Mapping of cosmid clones in Huntington's disease region of chromosome 4

Huntington's disease (HD) is tightly linked to genetic markers in 4p16.3. We have used a regional somatic cell hybrid mapping panel to isolate and map 25 cosmids to the proximal portion of 4p16.3 and 17 cosmids to the distal portion. The latter were positioned by long-range restriction mapping relative to previously mapped markers. One cosmid, L6 (D4S166), spans the critical breakpoint in the mapping panel that distinguishes proximal and distal 4p16.3. Four of the cosmids mapped distal toD4S90, the previous terminal marker on 4p, and stretched to within 75 kb of the telomere. Several of the cosmids that mapped between L6 andD4S90 were clustered near a number of previously isolated clones in a region with many NotI sites. Cosmid E4 (D4S168) was localized immediately proximal to the one remaining gap in the long-range restriction map of distal 4p16.3. Although pulsed field gel mapping with E4 failed to link the two segments of the map, the intervening gap was excluded as a potential site for theHD gene by genetic analysis.     

A yeast artificial chromosome contig from human chromosome 14q24 spanning the Alzheimer's disease locus AD3

Familial Alzheimer's disease has been previously linked to threegenetic loci on chromosomes 21, 19 and 14. The AD3 locus onchromosome 14 has not been cloned and the molecular defect inchromosome 14-linked AD3 families has yet to be identified.Genetic linkage analysis has placed the AD3 locus in band 14q24between the dinucleotide markers D14S61 and D14S289, a geneticdistance of approximately 6.4 cM. We have constructed a yeastartificial chromosome (YAC) contig that covers the entire minimalregion, encompassing all genetic markers that are non-recombinantfor the disease in AD3-linked families. This contig, constructedby using a combination of YAC end sequence walking and sequence-taggedsite (STS) mapping, consists of 63 YACs from three differentlibraries. The AD3 contig contains 12 polymorphic dinucleotiderepeat markers from D14S61 to D14S251, as well as an additional43 non-polymorphic STSs. This contiguous physical map of theregion will allow the physical distances between the markersto be determined, as well as providing a framework for the identificationof candidate genes.     

Detailed genetic mapping of the von Hippel-Lindau disease tumour suppressor gene.

Von Hippel-Lindau (VHL) disease is an autosomal dominant inherited familial cancer syndrome characterised by a predisposition to the development of retinal, cerebellar, and spinal haemangioblastomas, renal cell carcinoma, and phaeochromocytoma. The gene for VHL disease has been mapped to chromosome 3p25-p26 and flanking markers identified. We report the detailed genetic mapping of the VHL disease locus in 38 families. Significant linkage was detected between VHL disease and D3S601 (Zmax = 18.86 at theta = 0.0, CI 0.0-0.025), D3S18 (Zmax = 11.42 at theta = 0.03, CI 0.005-0.08), RAF1 (Zmax = 11.02 at theta = 0.04, CI 0.007-0.01), and D3S1250 (Zmax = 4.73 at theta = 0.05, CI 0.005-0.15). Multipoint linkage analysis mapped the VHL disease locus between D3S1250 and D3S18 close to D3S601. There was no evidence of locus heterogeneity. This study has (1) confirmed the tight linkage between VHL disease and D3S601, (2) identified D3S1250 as the first marker telomeric to RAF1 which maps centromeric to the VHL disease gene, and (3) narrowed the target region for isolation of the VHL disease gene by positional cloning techniques to a 4 cM interval between D3S1250 and D3S18. These findings will improve the clinical management of families with VHL disease by improving the accuracy of presymptomatic diagnosis using linked DNA markers, and will enhance progress towards isolating the VHL disease gene.     

Genetic linkage between Von Hippel--Lindau disease and three microsatellite polymorphisms refines the localisation of the VHL locus

Von Hippel—Lindau (VHL) disease is a dominantly inheritedfamilial cancer syndrome characterised by the development ofretinal and central nervous system haemangioblastomas, renalcell carcinoma and phaeochromocytoma. The gene for VHL diseasehas been mapped to chromosome 3p25–p26 and presymtomaticdiagnosis using linked DNA markers is available. We have previouslymapped the VHL disease gene to a 4 cM interval between D3S1250and D3S18. To increase access to presymptomatic diagnosis andto accelerate progress towards isolating the VHL disease genewe attempted to identify microsatellite DNA markers linked tothe disease gene by genetic linkage analysis in 29 families.We found significant linkage between the VHL disease gene anddinucleotide (CA) repeat polymorphisms at D3S1038 (Zmax = 22.24at     

