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CHELALA CLAUDE, DEVIGNES MARIEDOMINIQUE, IMBEAUD SANDRINE, ZOOROB RIMA, AUFFRAY CHARLES, CURIS EMMANUEL, BÉNAZETH SIMONE, COX DAVID. INCONSISTENCIES BETWEEN MAPS OF HUMAN CHROMOSOME 22 CORRELATE WITH INCREASED FREQUENCY OF DISEASE-RELATED LOCI. J BIOL SYST 2012. [DOI: 10.1142/s0218339002000743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The relationships between genetic or radiation hybrid (RH) and sequence maps of chromosome 22 have been reconsidered based on the sequence map. Integrated maps have been constructed by retaining only common markers between genetic or RH maps and the sequence map. Local inversions of markers have been detected. Ratios between either genetic or RH distances and sequence-based distances have been calculated for each map interval. Hot zones for recombination or radiation breakage have been delineated by merging together intervals displaying high distance ratios and located close to each other for sequence-constrained RH maps, and for female and male genetic maps. A statistically significant positive correlation was found between the distribution of disease-related genes and the hot zones for recombination or radiation breakage on both female genetic and Stanford-G3 RH maps. This observation indicates that investigation of chromosomal regions displaying inconsistencies between RH or genetic linkage and sequence-based maps can accelerate the initial phase of identification of disease-associated genes.
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Affiliation(s)
- CLAUDE CHELALA
- CNRS FRE 2571, Génomique Fonctionnelle et Biologie Systémique en Santé, 19 rue Guy Mocquet, B.P. 8, 94801 Villejuif Cedex, France
| | - MARIE-DOMINIQUE DEVIGNES
- CNRS FRE 2571, Génomique Fonctionnelle et Biologie Systémique en Santé, 19 rue Guy Mocquet, B.P. 8, 94801 Villejuif Cedex, France
| | - SANDRINE IMBEAUD
- CNRS FRE 2571, Génomique Fonctionnelle et Biologie Systémique en Santé, 19 rue Guy Mocquet, B.P. 8, 94801 Villejuif Cedex, France
| | - RIMA ZOOROB
- CNRS FRE 2571, Génomique Fonctionnelle et Biologie Systémique en Santé, 19 rue Guy Mocquet, B.P. 8, 94801 Villejuif Cedex, France
| | - CHARLES AUFFRAY
- CNRS FRE 2571, Génomique Fonctionnelle et Biologie Systémique en Santé, 19 rue Guy Mocquet, B.P. 8, 94801 Villejuif Cedex, France
| | - EMMANUEL CURIS
- Laboratoire de Biomathématique, Faculté de Pharmacie-Paris V, 4 avenue de l'Observatoire, 75006 Paris, France
| | - SIMONE BÉNAZETH
- Laboratoire de Biomathématique, Faculté de Pharmacie-Paris V, 4 avenue de l'Observatoire, 75006 Paris, France
| | - DAVID COX
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
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Fine mapping of familial prostate cancer families narrows the interval for a susceptibility locus on chromosome 22q12.3 to 1.36 Mb. Hum Genet 2007; 123:65-75. [PMID: 18066601 DOI: 10.1007/s00439-007-0451-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 12/02/2007] [Indexed: 10/22/2022]
Abstract
Genetic studies suggest that hereditary prostate cancer is a genetically heterogeneous disease with multiple contributing loci. Studies of high-risk prostate cancer families selected for aggressive disease, analysis of large multigenerational families, and a meta-analysis from the International Consortium for Prostate Cancer Genetics (ICPCG), all highlight chromosome 22q12.3 as a susceptibility locus with strong statistical significance. Recently, two publications have narrowed the 22q12.3 locus to a 2.18 Mb interval using 54 high-risk families from the ICPCG collaboration, as defined by three recombination events on either side of the locus. In this paper, we present the results from fine mapping studies at 22q12.3 using both haplotype and recombination data from 42 high-risk families contributed from the Mayo Clinic and the Prostate Cancer Genetic Research Study (PROGRESS) mapping studies. No clear consensus interval is present when all families are used. However, in the subset of 14 families with >/=5 affected men per family, a 2.53-Mb shared consensus segment that overlaps with the previously published interval is identified. Combining these results with data from the earlier ICPCG study reduces the three-recombination interval at 22q12.3 to approximately 1.36 Mb.
