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At least 19 recordsLinked to original sources
PubMed1992

Multipoint analysis for radiation hybrid mapping.

Radiation hybrid mapping is a somatic cell genetic technique that permits construction of fine-structure maps of human chromosomes. Radiation hybrid mapping uses X-ray breakage of chromosomes to order genetic loci and to estimate distances between them. Cox and colleagues described radiation hybrid mapping and derived methods for locus ordering based on two-point statistical analysis of radiation hybrid mapping data. In this paper, I describe alternative non-parametric and likelihood methods for radiation hybrid mapping that make use of information on many loci simultaneously, and efficiently include information on partially typed radiation hybrids. Locus orders are selected by minimum number of obligate chromosome breaks or maximum likelihood. I demonstrate the utility of these methods with an application to data on 14 markers and 99 hybrids for human chromosome 21.

Chromosome Aberrations↗
PubMed1995

Statistical methods for polyploid radiation hybrid mapping.

Radiation hybrid mapping is a somatic cell technique for ordering genetic loci along a chromosome and estimating physical distances between adjacent loci. This paper presents a model of fragment generation and retention for data involving two or more copies of the chromosome of interest per clone. Such polyploid data can be generated by initially irradiating normal diploid cells or by pooling haploid or diploid clones. The current model assumes that fragments are generated in the ancestral cell of a clone according to an independent Poisson breakage process along each chromosome. Once generated, fragments are independently retained in the clone with a common retention probability. On the basis of this and less restrictive retention models, statistical criteria such as minimum obligate breaks, maximum likelihood ratios, and Bayesian posterior probabilities can be used to decide locus order. Distances can be estimated by maximum likelihood. Likelihood computation is particularly challenging, and computing techniques from the theory of hidden Markov chains prove crucial. Within this context it is possible to incorporate typing errors. The statistical tools discussed here are applied to 14 loci on the short arm of human chromosome 4.

Chromosome Mapping↗
PubMedDate not supplied

Comparison of MultiMap and TSP/CONCORDE for constructing radiation hybrid maps.

Radiation hybrid (RH) map construction allows investigators to locate both type I and type II markers on a given genome map. The process is composed of two steps. The first consists of determining the pattern distribution of a set of markers within the different cell lines of an RH panel. This is mainly done by polymerase chain reaction (PCR) amplification and gel electrophoresis, and results in a series of numbers indicating the presence or the absence of each marker in each cell line. The second step consists of a comparison of these numbers, using various algorithms, to group and then order markers. Because different algorithms may provide (slightly) different orders, we have compared the merits of the MultiMap and TSP/CONCORDE packages using a data set of information currently under analysis for construction of the canine genome RH map.

Animals↗
PubMed1999

Point and interval estimates of marker location in radiation hybrid mapping.

Radiation hybrid (RH) mapping is a powerful method for ordering loci on chromosomes and for estimating the distances between them. RH mapping is currently used to construct both framework maps, in which all markers are ordered with high confidence (e.g., 1,000:1 relative maximum likelihood), and comprehensive maps, which include markers with less-confident placement. To deal with uncertainty in the order and location of markers, marker positions may be estimated conditional on the most likely marker order, plausible intervals for nonframework markers may be indicated on a framework map, or bins of markers may be constructed. We propose a statistical method for estimating marker position that combines information from all plausible marker orders, gives a measure of uncertainty in location for each marker, and provides an alternative to the current practice of binning. Assuming that the prior distribution for the retention probabilities is uniform and that the marker loci are distributed independently and uniformly on an interval of specified length, we calculate the posterior distribution of marker position for each marker. The median or mean of this distribution provides a point estimate of marker location. An interval estimate of marker location may be constructed either by using the 100(alpha/2) and 100(1-alpha)/2 percentiles of the distribution to form a 100(1-alpha) % posterior credible interval or by calculating the shortest 100(1-alpha) % posterior credible interval. These point and interval estimates take into account ordering uncertainty and do not depend on the assumption of a particular marker order. We evaluate the performance of the estimates on the basis of results from simulated data and illustrate the method with two examples.

