A sequence-based integrated map of chromosome 22.

The near-completion of the sequence for chromosome 22q revolutionizes map integration. We describe a sequence-based integrated map containing 968 loci including 516 known or predicted gene sequences, 317 STSs not included in these sequences, and 135 nonexpressed multinucleotide polymorphisms. The published sequence spans 34.6 Mb, inclusive of gaps estimated to total 1.1 Mb, compared with a top-down estimate of 43 Mb. This discrepancy is discussed, but will not be resolved until more of the genome is analyzed. The radiation hybrid map has 5% error in order and 34% error in location exceeding 1 Mb. The utility of a composite location based on evidence other than sequence is limited to regions not yet sequenced. A genetic map conditional on sequence order was constructed from pairwise lods. Its length of 74.8 cM in males and 80.2 cM in females is slightly less than the previous estimate not constrained by sequence order. Five recombination hot spots are detected, with differences in location between the sexes. Male recombination correlates with repetitive DNA, whereas female recombination does not. It remains to be seen whether this is true for other human chromosomes. An algorithm to improve the fit of cytogenetic bands sequence location reduces the discrepancies in cytogenetic assignment from 61 to 38. This sequence-based integrated map is represented in the genetic location database (LDB2000), which is available at http://cedar.genetics.soton.ac.uk/public_html/LDB2000.html.     

A microsatellite-based index map of human chromosome 11

We have constructed a continuous Index map of 25 micosatellitemarkers on human chromosome 11. The markers have been typedin 40 CEPH families, have heterozygositles of 69% or higherand can be typed by PCR. The odds against inversion of adjacentmarker loci order are at least 10⁵: 1. The sex average map coversa total of 162 cM with no gap exceeding 15 cM. Total lengthsfor female and male maps are 205 and 123 cM, respectively. Byuse of a hybrid cell panel or by in situ hybridization, 16 ofthe markers have also been mapped cytogenetically, providinga good correlation of the Index map with the cytogenetic map.The map will facilltate high resolution mapping of additionalpolymorphic loci and of disease genes on chromosome 11.     

An integrated map of chromosome 9

An integrated map of 211 loci on chromosome 9 is presented for which 198 loci have genetic locations. The results of the analysis indicate very strong interference for the chromosome and positional variations in recombination rates, most extreme in the male map where there is an excess of recombination near the p telomere and a marked suppression of recombination in a large region that includes the centromere.     

A high resolution physical map of 2.5 Mbp of the Down syndrome region on chromosome 21

The region surrounding D21S55 in band 21q22 of human chromosome21 has been implicated in the etiology of Down syndrome (DS).In this paper, we report the construction of a high resolutionmap of a 2.5 Mb region around the marker D21S55. Characterizationof YAC clones by accurate size determination, end isolationand marker assignment was used to build a refined YAC-basedmap. The YAC clones were then used to isolate 284 cosmid clones,covering 2.3 Mb, from a chromosome 21-specific cosmid library.The cosmid clones were ordered into overlapping groups and arestriction map of each group was determined. The groups ofcosmids were then ordered and oriented with respect to the YAC-basedmap. This high resolution map provides the framework for furtheranalysis of the region by transcribed sequence mapping and sequencedetermination.     

An integrated map of chromosome 18 CAG trinucleotide repeat loci

Expansions of trinucleotide CAG repeats have been demonstrated in at least eight neurodegenerative disorders, and suggested to occur in several others, including bipolar disorder and schizophrenia. Chromosome 18 loci have been implicated in bipolar disorder pedigrees by linkage analysis. To address this putative link between chromosome 18 CAG trinucleotide repeats and neuropsychiatric illness, we have screened a chromosome 18 cosmid library (LL18NCO2" AD") and identified 14 novel candidate loci. Characterisation of these loci involved repeat flank sequencing, estimation of polymorphism frequency and mapping using FISH as well as radiation hybrid panels. These mapped trinucleotide loci will be useful in the investigation of chromosome 18 in neurodegenerative or psychiatric conditions, and will serve to integrate physical and radiation hybrid maps of chromosome 18.     

A familial pericentric inversion of chromosome 8 analysed with a high resolution chromosome banding technique

A familial pericentric inversion of chromosome 8 is described. The break points were localized by a high resolution chromosome banding technique and found to be inv(8)(p23.108q12.100). None of the family members had an unbalanced product of the inversion. There were no phenotypical abnormalities in the carriers. The break points and segregation pattern are compared with those of previously reported pericentric inversions of chromosome 8.     

A revised map of chromosome 1

The genetic map of chromosome 1 reported by Keats, Morton & Rao (1981) has been updated using recent recombination data and regional assignments from the Galton Laboratory (King, 1982 a ) and from the current literature. A maximum likelihood mapping technique using pairwise recombination data without a chiasma map was developed, based on the principles of Rao et al . (1979) and Keats et al . (1981). The development of this new method was found to be necessary when inconsistencies were encountered using a method which combines recombination data and physical data through the chiasma map. These inconsistencies could be due to appreciable chiasma movement, incorrect physical assignments or technical and biological variation in lod scores.     

