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PubMed1994

Deletion map of the coloboma (Cm) locus on mouse chromosome 2.

The extent of the semidominant coloboma (Cm) mutation on mouse Chromosome 2 was determined by deletion mapping using interspecific hybrid mice. The Cm deletion mutation results in ophthalmic dysmorphology and behavioral deficits, including profound hyperactivity, and has been shown to encompass the gene Snap. In addition to Snap, the gene encoding phospholipase C beta-1 (Plcb-1), which maps 0.60 +/- 0.60 cM proximal to Snap, and simple sequence repeat (SSR) loci D2Mit19, D2Mit46, D2Mit28, and D2Mit136 were shown to be deleted at the Cm locus. In contrast, analysis of other closely linked SSRs and genes either proximal (Bmp-2a) or distal (Nec-1) to Snap, as well as a complementation test with the closely linked mutation lethal milk (lm), indicates that these gene sequences are unaffected by the Cm mutation. These data demonstrate that the Cm deletion represents a contiguous gene defect encompassing 1.1 to 2.2 cM that may be probed for genes, both in the mouse and in the syntenic region of human Chr 20, that independently affect elements of neurological behavior and eye development.

Animals↗

PubMed1994

The mouse neurofibromatosis type 2 gene maps to chromosome 11.

Neurofibromatosis type 2 (NF2) is a dominantly inherited disease characterized by the development of bilateral vestibular schwannomas and meningiomas, which together represent 30% of primary brain tumors. The NF2 gene, which has recently been isolated, maps to the long arm of human chromosome 22. Using recombinant inbred mice, we have determined the chromosomal position of the mouse homologue of the NF2 gene. Analysis of the allele distribution in AKXD recombinant inbred strains using a simple sequence repeat polymorphism (D11Mcg1) in the 3' untranslated region of the mouse cDNA maps the mouse NF2 gene to the proximal region of chromosome 11, closely linked to Pmv-2. This region also contains the genes for leukemia inhibitory factor and neurofilament heavy-chain polypeptide and thus represents a region of conserved synteny between human chromosome 22 and mouse chromosome 11. Using additional polymorphic markers, we established the following locus order from the centromere: D11Mit1/D11Mit72/D11Mcg1-D11Mit74-Pmv-2-D11Mi t2-D11Mit77/D11Mit78/D11Mit63.

Alleles↗

PubMed1994

Similar origins of two mouse minisatellites within transposon-like LTRs.

Tandem arrays of simple sequence repeat units are among the most unstable regions of mammalian genomes. Mutational instability at such loci depends on both repeat unit sequence and DNA sequences external to the tandem array, which have been recently implicated in polarized variability at human minisatellites. The characteristics of DNA sequences flanking the mouse minisatellite Ms6-hm have been investigated. This locus has a high mutation rate both in the germline and during early somatic development and is composed of a hypervariable tandem array of 500-2000 pentanucleotide repeat units flanked by a transposon-like long terminal repeat sequence of the mouse transcript (MT) family. A subpopulation of MT elements in the mouse genome are shown to flank a 1.1-kb internal sequence, consistent with their classification within a newly defined mammalian retrotransposon-like superfamily (MaLR). A second mouse minisatellite, Hm-2, also originates from within a MaLR LTR. Hm-2 is related to Ms6-hm in repeat unit sequence and profiles of germline and somatic instability; at both loci the tandem array has amplified from precisely the same point within the LTR. The similar origins of Ms6-hm and Hm-2 suggest that flanking MaLR sequences may be involved in mutational processes at these loci.

Animals↗

PubMed1994

A PCR-based genetic map for human chromosome 3.

Oligonucleotide primers for 125 simple sequence repeat microsatellite-based genetic markers have been assayed by polymerase chain reaction (PCR) in the CEPH reference family panel. These microsatellites include 101 dinucleotide repeats as well as 24 new tetranucleotide repeats. The average heterozygosity of this marker set was 72.4%. Genetic data were analyzed with the genetic mapping package LINKAGE. A subset of these microsatellite markers define a set of 56 uniquely ordered loci (> 1000:1 against local inversion) that span 271 cM. Sixty-seven additional loci were tightly linked to markers on the uniquely ordered map, but could not be ordered with such high precision. These markers were positioned by CMAP into confidence intervals. One hundred thirteen of the microsatellite markers were also tested on a chromosome 3 framework somatic cell hybrid panel that divides this chromosome into 23 cytogenetically defined regions, integrating the genetic and physical maps of this chromosome. The high density, high heterozygosity, and PCR format of this genetically and physically mapped set of markers will accelerate the mapping and positional cloning of new chromosome 3 genes.