Physical map of the region containing the gene for Batten disease (CLN3)

CLN3 has been mapped genetically to 16p12, to the interval between D16S288 and D16S383, a sex-averaged genetic distance of 2.1 cM. Analysis of disease haplotypes for four microsatellite markers in this interval, D16S288, D16S299, D16S298, and SPN, has shown significant allelic association between one allele at each of these loci and CLN3. All four of the associated markers were used as nucleation sites in the isolation of genomic clones (YACs). A contig was assembled which contains 3 of the 4 associated markers and which confirmed the relative order of these markers. Marker D16S272 has been located on the physical map between D16S288 and D16S299. Restriction mapping has demonstrated the location of possible CpG islands. One gene, STP, has been localised on the YAC contig proximal to D16S298 and is therefore a candidate for CLN3. Other genes, including IL4R, SGLT2, and UQCRC2, have been excluded from this region. © 1995 Wiley-Liss, Inc.     

Cloning of the Huntington disease region in yeast artificial chromosomes.

The gene responsible for Huntington disease has been localized to a 2.5 million base pair (Mb) region between the loci D4S10 and D4S168 on the short arm of chromosome 4. As part of a strategy to clone the HD gene on the basis of its chromosomal location, we isolated genomic DNA from the HD region as a set of overlapping yeast artificial chromosome (YAC) clones. Twenty-eight YAC clones were identified by screening human YAC libraries with twelve PCR-based sequence-tagged sites (STSs) from the region. We assembled the YAC clones into overlapping sets by hybridizing them to a large number of DNA probes from the HD region, including the STSs. In addition, we isolated the ends of the human DNA inserts of most of the YAC clones to assist in the construction of the contig. Although almost half of the YACs appear to contain chimeric inserts and several contain internal deletions or other rearrangements, we were able to obtain over 2.2 Mb of the HD region in YACs, including one continuous segment of 2.0 Mb covering the region that most likely contains the HD gene. Ten of the twenty eight YAC clones comprise a minimal set spanning the 2.2 Mb. These clones provide reagents for the complete characterization of this region of the genome and for the eventual isolation of the HD gene.     

Cloning of a novel, anonymous gene from a megabase-range YAC and cosmid contig in the neurofibromatosis type 2/meningioma region on human chromosome 22q12

In order to permit detailed characterization of meningioma casesshowing deletions within chromosomal band 22q12 and furthersystematically clone genes located within this region, we establisheda genomic YAC and cosmid contig which encompasses a region inexcess of 1000 kb of 22q12. The YAC contig consists of 6 YACclones arranged Into 5 overlapping steps covering more than1100 kb. Two corresponding cosmid contigs consisting of 40 stepsof overlapping groups of cosmids encompasses 900–1000kb. This set of genomic clones provides a detailed physicalmap of this part of chromosome 22 and constitutes a basis forthe Isolation and characterization of genes that may be locatedwithin this chromosomal region. Employing the exon-amplificationmethod on two cosmids from the contig, we cloned a novel, anonymousgene, pK1.3, which potentially encodes a protein of 683 aminoacids with a predicted molecular weight of of 78.5 kD. Its 2.7kb mRNA is expressed ubiquitously. We estimated the genomicsize of this gene to 100 –150 kb, and it is located inthe Immediate centromeric vicinity of the neurofibromatosis2 (NF2) tumor suppressor gene.     

8p11.2亚带ANK1位点附近区域YAC连续克隆群的构建

我们分离了３个８ｐ１１．２亚带ＡＮ中位点附近区域的单拷贝片段，应用这些片段之一Ｓ９２５作为探针筛到４个阳性ＣＥＰＨＹＡＣ克隆结合文献报道资料及其多态性位标检测结果。我们在ＡＮＫ１附近区域构建一个ＹＡＣ连续克隆群，从而填补了Ｄ８Ｓ５３２和Ｄ８Ｓ２６８之间的间隙。这个ＹＡＣ连续克隆群要用于分离基因，为筛选定位在这个区域的致病基因提供候选基因。     

Construction of cosmid contigs and high-resolution restriction mapping of the Huntington disease region of human chromosome 4