An integrated physical map for the short arm of human chromosome 5

The short arm of human chromosome 5 contains approximately 48 Mb of DNA and comprises 1.5% of the genome. We have constructed a mega-YAC/ STS map of this region that includes 436 YACs anchored by 216 STSs. By combining and integrating our map with the 5p maps of other groups using the same recombinant DNA library, a comprehensive map was constructed that includes 552 YACs and 504 markers. The YAC map covers >94% of 5p in four YAC contigs, bridges the centromere, and includes an additional 5 Mb of 5q DNA. The average marker density is 95 kb. This integrated 5p map will serve as a resource for the continuing localization of genes on the short arm of human chromosome 5 and as a framework for both generating and aligning the DNA sequence of this region.     

High resolution of a small pericentric inversion of chromosome 11.

A pericentric inversion 11 (p11q13.3) segragating in two generations is described. A high degree of resolution of the inversion was achieved by using prophase and prometaphase chromosomes from methotrexate-synchronised cells. The inversion occurred in a mother and three of her ten children. It had no detectable clinical consequences.     

A fine-structure deletion map of human chromosome 11p: Analysis of J1 series hybrids

Deletion analysis offers a powerful alternative to linkage and karyotypic approaches for human chromosome mapping. A panel of deletion hybrids has been derived by mutagenizing J1, a hamster cell line that stably retains chromosome 11 as its only human DNA, and selecting for loss of MIC1,a surface antigen encoded by a gene in band 11p13. A unique, self-consistent map was constructed by analyzing the pattern of marker segregation in 22 derivative cells lines; these carry overlapping deletions of 11p13, but selectively retain a segment near the 11p telomere. The map orders 35 breakpoints and 36 genetic markers, including 3 antigens, 2 isozymes, 12 cloned genes, and 19 anonymous DNA probes. The deletions span the entire short arm, dividing it into more than 20 segments and define a set of reagents that can be used to rapidly locate any newly identified marker on 11p, with greatest resolution in the region surrounding MIC1.The approach we demonstrate can be applied to map any mammalian chromosome. To test the gene order, we examined somatic cell hybrids from five patients, whose reciprocal translocations bisect band 11p13; these include two translocations associated with familial aniridia and two with acute T-cell leukemia. In each patient, the markers segregate in telomeric and centromeric groups as predicted by the deletion map. These data locate the aniridia gene (AN2)and a recurrent T-cell leukemia breakpoint (TCL2)in the marker sequence, on opposite sides of MIC1.To provide additional support, we have characterized the dosage of DNA markers in a patient with Beckwith-Wiedemann syndrome and an 11p15-11pter duplication. Our findings suggest the following gene order: TEL-(HRAS1, MER2, CTSD, TH/INS/IGF2, H19, D11S32)-(RRM1, D11S1, D11S25, D11S26)-D11S12-(HBBC, D11S30)-D11S20-(PTH, CALC)-(LDHA, SAA, TRPH, D11S18, D11S21)-D11S31-D11S17-HBVS1-(FSHB, D11S16)-AN2-MIC1-TCL2-J-CAT-MIC4-D11S9-D11S14-ACP2-(D11S33, 14L)-CEN.We have used the deletion map to show the distribution on 11p of two centromeric repetitive elements and the low-order interspersed repeat A36Fc.Finally, we provide evidence for an allelic segregation event in the hamster genome that underlies the stability of chromosome 11 in J1. The deletion map provides a basis to position hereditary disease loci on 11p, to distinguish the pattern of recessive mutations in different forms of cancer and, since many of these genes have been mapped in other mammalian species, to study the evolution of a conserved syntenic group.Deceased.     

Combined high resolution linkage and association mapping of quantitative trait loci

In this paper, we investigate variance component models of both linkage analysis and high resolution linkage disequilibrium (LD) mapping for quantitative trait loci (QTL). The models are based on both family pedigree and population data. We consider likelihoods which utilize flanking marker information, and carry out an analysis of model building and parameter estimations. The likelihoods jointly include recombination fractions, LD coefficients, the average allele substitution effect and allele dominant effect as parameters. Hence, the model simultaneously takes care of the linkage, LD or association and the effects of the putative trait locus. The models clearly demonstrate that linkage analysis and LD mapping are complementary, not exclusive, methods for QTL mapping. By power calculations and comparisons, we show the advantages of the proposed method: (1) population data can provide information for LD mapping, and family pedigree data can provide information for both linkage analysis and LD mapping; (2) using family pedigree data and a sparse marker map, one may investigate the prior suggestive linkage between trait locus and markers to obtain low resolution of the trait loci, because linkage analysis can locate a broad candidate region; (3) with the prior knowledge of suggestive linkage from linkage analysis, both population and family pedigree data can be used simultaneously in high resolution LD mapping based on a dense marker map, since LD mapping can increase the resolution for candidate regions; (4) models of high resolution LD mappings using two flanking markers have higher power than that of models of using only one marker in the analysis; (5) excluding the dominant variance from the analysis when it does exist would lose power; (6) by performing linkage interval mappings, one may get higher power than by using only one marker in the analysis.     