Animals↗

PubMed1995

Molecular mapping of SSRs for Pgm1 and C8b in the vicinity of the rat fatty locus.

Recessive mutations at the rat fatty locus (fa, facp), which produce obesity, insulin resistance, and diabetes, provide useful experimental models for similar phenotypes in humans. The molecular pathogenesis of the metabolic phenotype in animals segregating for fa is unknown and difficult to study once the confounding metabolic effects of obesity are present. Although various experimental methods distinguish preobese from lean rats (phenotypic markers and molecular markers genetically linked to fatty), technical difficulties limit their utility. We report the identification of two (GT)n simple sequence repeats (SSRs) near the rat phosphoglucomutase gene (Pgm1) gene and two SSRs, (GA)n and (GT)n, near the rat complement component 8 beta gene (C8b). These SSRs map to an approximately 4-cM interval flanking the fatty locus on rat chromosome 5. Use of these molecular markers in combination offers an improved method for early assessment of gene dosage for fa and hence for studying the fundamental molecular physiology underlying the derangements of metabolism and behavior resulting from mutations in this gene.

Alleles↗

PubMed1995

Microsatellite-centromere mapping in the zebrafish (Danio rerio).

Ten (CA)n microsatellite simple sequence repeat (SSR) markers, 1, 2, 12, 14, 16, 18, 20, 22, 26, and 29, were used to show high chiasma interference and to determine centromere-marker map distances in the zebrafish (Danio rerio). Of these, SSR 12 exhibited no recombinant tetratypes among 175 half-tetrad embryos, placing this marker within 1 cM of the centromere of Linkage Group XVII. Fractions of heterozygous half-tetrads for the remaining nine markers ranged from 0.64 to 0.89. Of these, six recombinant fractions were more than 0.67 (P < 0.05), indicating strong chiasma interference during female meiosis in the zebrafish. Consistent with previous mapping data, SSRs 2 and 20 of Linkage Group VI were tightly linked. Half-tetrad analysis will allow the mapping of the remaining centromeres and may be useful in the mapping of new genes and mutations in the zebrafish.

Animals↗

PubMed1997

Physical and linkage mapping of human chromosome 17 loci to dog chromosomes 9 and 5.

Genome mapping in the dog is in its early stages. Here we illustrate an approach to combined physical and linkage mapping of type 1 anchor (gene) loci in the dog using information on syntenic homology from human and mouse, an interbreed cross/backcross, and a strategy for isolation of dog genomic clones containing both gene-specific sequences and simple sequence repeat polymorphisms. Eleven gene loci from human chromosome 17q (HSA17q) were mapped to the centromeric two-thirds of dog chromosome 9 (CFA9), an acrocentric chromosome of medium size: P4HB, GALK1, TK1, GH1, MYL4, BRCA1, RARA, THRA1, MPO, NF1, and CRYBA1. Eight of these were also positioned on a linkage map spanning 38.6 cM. Based on combined fluorescence in situ hybridization and linkage mapping, the gene order on CFA9 is similar to that of the homologous genes on HSA17q and mouse chromosome 11 (MMU11), but in the dog the gene order is inverted with respect to the centromere. Canine loci, GALK1, TK1, GH1, MYL4, THRA1, and RARA constitute a closely linked group near the centromeric end of CFA9, spanning a genetic distance of only 4.7 cM. Canine NF1 and CRYBA1 lie distally, near the lower border of the Giemsa band adjacent to the distal one-third of CFA9. NF1 and CRYBA1 are loosely linked to the more centromeric group (31.2 cM). No HSA17 genes were found on the telomeric one-third of CFA9. Painting of dog chromosomes with a human whole chromosome 17 probe showed hybridization with only the proximal two-thirds of CFA9, consistent with the conclusion that the distal one-third corresponds to a segment or segments of other human chromosomes. Two loci, GLUT4 and PMP22, located on HSA17p, were mapped by FISH to dog chromosome 5 in a region also identified by the whole human chromosome 17 paint, indicating disruption of HSA17 syntenic homology at the centromere.