Bayes Theorem↗
PubMed1997

On constructing radiation hybrid maps.

Radiation hybrid (RH) mapping is a somatic cell method for obtaining ordering information of markers on a chromosome, using relatively few experiments. Given the results of a typical RH experiment, finding the true order of the markers is a challenging algorithmic problem. In this work we present several simple algorithms for ordering and mapping the markers, where the input is the genomic data obtained from RH experiments. We provide a rigorous analysis of these algorithms. In particular, we show that under the standard statistical model for RH, our algorithms are "statistically consistent." That is, given enough hybrids, the algorithms do reconstruct the true markers' order (with high probability). We also prove a simple lower bound for the number of hybrids required (by any algorithm) to correctly reconstruct the order. We have implemented these algorithms, and tested them on synthetic and real data. These simulations show that for practical input sizes (number of markers and hybrids) our algorithms produce outputs that are very close to the true ordering. The simulations also indicate that the true ordering of the markers is usually not the one which minimizes the number of obligate chromosome breaks.

Algorithms↗
PubMed1997

Estimating physical distances from radiation hybrid mapping data.

Radiation hybrid mapping has become an established tool for building physical maps. It represents a powerful way of constructing YAC contigs and high-resolution maps for positional cloning experiments. Ideally, radiation hybrids should not only provide support for the true order of the markers, but also accurate estimates of the physical distances between them. Statistical analysis of radiation hybrids has proved difficult because of the number of parameters (representing the fragment retention probabilities) that must be estimated, and simplifying assumptions are needed to analyze large numbers of markers simultaneously. The ramifications of these assumptions for the calculation of physical distances are investigated. A simple two-locus model is presented to demonstrate that variation in marker retention can lead to distortions in the estimates of distance. Multilocus simulations show that, when marker retention is constant across the chromosome, good estimates of physical distance can be derived using simple models of retention. However, further simulations exploring variable retention schemes demonstrate that significant errors in the estimates of map distances can occur. Ways of minimizing these distortions are discussed.

Chromosome Mapping↗
PubMed2002

Conservation of gene order between horse and human X chromosomes as evidenced through radiation hybrid mapping.

A radiation hybrid (RH) map of the equine X chromosome (ECAX) was obtained using the recently produced 5000(rad) horse x hamster hybrid panel. The map comprises 34 markers (16 genes and 18 microsatellites) and spans a total of 676 cR(5000), covering almost the entire length of ECAX. Cytogenetic alignment of the RH map was improved by fluorescent in situ hybridization mapping of six of the markers. The map integrates and refines the currently available genetic linkage, syntenic, and cytogenetic maps, and adds new loci. Comparison of the physical location of the 16 genes mapped in this study with the human genome reveals similarity in the order of the genes along the entire length of the two X chromosomes. This degree of gene order conservation across evolutionarily distantly related species has up to now been reported only between human and cat. The ECAX RH map provides a framework for the generation of a high-density map for this chromosome. The map will serve as an important tool for positional cloning of X-linked diseases/conditions in the horse.

Animals↗
PubMed1999

Extensive conservation of sex chromosome organization between cat and human revealed by parallel radiation hybrid mapping.

A radiation hybrid (RH)-derived physical map of 25 markers on the feline X chromosome (including 19 Type I coding loci and 6 Type II microsatellite markers) was compared to homologous marker order on the human and mouse X chromosome maps. Complete conservation of synteny and marker order was observed between feline and human X chromosomes, whereas the same markers identified a minimum of seven rearranged syntenic segments between mouse and cat/human X chromosome marker order. Within the blocks, the feline, human, and mouse marker order was strongly conserved. Similarly, Y chromosome locus order was remarkably conserved between cat and human Y chromosomes, with only one marker (SMCY) position rearranged between the species. Tight linkage and a conserved gene order for a segment encoding three genes, DFFRY-DBY-UTY in human, mouse, and cat Y chromosomes, coupled with demonstrated deletion effects of these genes on reproductive impairment in both human and mouse, implicates the region as critical for Y-mediated sperm production.