A linkage map of human chromosome 15 with an average resolution of 2 cM and containing 55 polymorphic microsatellites

We have constructed a 2.0 centiMorgan (cM) resolution geneticlinkage map for chromosome 15q that contains 55 polymorphicsatellites and 3 RFLPs that have placed on the map with oddsfor order of at least 1,000: 1. Genotypes from 67 polymorphicloci (64 polymorphic microsatellites) were used to constructthe map. Nine genes are Included in the 1,000: 1 map and 37markers have heterozygoslties of at least 70%. The sex-equalmap length is 128 cM and the largest genetic interval is 11cM (15.5 cM on the female map). The female and male map lengthsare 150 cM and 106 cM, respectively. The map was constructedwith ‘MultiMap’ and is based on the CEPH referencepedigrees and includes over 12, 000 new genotypes. A sub-setof 12 markers spanning the length of the linkage map were genotypedin a somatic cell hybrid panel with breakpoints that divided15q into five segments. Cytogenetic placement agreed with thelinkage positions for each of the microsatellites tested withthe exception of one (ACTC) which failed to give consistentresults. Ten spontaneous new mutations were identified froma subset of 42 polymorphic microsatellites (out of a total of20, 420 transmissions), giving an apparent observed spontaneousmutation rate of 5 x 10–4 per locus. An integrated mapof chromosome 15q was also constructed with the microsatellitemarkers described here and previously genotyped RFLP-based markers.The sex average map spans 144.7 cM with an average distancebetween unique map locations of 3.5 cM and a maximum intermarkerdistance of 11.5 cM. These genetic linkage maps can be consideredbaseline maps for 15q which will be useful for physical mappingand the localization of disease genes and other genes of interest.     

A 7.5 Mb sequence-ready PAC contig and gene expression map of human chromosome 11p13-p14.1

The region p13 of the short arm of human chromosome 11 has been studied intensely during the search for genes involved in the etiology of the Wilms' tumor, aniridia, genitourinary abnormalities, mental retardation (WAGR) syndrome, and related conditions. The gene map for this region is far from being complete, however, strengthening the need for additional gene identification efforts. We describe the extension of an existing contig map with P1-derived artificial chromosomes (PACs) to cover 7.5 Mb of 11p13-14.1. The extended sequence-ready contig was established by end probe walking and fingerprinting and consists of 201 PAC clones. Utilizing bins defined by overlapping PACs, we generated a detailed gene map containing 20 genes as well as 22 anonymous ESTs which have been identified by searching the RH databases. RH maps and our established gene map show global correlation, but the limits of resolution of the current RH panels are evident at this scale. Initial expression studies on the novel genes have been performed by Northern blot analyses. To extend these expression profiles, corresponding mouse cDNA clones were identified by database search and employed for Northern blot analyses and RNA in situ hybridizations to mouse embryo sections. Genomic sequencing of clones along a minimal tiling path through the contig is currently under way and will facilitate these expression studies by in silico gene identification approaches.     

Localization of the EPM1 gene for progressive myoclonus epilepsy on chromosome 21: linkage disequilibrium allows high resolution mapping

The gene for Progressive myoclonus epilepsy of Unverricht- Lundborgtype (EPM1) has previously been mapped by linkage to markerson chromosome 21q22.3. By analyzing crossover events in multiplexdisease families with newly detected markers from the regionwe were able to narrow the localization of EPM1 to an intervalof approximately 7 cM, between locl D21S212 and CD18. To furtherrefine the localization of the EPM1 gene we applied linkagedisequilibrium mapping In 38 Finnish families, consisting of12 with multiple affected children and 26 with a single affectedchild. Based on existing knowledge about the structure and historyof the Isolated Finnish population, we estimated genetic distancesbased on strong linkage disequilibrium to several marker lociand found that EPM1 resides within 0.3 cM or less of loci PFKL,D21S25 and D21S154. As this genetic distance translates intoa likely physical distance of 300 kb or less, these data providea basis for highly focused attempts to clone EPM1.     

A panel of partial chromosome paints and YAC probes specific for human chromosome 2

Twenty nine hybrids retaining fragments of human chromosome 2 were characterized by reverse-FISH and by a panel of 106 STSs. Most of the hybrids are radiation hybrids retaining fragments of chromosome 2 as the only human contribution. The hybrid panel dissected chromosome 2 in 69 distinct physical regions, allowing a fine mapping of the sequences. These hybrids are particularly useful as starting points for generation, via Alu-PCR, of specific partial chromosome paints (PCP). We also report the mapping by FISH of 60 YACs located on chromosome 2. These resources can be advantageously used in cytogenetic investigations, with particular reference to cancer cytogentics, as illustrated with the renal carcinoma cell line KRC/Y.