Animals↗

PubMed1997

Human cholecystokinin type A receptor gene: cytogenetic localization, physical mapping, and identification of two missense variants in patients with obesity and non-insulin-dependent diabetes mellitus (NIDDM).

The human CCKAR gene was previously mapped to chromosome 4 using a panel of human/hamster somatic cell hybrids. We now report the cytogenetic and physical localization of the CCKAR gene. Using fluorescence in situ hybridization, we determined that CCKAR maps to 4p15.1-p15.2. On the physical map, CCKAR was adjacent to the marker AFMa283yh5, between AFMb355ya5 and WI-4086. A simple sequence repeat (D4S391) with high heterozygosity was found in the database, and CCKAR and this genetic marker were colocalized on two YACs (933D9 and 928A5). We also characterized the genomic structure and determined the exon-intron boundaries of the gene. This provided the opportunity to screen the gene in patients with non-insulin-dependent diabetes mellitus and/or obesity for single nucleotide changes using a single-strand conformational polymorphism strategy. Five sequence variants were identified in the coding sequence of the gene, including two missense variants (G21R and V365I). The results of these studies provide (1) precise genetic and physical mapping data, (2) exon-intron sequences for single nucleotide analysis, and (3) identification of two missense mutations in the CCKAR gene. The contribution of these CCKAR variants to normal physiology, to obesity, and to diabetes can now be evaluated.

Animals↗

PubMed1997

The human homogentisate 1,2-dioxygenase (HGO) gene.

Alkaptonuria (AKU; McKusick No. 203500), a rare hereditary disorder of the phenylalanine catabolism, was the first disease to be interpreted as an inborn error of metabolism (A. E. Garrod, 1902, Lancet 2: 1616-1620). AKU patients are deficient for homogentisate 1,2-dioxygenase (HGO; EC 1.13.11.5). This enzymatic deficiency causes homogentisic aciduria, ochronosis, and arthritis. Recently we cloned the human HGO gene and showed that AKU patients carry two copies of a loss-of-function HGO allele. Here we describe the complete nucleotide sequence of the human HGO gene and the identification of its promoter region. The human HGO gene spans 54,363 bp and codes for a 1715-nt-long transcript that is split into 14 exons ranging from 35 to 360 bp. The HGO introns, 605 to 17,687 bp in length, contain representatives of the major classes of repetitive elements, including several simple sequence repeats (SSR). Two of these SSRs, a (CT)n repeat in intron 4 and a (CA)n repeat in intron 13, were found to be polymorphic in a Spanish population sample. The HGO transcription start site was determined by primer extension. We report that sequences from -1074 to +89 bp (relative to the HGO transcription start site) are sufficient to promote transcription of a CAT reporter gene in human liver cells and that this fragment contains putative binding sites for liver-enriched transcription factors that might be involved in the regulation of HGO expression in liver.

Alkaptonuria↗

PubMed1997

Identification of a human LMX1 (LMX1.1)-related gene, LMX1.2: tissue-specific expression and linkage mapping on chromosome 9.

LMX1 is a LIM-homeodomain (LIM-HD)-containing protein expressed selectively in insulin-producing beta-cell lines, and it it has been shown to activate insulin gene transcription. The human LMX1 gene was mapped by fluorescence in situ hybridization to chromosome region 1q22-q23, yet Church et al. (1994, Nat. Genet. 6: 98-105) identified two exon-trapping products from human chromosome 9 that were highly homologous to hamster LMX1. In the current study, we demonstrate tissue-specific expression of an LMX1 (now known as LMX1.1)-related gene, named LMX1.2. The chicken C-LMX1 gene, recently cloned using the hamster LMX1.1 sequence and shown to specify dorsal cell fate during vertebrate limb development (9), is actually more related to human LMX1.2 than LMX1.1. We have identified a unique simple sequence repeat polymorphic marker (hLMX1.2CA1) in a P1 genomic clone containing the human LMX1.2 gene and genetically mapped the marker on chromosome 9 between markers D9S1825 and D9S290 with odds of at least 1000:1. In addition, we localized the human LMX1.1 gene to three CEPH "B" yeast artificial chromosome clones (907A11, 935B12, and 947B2), along with two nearby polymorphic markers (D1S426 and D1S194)). Identification of this new LIM-HD-related gene may provide the opportunity to elucidate further the function of LIM class homeobox genes. Nearby polymorphic markers will be useful in testing the hypothesis that mutations in these LIM-HD genes result in genetic diseases such as non-insulin-dependent diabetes mellitus.