The gene responsible for Huntington disease (HD) has been localizedto a 2.2 million base pair (Mbp) region between the loci D4S10and D4S98 on the short arm of human chromosome 4. As part ofa strategy originally designed to clone the gene based on itschromosomal location, we and others previously identified overlappingyeast artificial chromosome (YAC) clones covering most of thisregion. While these YAC clones were useful for initially obtaininglong-range clone continuity, a number of features of the YACsindicated that smaller clones are generally more useful in thesubsequent steps of the positional cloning strategy. In thispaper, we use these YAC clones to generate sets of overlappingcosmid clones covering most of the HD region. We Isolated alarge number of cosmids by screening a chromosome 4-specificcosmld library with labeled DNA from a minimal overlapping setof YAC clones. These cosmid clones were further analyzed byrestriction mapping and hybridization experiments, leading tothe assembly of 185 cosmids Into eleven contigs covering morethan 1.65 Mbp and to a fine-structure restriction map of theregion. Nine of these contigs cover 90 percent of the 1.7 Mbpsubregion between loci D4S125 and D4S98 where the HD gene isnow known to lie. The detailed restriction map and the cosmidclones should facilitate the identification and localizationof cDNAs and polymorphic markers, and they provide reagentsfor large scale DNA sequencing of this region of the human genome.Our results suggest that this strategy should be generally usefulfor converting YAC clones into cosmid contigs and generatinghigh-resolution restriction maps of genomioc regions of interest.     

Construction of a YAC contig and a STS map spanning at least seven megabasepairs in chromosome 5q34-35

We have constructed a YAC contig containing 54 clones and aminimum of 7 Mbp of human DNA, that maps to bands q34–35on chromosome 5. The contig was nucleated using FISH mappedcosmid clones shown to flank the t(2; 5)(p23;q35) translocationbreakpoint in a CD30–positive large cell lymphoma cellline. Thirty of the 54 YAC clones are non-chimeric and six spanthe translocation breakpoint, as determined by FISH analysis.A total of 28 YAC clone end fragments, 14 non-polymorphic YACend STS probes and 13 polymorphic microsatellite STS markershave been used to order clones within the contig. The most distalgenetic markers (D5S498 and D5S619) are separated by 15 cM basedon multipoint linkage analysis. This map of overlapping clonesand the set of densely spaced physical markers will promoteour understanding of the 5q34–35 reglon and its associatedgenes.     

Mapping the Von Hippel -- Lindau disease tumour suppressor gene: identification of germline deletions by pulsed field gel electrophoresis

Von Hlppel—Lindau (VHL) disease is a dominantly Inheritedfamillal cancer syndrome In which affected individuals havea greatly increased predisposition to the development of haemangloblastomasof the central nervous system and retina, renal cell carcinomaand phaeochromocytoma. The VHL gene has been mapped to chromosome3p25 -p26 by genetic linkage studies and we have previouslydemonstrated that the VHL gene is tightly linked to the D3S601locus (Zmax = 18.86 at     

Relationship between Charcot - Marie-Tooth 1A and Smith - Magenis regions. snU3 may be a candidate gene for the Smith - Magenis syndrome

The juxtacentromeric region of the human chromosome 17 shortarm (17p11.2-p12) contains genes Involved in the Charcot - Marie- Tooth type 1A disease (CMT1A) and the Smith-Magenis syndrome(SMS). CMT1A Is associated with a duplication of a short segmentwhereas SMS is linked to microdeletions, extending toward thecentromere. We describe the construction and analysis of a 5Mb YAC contig spanning the CMT1A duplicated segment and thedistal part of four SMS microdeletions. We concluded that theYAC contig contains about 1Mb of genomic DNA which is deletedin the four SMS patients analysed. Moreover two YACs containboth STS deleted in SMS (U3) and STS duplicated in CMT1A (5H5),but the proximal breakpoint associated with the CMT1A duplicationis not the same as the distal SMS breakpoint we studied. Finallywe located five new STS In SMS deletion. Two of them, a microsatellite(D17S805(23)) and the gene coding for small nuclear RNA U3,have been localized In the contig we described. We may alsonote that snU3 Is the first expressed sequence localized Inan SMS deletion so far. The possible participation of this genein the SMS phenotype is discussed.     