Animals↗
PubMed1997

Markov chain Monte Carlo methods for radiation hybrid mapping.

The ordering of genetic loci is central to genetic mapping at all levels. Markov chain Monte Carlo (MCMC) techniques can provide estimates of the posterior density of orders while accounting naturally for missing data, data errors, and unknown parameters. MCMC sampling schemes have been proposed for mapping problems such as linkage mapping and radiation hybrid mapping. The sampling schemes tend, however, to suffer from poor mixing caused by strong correlations between the model parameters. The method described here investigates the effect of using a modified sampling scheme, simulated tempering, on the mixing characteristics of the Markov chain. The method is illustrated by the analysis of haploid radiation hybrid mapping data; the principles are, however, applicable to a range of mapping problems. The results demonstrate that simulated tempering greatly improves the performance of the MCMC sampling scheme. For the radiation hybrid problem, the approach is probably not suitable for simultaneously ordering very large number of loci (> 100); it could, however, be useful for fine scale mapping of subsections of chromosomes.

Algorithms↗
PubMed2000

Human Na+/H+ exchanger genes : identification of polymorphisms by radiation hybrid mapping and analysis of linkage in end-stage renal disease.

The Na+/H+ exchangers (NHEs) are membrane-bound transporters that catalyze the electro-neutral movement of extracellular Na+ for intracellular H+. NHE genes play a critical role in pH homeostasis and cellular volume regulation and can be considered candidate genes for essential hypertension and renal disease. This study was performed to determine whether the NHE genes contributed to genetic susceptibility in end-stage renal disease (ESRD). To date, 5 isoforms of NHE have been cloned in mammals (NHE1 to NHE5). The complementary DNA (cDNA) sequences of NHE1 to NHE3 and NHE5 are known in humans. Because the chromosomal structure of the NHE genes is unknown, we used cDNA sequences to design polymerase chain reaction primers for use in radiation hybrid mapping. Radiation hybrid mapping of NHE genes identified nearby polymorphic markers for NHE1 to NHE3 (NHE1: D1S197, D1S2677; NHE2: D2S373, D2S1789; and NHE3: D5S678, D5S2005). We used these markers, and other previously identified polymorphic markers for NHE5, in linkage and association analyses of ESRD. The NHE1 to NHE3 and NHE5 loci did not demonstrate evidence for linkage to ESRD. However, NHE5 showed significant evidence for association (P</=1.0x10(-4)). The strongest evidence for association was observed with allele 6 of NHE5 (P</=0.001 to 0. 01). Allele 6 appeared to have a renoprotective effect, with a frequency of 0.15 in the control population and 0.06 to 0.09 in patients with ESRD. The combined approach of designing primers from cDNA and radiation hybrid mapping has proven successful in identifying polymorphisms for human genes of which only cDNA sequences were previously available. The NHE primers and associated polymorphic loci identified in this study can be used in genomic, linkage, and association analysis of NHE genes in future genetic studies of hypertension and renal failure. Given the allelic association, further evaluation of the role of NHE5 in ESRD susceptibility appears warranted.

Alleles↗
PubMed1999

Cytogenetic and radiation hybrid mapping of human arachidonate 5-lipoxygenase-activating protein (ALOX5AP) to chromosome 13q12.

Arachidonate 5-lipoxygenase-activating protein (ALOX5AP) is an arachidonic acid binding protein that has been shown to be critical in the biosynthesis of leukotrienes. We mapped the ALOX5AP gene to the chromosome 13q12 region by cytogenetic mapping, yeast artificial chromosome (YAC) pool screening, and radiation hybrid mapping. It was mapped to YAC contig WC13.2 by YAC pool screening with an unambiguous hit to WI-4874, which is at 78 cR on the radiation hybrid map, 3.36 cR, by radiation hybrid mapping, from WI-4874.