Amino Acid Sequence↗

PubMed1999

A radiation hybrid map of mouse chromosome 13.

A mouse radiation hybrid (RH) panel was used to make a framework map for the entire length of mouse chromosome (Chr) 13. Forty-one loci were typed, and while most used primers flanking simple sequence repeats, some genes were included. The most proximal and distal loci are D13Mit132 and D13Mit35. The estimate of map length for Chr 13 is 1328 cR. The map is compared with the same set of loci from the consensus map for Chr 13, which is 70 cM in length, and also with a recombinational map derived from an intraspecies cross typed for many of the same loci. The mouse RH panel gave good resolution for Chr 13 and at the distal end allowed separation of previously nonrecombinant markers that are present on a single 620-kb YAC clone. Data analysis was performed using the RH option for Map Manager QT. This framework RH map of Chr 13 is the second of a series of RH maps for mouse chromosomes.

Animals↗

PubMed2000

A 6-Mb high-resolution physical and transcription map encompassing the hereditary prostate cancer 1 (HPC1) region.

Several hereditary disease loci have been genetically mapped to the chromosome 1q24-q31 interval, including the hereditary prostate cancer 1 (HPC1) locus. Here, we report the construction of a 20-Mb yeast artificial chromosome contig and a high-resolution 6-Mb sequence-ready bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) contig of 1q25 by sequence and computational analysis, STS content mapping, and chromosome walking. One hundred thirty-six new STSs, including 10 novel simple sequence repeat polymorphisms that are being used for genetic refinement of multiple disease loci, have been generated from this contig and are shown to map to the 1q25 interval. The integrity of the 6-Mb BAC/PAC contig has been confirmed by restriction fingerprinting, and this contig is being used as a template for human chromosome 1 genome sequencing. A transcription mapping effort has resulted in the precise localization of 18 known genes and 31 ESTs by database searching, exon trapping, direct cDNA hybridization, and sample sequencing of BACs from the 1q25 contig. An additional 11 known genes and ESTs have been placed within the larger 1q24-q31 interval. These transcription units represent candidate genes for multiple hereditary diseases, including HPC1.

Base Sequence↗

PubMed1996

Analysis and comparison of the mouse and human immunoglobulin heavy chain JH-Cmu-Cdelta locus.

We report here 23,686 bases of contiguous DNA sequences from the mouse germline immunoglobulin heavy chain (H) constant (C) mu delta region. The sequence spans the joining (JH) regions, the mu constant region (C mu), the delta constant region (C delta) coding regions, a domain relic, the mu switch region (S mu), seven blocks of simple sequence repeats, a large unique sequence inverted repeat, a large unique sequence forward repeat, and all of the intervening material. A comparison of this 23.7-kb region with the corresponding human C mu/C delta region reveals clear homology in the coding and introns of C mu but not in the 5' flanking J gene segments nor in the intergenic and C delta regions. This mixed pattern of similarity between the human and the mouse sequences contrasts with high levels of similarity found in the T-cell receptor C alpha/C delta region and alpha and beta myosin genes and the very low levels found in the gamma-crystallin, XRCC1, and beta-globin gene clusters. The human and mouse comparison further suggests the incorporation of novel sequences into expressed genes of IgD.

Animals↗

PubMed1995

Barley microsatellites: allele variation and mapping.

Microsatellites have developed into a powerful tool for mapping mammalian genomes and first reports about their use in plants have been published. A database search of 228 barley sequences from GenBank and EMBL was made to determine which simple sequence repeat (SSR) motif prevails in barley. Nearly all types of SSRs were found. The (A)n and (T)n SSRs occurred more often than (C)n and (G)n for n > or = 10. Among the dinucleotide repeats, the (CG)n SSRs occurred least often. Trinucleotide repeats did not occur with n > 7 and there is no correlation between the GC content in the trinucleotide motifs and the number of observed SSRs. Analysing 15 different microsatellites with 11 barleys yielded 2.1 alleles per microsatellite. Sequencing 25 putative microsatellites showed that the resolution capacity of high-quality agarose gels was sufficient to determine differences of only three base pairs. Five microsatellites were mapped on three different chromosomes of a barley RFLP map.