Genetic and physical characterization of the early-onset Alzheimer's disease AD3 locus on chromosome 14q24.3

Genetic linkage studies have provided significant evidence thata major gene defect, AD3, for familial early-onset Alzheimer'sdisease (EOAD) is located at chromosome 14q24.3, between theshort tandem repeat (STR) markers D14S52 and D14S53 defininga genetic size of 22.7 cM for the AD3 candidate region. We constructeda physical map of the AD3 region using yeast artificial chromosomes(YACs) selected from both the CEPH and megaCEPH YAC librariesusing the AD3 linked STR markers as well as new sequence-taggedsites (STSs) designed based on YAC terminal sequences. The YACmap is contiguous in the region between D14S258 and D14S53,a region of 8.2 cM, and has an estimated physical size of 4–8Mb. The YAC contig map was used as a framework to localize threeknown genes, a pseudogene and two brain expressed sequence tags(ESTs). Linkage analysis studies in two Belgian chromosome 14EOAD families AD/A and AD/B, identified obligate recombinantsin family AD/A with D14S289 and D14S61 reducing the geneticsize of the candidate AD3 region substantially. The minimalAD3 candidate region measured 6.4 cM on the genetic map andis contained within six overlapping megaCEPH YACs that covereda physical distance estimated between 2 and 6 Mb. These YACsas well as other YACs in the YAC contig map are valuable resourcesin gene cloning efforts or genomic sequencing experiments aimingat isolating the AD3 gene.     

High-resolution physical and transcript map of human chromosome 2p21 containing the sitosterolaemia locus

Sitosterolaemia (phytosterolaemia) is an autosomal recessive disorder characterised by the presence of tendon xanthomas in the face of normal or mildly elevated plasma cholesterol levels, premature atherosclerotic disease and has diagnostically elevated plasma and tissue plant sterol concentrations. Affected individuals show an increased absorption of both cholesterol and sitosterol from the diet, decreased bile clearance of these sterols and their metabolites resulting in markedly expanded whole body cholesterol and sitosterol pools. The defective gene is therefore hypothesised to play a crucial role in regulating dietary cholesterol absorption, and its elucidation may shed light on these molecular processes. We have previously localised the defective gene to human chromosome 2p21, between microsatellite markers D2S1788 and D2S1352, a distance of approximately 15 cM. Recently, the disease locus interval has been narrowed to lie between D2S2294 and D2S2291/D2S2174. We have constructed a high-resolution YAC and BAC contigs by using known STSs and generating novel STSs from the minimal interval. Eight previously identified genes and 60 ESTs were mapped to these contigs. The BAC contig contains 60 BAC clones and 108 STSs and encompasses a physical distance of approximately 2.0 cM between microsatellite markers D2S2294 and D2S2291. These results will not only facilitate cloning of the sitosterolaemia gene, but also other disease genes located in this region, and accelerate sequencing of the corresponding genomic clones.     

A 3-Mb High-Resolution BAC/PAC Contig of 12q22 Encompassing the 830-kb Consensus Minimal Deletion in Male Germ Cell Tumors

Cytogenetic and molecular genetic analyses have shown that the 12q22 region is recurrently deleted in male germ cell tumors (GCTs), suggesting that this site may harbor a tumor suppressor gene (TSG). Previous loss of heterozygosity (LOH) analyses identified a consensus minimal deleted region between the markers D12S377 and D12S296, and a YAC clone contig covering the region was generated. Here, we describe a high-resolution sequence-ready physical map of this contig covering a 3-Mb region. The map comprised of 52 cosmids, 49 PACs, and 168 BACs that were anchored to the previous YAC contig; 99 polymorphic, nonpolymorphic, EST, and gene-based markers are now placed on this map in a unique order. Of these, 61 markers were isolated in the present study, including one that was polymorphic. In addition, we have narrowed the minimal deletion to approximately 830 kb between D12S1716 (proximal) and P382A8-AG (distal) by LOH analysis of 108 normal-tumor DNAs from GCT patients using 21 polymorphic STSs. These physical and deletion maps should prove useful for identification of the candidate TSG in GCTs, provide framework to generate complete DNA sequence, and ultimately generate a gene map of this segment of the chromosome 12. [The sequence data described in this paper have been submitted to the Genome Survey Sequence under accession nos. AQ254896-AQ254955 and AQ269251-AQ269266. Online supplementary material is available at http://www.genome.org]     

Refinement of the RP17 locus for autosomal dominant retinitis pigmentosa, construction of a YAC contig and investigation of the candidate gene retinal fascin

The RP17 locus for autosomal dominant retinitis pigmentosa has previously been mapped to chromosome 17q by linkage analysis. Two unrelated South African families are linked to this locus and the identification of key recombination events assigned the RP17 locus to a 10 cM interval on 17q22. The work reported here refines the mapping of the locus from a 10 cM to a 1 cM interval between the microsatellite markers D17S1604 and D17S948. A physical map of this interval was constructed using information from the Whitehead/MIT YAC contig WC 17.8. Sequence-tagged site (STS) content mapping of seven overlapping YACs from this contig was employed in order to build the map. A BAC library was screened to cover a gap in the YAC contig and two positive BACs were identified. Intragenic polymorphisms in the retinal fascin gene provided evidence for the exclusion of this candidate as the RP17 disease gene.     

