sample sequencing, a technique which generates random genomic sequence from cosmid clones and compares them with sequences deposited in the GenBank databases, to identify new genes in the class I region of the human major histocompatibility region. We isolated and ordered cosmid clones from a flow-sorted chromosome (Chr) 6 cosmid library, generating cosmid contigs covering approximately one third of the HLA class I region. Fifteen of these cosmids were then sample sequenced. A total of 216,694 bp of genomic sequence was generated and compared with sequences deposited in GenBank databases. In addition to identifying established class I region genes, a number of potential new genes were identified, including several which were not included in the recent major histocompatibility complex (MHC) consensus sequence map. Of particular interest are several new transcripts in the psoriasis susceptibility region.

Cloning, Molecular↗
PubMed1997

Identification of positional candidates for neurological disorders on chromsome 13q14-->q22.

In the course of a research project aimed at the molecular characterization of balanced chromosome rearrangements associated with mental retardation (MR), several YACs spanning MR-associated chromosomal rearrangements in the 13q14-->q22 region were identified. To facilitate the search for relevant candidate genes, we have analyzed a total of 102 EST clones from this region. Sequence comparisons revealed that these 102 clones represent up to 72 distinct transcripts. When no physical mapping data were available, a minimal YAC contig was screened for each unique transcript by the polymerase chain reaction (PCR) or hybridization. Fifty-eight independent ESTs could be localized to YAC clones between the markers D13S1248 and D13S1201. Several ESTs are located on YAC clones detecting chromosomal rearrangements in MR patients. One EST was mapped within the critical region for Rieger syndrome type 2, and three transcripts were identified in the region for the nocturnal enuresis type 1. Some ESTs showed homologies to known genes, including the cadherin-related tumor suppressor gene from Drosophila, the yeast mitotic control protein DIS3, and the human alpha-2-macroglobulin receptor associated protein.

Chromosome Aberrations↗
PubMed1993

Long-range restriction map of human chromosome 22q11-22q12 between the lambda immunoglobulin locus and the Ewing sarcoma breakpoint.

A long-range restriction map of the region between the immunoglobulin lambda locus and the Ewing sarcoma breakpoint has been constructed using the rare-cutting enzymes NotI, NruI, AscI, and BsiWI. The map spans approximately 11,000 kb and represents about one-fifth of the long arm of chromosome 22. Thirty-nine markers, including seven NotI junction clones as well as numerous genes and anonymous sequences, were mapped to the region with a somatic cell hybrid panel. These probes were then used to produce the map. The seven NotI junction clones each identified a possible CpG island. The breakpoints of the RAJ5 hybrid and the Ewing sarcoma t(11;22) were also localized in the resulting map. This physical map will be useful in studying chromosomal rearrangements in the region, as well as providing the details to examine the fidelity of the YAC and cosmid contigs currently under construction. Comparisons of this physical map to genetic and radiation hybrid maps are discussed.

Azacitidine↗
PubMed2005

Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5.

We constructed a bacterial artificial chromosome (BAC) library, designated as KBrH, from high molecular weight genomic DNA of Brassica rapa ssp. pekinensis (Chinese cabbage). This library, which was constructed using HindIII-cleaved genomic DNA, consists of 56,592 clones with average insert size of 115 kbp. Using a partially duplicated DNA sequence of Arabidopsis, represented by 19 and 9 predicted genes on chromosome 4 and 5, respectively, and BAC clones from the KBrH library, we studied conservation and microsynteny corresponding to the Arabidopsis regions in B. rapa ssp. pekinensis. The BAC contigs assembled according to the Arabidopsis homoeologues revealed triplication and rearrangements in the Chinese cabbage. In general, collinearity of genes in the paralogous segments was maintained, but gene contents were highly variable with interstitial losses. We also used representative BAC clones, from the assembled contigs, as probes and hybridized them on mitotic (metaphase) and/or meiotic (leptotene/pachytene/metaphase I) chromosomes of Chinese cabbage using bicolor fluorescence in situ hybridization. The hybridization pattern physically identified the paralogous segments of the Arabidopsis homoeologues on B. rapa ssp. pekinensis chromosomes. The homoeologous segments corresponding to chromosome 4 of Arabidopsis were located on chromosomes 2, 8 and 7, whereas those of chromosome 5 were present on chromosomes 6, 1 and 4 of B. rapa ssp. pekinensis.

Arabidopsis↗
PubMed2004

Visualization of the S-locus region in Ipomoea trifida: toward positional cloning of self-incompatibility genes.