5-Lipoxygenase-Activating Proteins↗
PubMed1994

A method for constructing radiation hybrid maps of whole genomes.

In radiation hybrid mapping, chromosomes in human-rodent hybrid cells are fragmented by X-rays and fragments rescued by fusion of the donor cell to a recipient rodent cell. The co-retention frequencies of markers in 100-200 hybrids are used to map individual chromosomes, but mapping the whole genome in this way is impractical. We have reverted to the original protocols of Goss and Harris and have produced a panel of 44 hybrids using irradiated human fibroblasts as donors. This panel has been used to make a map of human chromosome 14 containing 40 ordered markers. The map integrates previously published maps and localizes nine new markers. We suggest that the construction of a high resolution map of the whole human genome is feasible with a single panel of 100-200 hybrids.

Animals↗
PubMed2002

The functional significance of absence: the chromosomal segment harboring Tp53 is absent from the T55 rat radiation hybrid mapping panel.

The T55 rat radiation hybrid (RH) mapping panel has been reported to retain the entire rat genome at retention frequencies between 22% and 37%. However, we found that a small segment of rat chromosome 10 harboring at least four different genes, including Tp53, was completely absent from the panel (retention frequency = 0%). Two other markers located in the vicinity exhibited much reduced retention (2-6%). RH clones are generated by transferring highly fragmented DNA into a recipient cell. There might be a strong selection against the transfer and retention of chromosome segments harboring an intact Tp53, as the action of this gene might prevent proliferation and establishment of the RH clone. Our finding further suggests that unexpected low retention or absence of chromosome segments in an RH panel may represent indications that the segments harbor genes with important functions in cell proliferation control.

Animals↗
PubMed2004

Radiation hybrid mapping of the species cytoplasm-specific (scsae) gene in wheat.

Radiation hybrid (RH) mapping is based on radiation-induced chromosome breakage and analysis of chromosome segment retention or loss using molecular markers. In durum wheat (Triticum turgidum L., AABB), an alloplasmic durum line [(lo) durum] has been identified with chromosome 1D of T. aestivum L. (AABBDD) carrying the species cytoplasm-specific (scsae) gene. The chromosome 1D of this line segregates as a whole without recombination, precluding the use of conventional genome mapping. A radiation hybrid mapping population was developed from a hemizygous (lo) scsae--line using 35 krad gamma rays. The analysis of 87 individuals of this population with 39 molecular markers mapped on chromosome 1D revealed 88 radiation-induced breaks in this chromosome. This number of chromosome 1D breaks is eight times higher than the number of previously identified breaks and should result in a 10-fold increase in mapping resolution compared to what was previously possible. The analysis of molecular marker retention in our radiation hybrid mapping panel allowed the localization of scsae and 8 linked markers on the long arm of chromosome 1D. This constitutes the first report of using RH mapping to localize a gene in wheat and illustrates that this approach is feasible in a species with a large complex genome.

Chromosomes, Plant↗
PubMed1999

A radiation hybrid map of bovine chromosome one.

Radiation hybrid (RH) mapping has proven to be an extremely powerful approach to constructing high density maps of human chromosomes and is experiencing increased use in other animals, including cattle. A 5000 rad bovine whole-genome radiation hybrid panel was recently constructed in order to integrate existing cattle linkage maps with evolutionarily conserved genes and provide high resolution comparative maps relative to humans and mice. We utilized this panel to construct a 19 marker framework map of bovine chromosome 1 (BTA1), which included 8 Type I loci and 11 Type II loci ordered with at least 1000:1 odds. A 35 marker comprehensive map including 15 Type I loci and 20 Type II loci was also produced. Of the 15 Type I loci ordered on the comprehensive map, three are ordered on HSA3 and five are ordered in three blocks on HSA21 on the human cytogenetic maps.