Alleles↗

PubMed1994

Linkage analysis of the genetic determinants of high density lipoprotein concentrations and composition: evidence for involvement of the apolipoprotein A-II and cholesteryl ester transfer protein loci.

We have tested for evidence of linkage between the genetic loci determining concentrations and composition of plasma high density lipoproteins (HDL) with the genes for the major apolipoproteins and enzymes participating in lipoprotein metabolism. These genes include those encoding various apolipoproteins (apo), including apoA-I, apoA-II, apoA-IV, apoB, apoC-I, apoC-II, apoC-III, apoE, and apo(a), cholesteryl ester transfer protein (CETP), HDL-binding protein, lipoprotein lipase, and the low density lipoprotein (LDL) receptor. Polymorphisms of these genes, and nearby highly polymorphic simple sequence repeat markers, were examined by quantitative sib-pair linkage analysis in 30 coronary artery disease families consisting of a total of 366 individuals. Evidence for linkage was observed between a marker locus D16S313 linked to the CETP locus and a locus determining plasma HDL-cholesterol concentration (P = 0.002), and the genetic locus for apoA-II and a locus determining the levels of the major apolipoproteins of HDL, apoA-I and apoA-II (P = 0.009 and 0.02, respectively). HDL level was also influenced by the variation at the apo(a) locus on chromosome 6 (P = 0.02). Thus, these data indicate the simultaneous involvement of at least two different genetic loci in the determination of the levels of HDL and its associated lipoproteins.

Apolipoprotein A-II↗

PubMed1993

Inter-ethnic polymorphism of the beta-globin gene locus control region (LCR) in sickle-cell anemia patients.

Sequence polymorphisms within the 5'HS2 segment of human locus control region is described among sickle cell anemia patients. Distinct polymorphic patterns of a simple sequence repeat are observed in strong linkage disequilibrium with each of the five major beta s haplotypes. Potential functional relevance of this polymorphic region in globin gene expression is discussed.

Algeria↗

PubMed1993

Genetic mapping of the erythropoietin receptor gene.

We describe a novel, highly informative (polymorphism information content, PIC, = 0.86) simple sequence repeat polymorphism at the 5' end of the gene encoding the human erythropoietin receptor (EPOR) previously assigned to 19p13.2 by in situ hybridization. Fourteen different allelic size variants were identified in 12 families of the CEPH (Centre d'Etude du Polymorphisme Humain) family panel of 40 families. In pairwise linkage 16 of the 65 chromosome 19 markers reported to the CEPH database gave a lod score exceeding 3.0 when tested against EPOR. The most likely location of EPOR within a framework of 10 markers including orientation and information on reported physical assignments was pter-[INSR-D19S177-D19S176]-D19S24-LDLR-++ +EPOR-cen-D19S7-D19S49-D19S75-D19S47-AP OC2-qter, placing EPOR as the most proximal of the tested loci on the short arm. On an 11-point map the position and order for all other loci except INSR were supported by the data with odds exceeding 1,000:1. The polymorphism at the 5' end of EPOR should provide a useful landmark marker for future mapping studies of this region.

Base Sequence↗

PubMed1994

Characterization of 65 bovine microsatellites.

Microsatellites or simple sequence repeat (SSR) polymorphisms are used widely in the construction of linkage maps in many species. High levels of polymorphism coupled with the ease of analysis of the polymerase chain reaction (PCR) have resulted in this type of maker being one of the most widely used for genetic analysis. In this paper we describe 58 polymorphic bovine microsatellites that were isolated from insert size selected bovine genomic libraries. Primer sequences, number of alleles, and heterozygosity levels in cattle reference families are reported. Chromosomal locations for 47 of these microsatellites as well as for 7 previously described systems derived from entries in the Genbank or EMBL databases have been determined. The markers map to 24 syntenic or chromosomal locations. Polymorphic bovine microsatellites were estimated to occur, on average, every 320 kb, and there is no evidence of clustering in the genome. Thirty of the bovine-derived microsatellite systems gave specific and polymorphic products in sheep, adding to the number of useful markers in that species.

Animals↗