Self-incompatibility (SI) in Ipomoea trifida is regulated by a single S locus with multiple alleles. Identification of SI genes in the S -locus region by positional cloning is one of the most important goals for understanding sexual reproduction in this species. Despite our intensive efforts to construct bacterial artificial chromosome (BAC) contigs covering the S -locus region, a gap was observed in the core region of the potential S locus. In order to confirm the physical linkage of two non-overlapping BAC contigs in the S -locus region and to determine the size of the gap between them, fluorescence in-situ hybridization (FISH) was performed on mitotic chromosomes and extended DNA fibres using previously isolated S -linked BAC clones as probes. The information obtained from this work would be useful for molecular cloning of the SI genes by a chromosome walking approach. In addition, we showed that strong suppression of recombination in the S locus was not related to the centromere because the S locus was mapped to one end of a chromosome.

Chromosomes, Artificial, Bacterial↗
PubMed1998

A 500-kb YAC and BAC contig encompassing the high-growth deletion in mouse chromosome 10 and identification of the murine Raidd/Cradd gene in the candidate region.

The mouse high growth (hg) gene was identified in a selection experiment for rapid growth. It produces a 30-50% increase in weight gain of homozygous individuals without resulting in obesity. Recently, hg was mapped to a deletion around marker D10Mit69. Here we report a map of yeast artificial chromosome and bacterial artificial chromosome clones spanning the entire region deleted in high-growth mice. The size of the deletion estimated from the clone lengths is approximately 500 kb. Using exon trapping, the murine Raidd/Cradd gene was identified in the hg region, and its cDNA sequence and expression pattern were determined. The human RAIDD/CRADD was mapped using radiation hybrid mapping to human chromosome 12, 2.9 cR distal to marker AFMB311WC5. The identified Raidd/Cradd gene, which is deleted in high-growth mice, presents a potential candidate for hg.

Adaptor Proteins, Signal Transducing↗
PubMed1995

Regional localization of 64 cosmid contigs, including 18 genes and 14 markers, to intervals on human chromosome 9q34.

A fluorescence in situ hybridization map of distal human chromosome 9q has been produced by mapping cosmid clones to metaphase chromosomes with balanced reciprocal translocations. This is a very accurate method of mapping, as clones are localized by their position with respect to the breakpoint in addition to cytogenetic banding. By using three lymphoblastoid cell lines with translocation breakpoints within 9q34, we have localized 18 genes and 14 DNA markers to one of four intervals on the chromosome. Cosmid contigs exist around 16 of these genes and 12 of these markers. A further 43 contigs have also been mapped, but they are as yet anonymous.

Animals↗
PubMed2000

Genetic and physical mapping of the locus for autosomal dominant renal Fanconi syndrome, on chromosome 15q15.3.

Autosomal dominant renal Fanconi syndrome is a genetic model for the study of proximal renal tubular transport pathology. We were able to map the locus for this disease to human chromosome 15q15.3 by genotyping a central Wisconsin pedigree with 10 affected individuals. After a whole-genome scan with highly polymorphic simple sequence repeat markers, a maximum LOD score of 3.01 was calculated for marker D15S659 on chromosome 15q15.3. Linkage and haplotype analysis for an additional 24 markers flanking D15S659 narrowed the interval to approximately 3 cM, with the two highest single-point LOD scores observed being 4.44 and 4.68 (for D15S182 and D15S537, respectively). Subsequently, a complete bacterial artificial chromosome contig was constructed, from the High Throughput Genomic Sequence Database, for the region bounded by D15S182 and D15S143. The identification of the gene and gene product altered in autosomal dominant renal Fanconi syndrome will allow the study of the physiology of proximal renal tubular transport.

Chromosome Mapping↗
PubMed2005

A BAC-based physical map of the Drosophila buzzatii genome.

Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps, and provide useful resources for sequencing entire genomes. Drosophila buzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in studies of genome evolution, ecological adaptation, and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and an approximately 18x expected representation of the D. buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be approximately 23x. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9555 clones, and assembled them using FingerPrint Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670 singletons. Finally, we anchored 181 large contigs (containing 7788 clones) to the D. buzzatii salivary gland polytene chromosomes by in situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available to the research community.

Animals↗
PubMed2001

Using PAC nested deletions to order contigs and microsatellite markers at the high repetitive sequence containing Npr3 gene locus.