Animals↗
PubMed2000

Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping.

A whole genome cattle-hamster radiation hybrid cell panel was used to construct a map of 54 markers located on bovine chromosome 5 (BTA5). Of the 54 markers, 34 are microsatellites selected from the cattle linkage map and 20 are genes. Among the 20 mapped genes, 10 are new assignments that were made by using the comparative mapping by annotation and sequence similarity strategy. A LOD-3 radiation hybrid framework map consisting of 21 markers was constructed. The relatively low retention frequency of markers on this chromosome (19%) prevented unambiguous ordering of the other 33 markers. The length of the map is 398.7 cR, corresponding to a ratio of approximately 2.8 cR(5,000)/cM. Type I genes were binned for comparison of gene order among cattle, humans, and mice. Multiple internal rearrangements within conserved syntenic groups were apparent upon comparison of gene order on BTA5 and HSA12 and HSA22. A similarly high number of rearrangements were observed between BTA5 and MMU6, MMU10, and MMU15. The detailed comparative map of BTA5 should facilitate identification of genes affecting economically important traits that have been mapped to this chromosome and should contribute to our understanding of mammalian chromosome evolution.

Animals↗
PubMed1994

High-resolution physical mapping of human 5q31-q33 using three methods: radiation hybrid mapping, interphase fluorescence in situ hybridization, and pulsed-field gel electrophoresis.

Three physical mapping methods, radiation hybrid (RH) mapping, pulsed-field gel electrophoresis (PFGE), and fluorescence in situ hybridization (FISH) of interphase nuclei, were used to determine the order and relative distances between 12 loci in the q31-q33 region of human chromosome 5. The information obtained by each of the methods was compared to determine whether they gave consistent results. Based upon a combination of data, the predicted order of the 12 loci is cen-ADRB2-PDEA-CSF1R-RPS14-ANX6-SPARC++ +-GLRA1-GLUR1-ADRA1B-IL12- GABRG2-GABRA1-tel. Over the 5-Mb region spanned by these loci, we determined that an RH mapping unit (centiray, cR6500) is equivalent to 21 kb, in good agreement with previous estimates of 27-34 kb/cR6500 using the same set of radiation hybrids to map other regions. Of the three methods, RH mapping was by far the easiest and most efficient method for determining both order and distances. In addition, the range of resolution of RH mapping was the broadest, ranging from approximately 200 kb to several megabasepairs. Interphase FISH was the most informative method for clarifying the order of closely linked markers. The FISH distances obtained in this study will be useful as an internal reference for high-resolution mapping studies of other regions on the long arm of human chromosome 5. In contrast to RH mapping and FISH, PFGE was the least reliable of the three methods, producing some data that were inconsistent with the distances determined by the other two methods.

Chromosome Mapping↗
PubMed1992

A radiation hybrid map of the proximal short arm of the human X chromosome spanning incontinentia pigmenti 1 (IP1) translocation breakpoints.

Radiation hybrid mapping was used in combination with physical mapping techniques to order and estimate distances between 14 loci in the proximal region of the short arm of the human X chromosome. A panel of radiation hybrids containing human X-chromosomal fragments was generated from a Chinese hamster-human cell hybrid containing an X chromosome as its only human DNA. Sixty-seven radiation hybrids were screened by Southern hybridization with sets of probes that mapped to the region Xp11.4-Xcen to generate a radiation hybrid map of the area. A physical map of 14 loci was constructed based on the segregation of the loci in the hybrid clones. Using pulsed-field gel electrophoresis (PFGE) analyses and a somatic cell hybrid mapping panel containing naturally occurring X; autosome translocations, the order of the 14 loci was verified and the loci nearest to the X-chromosomal translocation breakpoints associated with the disease incontinentia pigmenti 1 (IP1) were identified. The radiation hybrid panel will be useful as a mapping resource for determining the location, order, and distances between other genes and polymorphic loci in this region as well as for generating additional region-specific DNA markers.

Animals↗