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Abstract
Linkage maps have been invaluable for the positional cloning of many genes involved in severe human diseases. Standard genetic linkage maps have been constructed for this purpose from the Centre d'Etude du Polymorphisme Humain and other panels, and have been widely used. Now that attention has shifted towards identifying genes predisposing to common disorders using linkage disequilibrium (LD) and maps of single nucleotide polymorphisms (SNPs), it is of interest to consider a standard LD map which is somewhat analogous to the corresponding map for linkage. We have constructed and evaluated a cosmopolitan LD map by combining samples from a small number of populations using published data from a 10-megabase region on chromosome 20. In support of a pilot study, which examined a number of small genomic regions with a lower density of markers, we have found that a cosmopolitan map, which serves all populations when appropriately scaled, recovers 91 to 95 per cent of the information within population-specific maps. Recombination hot spots appear to have a dominant role in shaping patterns of LD. The success of the cosmopolitan map might be attributed to the co-localisation of hot spots in all populations. Although there must be finer scale differences between populations due to other processes (mutation, drift, selection), the results suggest that a whole-genome standard LD map would indeed be a useful resource for disease gene mapping.
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Affiliation(s)
- Jane Gibson
- Department of Human Genetics, School of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - William Tapper
- Department of Human Genetics, School of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Weihua Zhang
- Department of Human Genetics, School of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Newton Morton
- Department of Human Genetics, School of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Andrew Collins
- Department of Human Genetics, School of Medicine, University of Southampton, Southampton, SO16 6YD, UK
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Khatkar MS, Collins A, Cavanagh JAL, Hawken RJ, Hobbs M, Zenger KR, Barris W, McClintock AE, Thomson PC, Nicholas FW, Raadsma HW. A first-generation metric linkage disequilibrium map of bovine chromosome 6. Genetics 2006; 174:79-85. [PMID: 16816421 PMCID: PMC1569786 DOI: 10.1534/genetics.106.060418] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We constructed a metric linkage disequilibrium (LD) map of bovine chromosome 6 (BTA6) on the basis of data from 220 SNPs genotyped on 433 Australian dairy bulls. This metric LD map has distances in LD units (LDUs) that are analogous to centimorgans in linkage maps. The LD map of BTA6 has a total length of 8.9 LDUs. Within the LD map, regions of high LD (represented as blocks) and regions of low LD (steps) are observed, when plotted against the integrated map in kilobases. At the most stringent block definition, namely a set of loci with zero LDU increase over the span of these markers, BTA6 comprises 40 blocks, accounting for 41% of the chromosome. At a slightly lower stringency of block definition (a set of loci covering a maximum of 0.2 LDUs on the LD map), up to 81% of BTA6 is spanned by 46 blocks and with 13 steps that are likely to reflect recombination hot spots. The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming extensive LD in Holstein-Friesian dairy cattle, which makes such populations ideal for whole-genome association studies.
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Affiliation(s)
- Mehar S Khatkar
- Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney and CRC for Innovative Dairy Products, Camden NSW 2570, Australia.
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Collins A, Lau W, De La Vega FM. Mapping genes for common diseases: the case for genetic (LD) maps. Hum Hered 2005; 58:2-9. [PMID: 15604559 DOI: 10.1159/000081451] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2004] [Accepted: 06/22/2004] [Indexed: 02/03/2023] Open
Abstract
We examine the current effort to develop a haplotype map of the human genome and suggest an alternative approach which represents linkage disequilibrium patterns in the form of a metric LD map. LD maps have some of the useful properties of genetic linkage maps but have a much higher resolution which is optimal for SNP-based association mapping of common diseases. The studies that have been undertaken to date suggest that LD and recombination maps show some close similarities because of abundant, narrow, recombination hot spots. These hot spots are co-localised in all populations but, unlike linkage maps, LD maps differ in scale for different populations because of differences in population history. The prospects for developing optimized panels of SNPs and the use of linkage disequilibrium maps in disease gene localisation are assessed in the light of recent evidence.
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Affiliation(s)
- Andrew Collins
- Human Genetics, School of Medicine, University of Southampton, Southampton, UK.