Highly polymorphic di- and tetranucleotide repeats in and around Npr3, a potential candidate gene for hypertension, have been identified using a novel approach. Because this chromosomal site is rich in repetitive DNA and difficult to sequence, P1 artificial chromosomes were retrofitted with a loxP transposon to map the gene sequence within a clone using a series of nested deletions. Sequences from ends of deletions 1-3 kb apart identified a (CA)(20) and a (TA)(18)-(CA)(8) repeat 8 kb upstream and within an intron of Npr3, respectively. DNA from 17 individuals was analyzed for length polymorphisms in these and eight additional repeats identified in 200 kb of working draft sequence from this region in GenBank. The sequence contigs and microsatellite repeats from GenBank were ordered using the P1-derived artificial chromosome deletion series. Several of these repeats were found to vary considerably in length in the set of genomic DNA tested. Since this site in chromosome 5p has recently been implicated in disease in studies with genetically hypertensive rats, the microsatellite markers reported here will be useful for genetic analysis and may even be implicated in the disease process in humans. We discuss how these types of data are useful for interpreting draft DNA sequence coming out of the genome projects, and the utility of deletion clones as a resource for ordering contigs and gap filling.

Alleles↗
PubMed1992

A cluster of CpG islands at D10S94, near the locus responsible for multiple endocrine neoplasia type 2A (MEN2A).

We report the characterization of a dense cluster of CpG islands at D10S94 in proximal 10q11.2. D10S94 is tightly linked to the gene responsible for multiple endocrine neoplasia type 2A (MEN 2A), a dominantly inherited tumor syndrome characterized by medullary thyroid carcinoma (MTC), pheochromocytoma, and/or parathyroid adenoma. To date, no recombinants between D10S94 and MEN2A have been identified. The gene(s) responsible for two additional dominantly inherited disorders involving cancer of the medullary thyroid, MEN 2B (MEN2B), and dominantly inherited MTC without additional clinical features (MTC1), also map to this region. The gene or genes responsible for these disorders may be located at or near the D10S94 locus. A 570-kb long-range restriction map has been generated by pulsed-field gel electrophoresis using probes developed during a 160-kb bidirectional cosmid walk at D10S94. Six CpG islands are clustered within a 180-kb region; five fall within a 145-kb NotI restriction fragment that is contained in its entirety in our cosmid contig. The SacII, SfiI, and NotI restriction maps for lymphoblast and cloned DNA are concordant. These CpG islands may represent the 5' ends of candidate genes for MEN2A, MEN2B, and/or MTC1. One gene designated mcs94-1, which is associated with one of the CpG islands in this cluster, has been isolated and characterized in detail.

Base Sequence↗
PubMed2000

A first high-density map of 981 biallelic markers on human chromosome 14.

As the largest set of sequence variants, single-nucleotide polymorphisms (SNPs) constitute powerful assets for mapping genes and mutations related to common diseases and for pharmacogenetic studies. A major goal in human genetics is to establish a high-density map of the genome containing several hundred thousand SNPs. Here we assayed 3.7 Mb (154,397 bp in 24 alleles) of chromosome 14 expressed sequence tags (ESTs) and sequence-tagged sites, for sequence variation in DNA samples from 12 African individuals. We identified and mapped 480 biallelic markers (459 SNPs and 21 small insertions and deletions), equally distributed between EST and non-EST classes. Extensive research in public databases also yielded 604 chromosome 14 SNPs (dbSNPs), 520 of which could be mapped and 19 of which are common between CNG (i.e., identified at the Centre National de Génotypage) and dbSNP polymorphisms. We present a dense map of SNP variation of human chromosome 14 based on 981 nonredundant biallelic markers present among 1345 radiation hybrid mapped sequence objects. Next, bioinformatic tools allowed 945 significant sequence alignments to chromosome 14 contigs, giving the precise chromosome sequence position for 70% of the mapped sequences and SNPs. In addition, these tools also permitted the identification and mapping of 273 SNPs in 159 known genes. The availability of this SNP map will permit a wide range of genetic studies on a complete chromosome. The recognition of 45 genes with multiple SNPs, by allowing the construction of haplotypes, should facilitate pharmacogenetic studies in the corresponding regions.

Alleles↗
PubMed1994

Integration of physical, genetic and cytogenetic maps of human chromosome 7: isolation and analysis of yeast artificial chromosome clones for 117 mapped genetic markers.

An important goal for the human genome project is to assemble fully integrated physical, genetic and cytogenetic maps for each human chromosome. Towards that end, we have isolated yeast artificial chromosome (YAC) clones containing 117 of the 119 genetic markers that constitute a recently constructed, detailed genetic map of human chromosome 7. Analysis of these clones reveals numerous examples where adjacent genetic markers have been physically connected, either in individual YACs or in multi-YAC contigs. At present, the 117 genetic markers are contained in fewer than 80 YAC contigs, with most of these contigs uniquely ordered relative to one another based on the genetic map positions of the corresponding markers. These YACs and YAC contigs are estimated to contain approximately 60-85% of the DNA from human chromosome 7. YACs representing 36 genetic markers were mapped by fluorescence in situ hybridization (FISH) to metaphase chromosomes, allowing assignment of these genetic markers to cytogenetic bands along chromosome 7 and placement of the centromere within the genetic map. Together, these studies provide genetically and cytogenetically anchored YAC clones covering the majority of chromosome 7 that will be useful both for the positional cloning of genes and as a framework for assembling a complete YAC-based physical map of the chromosome.