Detailed analysis of loss of heterozygosity on chromosome band 17p13 in breast carcinoma on the basis of a high-resolution physical map with 29 markers

We have constructed a physical map of chromosome band 17p 13, using 29 markers that had been localized to 17p 13 by means of fluorescence in situ hybridization (FISH) and analysis by pulsed-field gel electrophoresis (PFGE). The map spans nearly 8 Mb of genomic DNA, and the estimated average distance between each marker is roughly 290 kb. The p 13 band of chromosome 17 is thought to contain a putative tumor suppressor gene in addition and distal to TP53. Deletion mapping in a large number of breast carcinomas indicated that the tumor suppressor gene lies between the loci defined by cC117-708 (D17S878) and p144D6 (D17S34), which are an estimated 7 Mb apart. Our results should contribute to construction of a contig map of chromosome band 17p 13 with cosmid and/or YAC (yeast artificial chromosome) clones, and to isolation of the putative tumor suppressor gene. Genes Chrom Cancer 9:173-179 (1994). © 1994 Wiley-Liss, Inc.     

Identification and mapping of novel tumor suppressor loci on 6p in diffuse large B-cell non-Hodgkin's lymphoma.

Allelic deletions have been thought to be indicators of the presence of tumor suppressor genes (TSGs). As indicated by this allelotype study using 39 highly informative microsatellite markers distributed among all autosomal chromosomes, frequent loss of heterozygosity (LOH) has been found at 6p in B-cell non-Hodgkin's lymphoma. To identify the commonly deleted regions (CDRs), we performed fine deletion mapping using 26 highly polymorphic microsatellite markers on 6p. The most frequent LOH occurred at D651721, where 9 of 18 of the informative cases (50%) had allelic losses. Seventeen of 32 cases (53%) exhibited LOH at least at one locus on 6p. Ten of these 17 cases showed interstitial deletions, and their LOH patterns indicated two CDRs on 6p; one between D6S1721 and D6S260 (at 6p23-24), and the other between D6S265 and D6S291 (at 6p21). The genetic distance of both CDRs was 6 cM. The CDKN1A (p21) gene is reported to be located within the interval of the CDR at 6p21, but no mutation of the gene was found in these 32 patients. These data suggested that these two loci might harbor novel putative TSGs responsible for the pathogenesis of malignant lymphoma. We have constructed a contig of yeast artificial chromosome (YAC) clones spanning the most frequent CDR at 6p23-24. This YAC contig can be used for fine physical mapping of the region and cloning of candidate TSGs.     

A YAC-based binning strategy facilitating the rapid assembly of cosmid contigs: 1.6 Mb of overlapping cosmids in Xp22

We have applied a yeast artificial chromosome (YAC)-based cosmidisolation and binning strategy to convert a YAC contig in Xp22into 1.6 Mb of overlapping cosmids. This strategy is based onthe screening of a high-density arrayed X chromosome-specificcosmid library with large YAC-derived restriction fragmentsand entire YAC probes. Cosmids selected in this way were griddedon dot blots and further mapped into bins defined by the overlapintervals of the YACs and YAC fragments. This rapid binningof cosmids simplified the subsequent assembly of cosmid contigsby restriction fingerprint hybridization. In total, we identified139 cosmids spanning the entire 1.6 Mb region with a minimaloverlap set of 53 clones. These cosmids were assigned to 17bins and 9 contigs. One of the contigs is 665 kb in length andis one of the largest uninterrupted cosmid contigs in humansreported to date. The gaps between the contigs are minor and,together, they represent less than 7% of the region covered.Two previously identified genes are contained in these cosmids,the gene for amelogenin (AMG) and the recently isolated putativechloride channel gene CICN4. In addition, two disease loci havebeen mapped to this region: X-linked ocular albinism type 1(OA1) and the microphthalmia with linear skin defects (MLS)syndrome. The assembly of the cosmid maps allowed us to determinethe size of the deletion intervals for these two loci, whichwere estimated to be 110 kb for OA1 and 570 kb for MLS. Thesecosmid contigs will greatly facilitate the positional cloningof the OA1 and MLS disease genes. Together with the Huntingtondisease gene region on chromosome 4, this region in Xp22 representsone of the best characterized large regions in the human genome.