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Liu Z, Womack JE, Antoniou E. A high-resolution comparative RH map of the telomeric end of bovine chromosome 2 with human chromosomes 1 and 2. Cytogenet Genome Res 2004; 103:89-93. [PMID: 15004470 DOI: 10.1159/000076295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2003] [Accepted: 09/01/2003] [Indexed: 11/19/2022] Open
Abstract
High density livestock to human comparative maps are necessary for the implementation of comparative positional candidate gene cloning. We have constructed a high-density comparative radiation hybrid (RH) map of the telomeric end of bovine chromosome 2 (BTA2) using a 12,000-rad whole genome cattle-hamster radiation hybrid (WGRH) panel. Eighteen bovine EST markers with orthologues on human chromosomes 1 and 2 (HSA1 and HSA2), together with nine microsatellite markers, were typed against the 180 cell lines of the WGRH panel. Twenty-one markers were included in the multi-point framework map at LOD =3.0. The comparative analysis reveals a new segment of highly conserved synteny between HSA2 and BTA2.
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Affiliation(s)
- Z Liu
- Department of Animal Science, University of Missouri-Columbia, Columbia, Missouri, USA
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Nievergelt CM, Smith DW, Kohlenberg JB, Schork NJ. Large-scale integration of human genetic and physical maps. Genome Res 2004; 14:1199-205. [PMID: 15140834 PMCID: PMC419799 DOI: 10.1101/gr.1475304] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genetic maps are used routinely in family-based linkage studies to identify the rough location of genes that influence human traits and diseases. Unlike physical maps, genetic maps are based on the amount of recombination occurring between adjacent loci rather than the actual number of bases separating them. Genetic maps are constructed by statistically characterizing the number of crossovers observed in parental meioses leading to the transmission of alleles to their offspring. Considerations such as the number of meioses observed, the heterozygosity and physical distance between the loci studied, and the statistical methods used can impact the construction and reliability of a genetic map. As is well known, poorly constructed genetic maps can have adverse effects on linkage mapping studies. With the availability of sequence-based maps, as well as genetic maps generated by different researchers (such as those generated by the Marshfield and deCODE groups), one can investigate the compatibility and properties of different maps. We have integrated information from the most current human genome sequence data (UCSC genome assembly Human July 2003) as well as 8399 microsatellite markers used in the Marshfield and deCODE maps to reconcile the these maps. Our efforts resulted in updated sex-specific genetic maps.
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Affiliation(s)
- Caroline M Nievergelt
- Polymorphism Research Laboratory, Department of Psychiatry, University of California at San Diego, La Jolla, California 92093-0603, USA
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Morton NE. Genetic epidemiology, genetic maps and positional cloning. Philos Trans R Soc Lond B Biol Sci 2004; 358:1701-8. [PMID: 14561327 PMCID: PMC1693267 DOI: 10.1098/rstb.2003.1357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic epidemiology developed in the middle of the last century, focused on inherited causes of disease but with methods and results applicable to other traits and even forensics. Early success with linkage led to the localization of genes contributing to disease, and ultimately to the Human Genome Project. The discovery of millions of DNA markers has encouraged more efficient positional cloning by linkage disequilibrium (LD), using LD maps and haplotypes in ways that are rapidly evolving. This has led to large international programmes, some promising and others alarming, with laws about DNA patenting and ethical guidelines for responsible research still struggling to be born.
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Affiliation(s)
- Newton E Morton
- University of Southampton, Human Genetics Division, Duthie Building, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.
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Abstract
We used LDMAP (Maniatis et al. 2002) to analyse SNP data spanning chromosome 22 (Dawson et al. 2002), to obtain a whole-chromosome metric LD map. The LD map, with map distances analogous to the centiMorgan scale of linkage maps, identifies regions of high LD as plateaus ('blocks') and characterises steps which define the relationship between these regions. From this map we estimate that block regions comprise between 32% and 55% of the euchromatic portion of chromosome 22 and that increasing marker density within steps may increase block coverage. Steps are regions of low LD which correspond to areas of variable recombination intensity. The intensity of recombination is related to the height of the step and thus intense recombination hot-spots can be distinguished from more randomly distributed historical events. The LD maps are more closely related to the high-resolution linkage map (Kong et al. 2002) than average measures of rho with recombination accounting for between 34% and 52% of the variance in patterns of LD (r=0.58 - 0.71, p=0.0001). Step regions are closely correlated with a range of sequence motifs including GT/CA repeats. The LD map identifies holes in which greater marker density is required and defines the optimal SNP spacing for positional cloning, which suggests that some multiple of around 50,000 SNPs will be required to efficiently screen Caucasian genomes. Further analyses which investigate selection of informative SNPs and the effect of SNP allele frequency and marker density will refine this estimate.
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Affiliation(s)
- W J Tapper
- Human Genetics Division, School of Medicine, Southampton General Hospital, University of Southampton, Southampton, SO16 6YD, UK.