Chromosome Mapping↗
PubMed1997

The organization of the gamma-glutamyl transferase genes and other low copy repeats in human chromosome 22q11.

A clone map consisting of YACs, cosmids, and fosmids has been constructed covering low copy repeat regions of human chromosome 22q11. A combination of clone restriction digest analysis, single-copy landmark content analysis, HindIII-Sau3AI fingerprinting, and sequencing of PCR products derived from clones was required to resolve the map in this region. Seven repeat-containing contigs were placed in 22q11, five containing gamma-glutamyl transferase (GGT) sequences described previously. In one case, a single interval at the resolution of the YAC map was shown to contain at least three GGT sequences after higher resolution mapping. The sequence information was used to design a rapid PCR/restriction digest technique that distinguishes the GGT loci placed in the YAC map. This approach has allowed us to resolve the previous cDNA and mapping information relating to GGT and link it to the physical map of 22q11.

Bacteria↗
PubMed1999

A 1-Mb PAC contig spanning the common eliminated region 1 (CER1) in microcell hybrid-derived SCID tumors.

We have developed an elimination test to identify chromosomal regions that contain tumor inhibitory genes. Monochromosomal human/mouse microcell hybrids are generated and passaged through SCID mice. Derived tumors are then analyzed for deletions on the transgenomic chromosome. Using this strategy, we have previously identified a 1.6-cM common eliminated region 1 (CER1) on human 3p21. 3. We now report that CER1 contains 14 markers that are deleted in 19 SCID-derived tumors. A 1-Mb PAC contig that spans CER1 was assembled. Five chemokine receptor genes (CCR1, CCR3, CCR2, CCR5, and CCR6) were localized in CER1 in a 225-kb cluster. The lactotransferrin gene (LTF, or lactoferrin, LF), which reportedly has tumor inhibitory activity, also maps to CER1. Our results create a basis for characterization and further functional testing of genes within CER1.

Animals↗
PubMed2000

A novel locus for autosomal recessive peripheral neuropathy in the EGR2 region on 10q23.

During our studies of Romany (Gypsy) families with hereditary motor and sensory neuropathy-Lom, we have identified a large kindred with two independently segregating autosomal recessive neuropathies. The novel disorder, named "hereditary motor and sensory neuropathy-Russe" (HMSNR), presented as a severe disabling form of Charcot-Marie-Tooth disease with prominent sensory loss, moderately reduced motor nerve conduction velocity, and a high threshold for electrical nerve stimulation. A genome scan in two branches of the large kindred detected linkage to the 10q22-q23 region containing the early growth response 2 gene (EGR2), a transcription factor with a key role in peripheral nerve myelination. The results of sequence analysis and the detection of an intragenic polymorphism allowed us to exclude EGR2 as the HMSNR gene. Further analysis done using linkage and recombination mapping refined the position of the HMSNR gene to a small interval on 10q23.2, flanked by markers D10S581 and D10S1742, telomeric to EGR2. In this interval, a conserved seven-marker haplotype is shared by all disease chromosomes, suggesting a single founder mutation. The homozygosity region is contained in bacterial-artificial-chromosome contig 1570 of the Sanger Centre physical map and has an estimated physical size of approximately 500 kb.

Charcot-Marie-Tooth Disease↗
PubMed2000

Localization of the mouse kidney disease (kd) gene to a YAC/BAC contig on Chromosome 10.

Mice that are homozygous for the kidney disease (kd) gene on Chromosome (Chr) 10 spontaneously develop a progressive and fatal interstitial nephritis. The disease phenotype is similar to that of the human disease, juvenile nephronophthisis. Using a backcross and intercross breeding strategy and analysis of over 900 resultant progeny, this genetic locus has now been mapped to a minimal co-segregating region of approximately two megabases between D10Mit 193 and D10Mit 38. The location assigned to kd by this study is over 3 cM from the current Mouse Genome Database location. The entire interval has been cloned in yeast artificial chromosome (YAC) and bacterial artificial chromosome (BAC) clones. Recombinant analysis has permitted assignment of 13 Mit microsatellite markers to positions near or within the region. Two new markers have been identified by using single-strand conformation polymorphism (SSCP) analysis of sequenced BAC ends. Several BAC end sequences align with human BAC clones from Chr 6q2 that contain NR2E1. Snx3, and Ros1. Three murine genes, CD24a, fyn, and ColX reported to map in or near the kd region as defined by this study have been evaluated. Though not definitely excluded, they appear to be unlikely candidates.

Animals↗