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Kolpakov R, Bana G, Kucherov G. mreps: Efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 2003; 31:3672-8. [PMID: 12824391 PMCID: PMC169196 DOI: 10.1093/nar/gkg617] [Citation(s) in RCA: 221] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The presence of repeated sequences is a fundamental feature of genomes. Tandemly repeated DNA appears in both eukaryotic and prokaryotic genomes, it is associated with various regulatory mechanisms and plays an important role in genomic fingerprinting. In this paper, we describe mreps, a powerful software tool for a fast identification of tandemly repeated structures in DNA sequences. mreps is able to identify all types of tandem repeats within a single run on a whole genomic sequence. It has a resolution parameter that allows the program to identify 'fuzzy' repeats. We introduce main algorithmic solutions behind mreps, describe its usage, give some execution time benchmarks and present several case studies to illustrate its capabilities. The mreps web interface is accessible through http://www.loria.fr/mreps/.
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Affiliation(s)
- Roman Kolpakov
- French-Russian Institute for Informatics and Applied Mathematics, Moscow University, 119899 Moscow, Russia
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Leal SM. Genetic maps of microsatellite and single-nucleotide polymorphism markers: are the distances accurate? Genet Epidemiol 2003; 24:243-52. [PMID: 12687641 PMCID: PMC6141025 DOI: 10.1002/gepi.10227] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Genetic maps play an important role in gene mapping. Inaccurate genetic maps can hinder gene mapping by biasing lod scores and reducing the power to map a trait to a particular region. Although sequence-based physical maps can provide a unique order for markers, they do not provide information on genetic map distances. By simulation studies, I investigated how many meioses are necessary to accurately estimate genetic map distances for maps constructed from microsatellite and single-nucleotide polymorphism (SNP) markers for various intermarker distances and marker heterozygosity. To evaluate the accuracy of the generated genetic maps, the length of the 95% confidence interval for intermarker genetic distances was examined. In addition, the power to separate two adjacent markers by a nonzero map distance was investigated. The number of meioses necessary to accurately estimate map distances depends greatly not only on intermarker distances but also on marker heterozygosity. For example, for a genetic map with intermarker distances of 0.5 cM generated with 1,000 meioses, when marker heterozygosity was high (0.90), for 96% of the markers there was a nonzero map distance between adjacent markers. However, when marker heterozygosity was low (0.32), only 48% of the markers mapped to a unique position. For identical numbers of meioses and intermarker distances, genetic maps constructed from microsatellite markers will be more precise than maps assembled from SNP markers, due to the higher levels of heterozygosity for microsatellite markers.
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Affiliation(s)
- Suzanne M Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
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Matise TC, Porter CJ, Buyske S, Cuttichia AJ, Sulman EP, White PS. Systematic evaluation of map quality: human chromosome 22. Am J Hum Genet 2002; 70:1398-410. [PMID: 11992248 PMCID: PMC379125 DOI: 10.1086/340605] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2001] [Accepted: 02/28/2002] [Indexed: 11/03/2022] Open
Abstract
Marker positions on nine genetic linkage, radiation hybrid, and integrated maps of human chromosome 22 were compared with their corresponding positions in the completed DNA sequence. The proportion of markers whose map position is <250 kb from their respective sequence positions ranges from 100% to 35%. Several discordant markers were identified, as well as four regions that show common inconsistencies across multiple maps. These shared discordant regions surround duplicated DNA segments and may indicate mapping or assembly errors due to sequence homology. Recombination-rate distributions along the chromosome were also evaluated, with male and female meioses showing significantly different patterns of recombination, including an 8-Mb male recombination desert. The distributions of radiation-induced chromosome breakage for the GB4 and the G3 radiation hybrid panels were also evaluated. Both panels show fluctuations in breakage intensity, with different regions of significantly elevated rates of breakage. These results provide support for the common assumption that radiation-induced breaks are generally randomly distributed. The present studies detail the limitations of these important map resources and should prove useful for clarifying potential problems in the human maps and sequence assemblies, as well as for mapping and sequencing projects in and across other species.
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Affiliation(s)
- Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA.
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DeWan AT, Parrado AR, Matise TC, Leal SM. Map error reduction: using genetic and sequence-based physical maps to order closely linked markers. Hum Hered 2002; 54:34-44. [PMID: 12446985 PMCID: PMC6143171 DOI: 10.1159/000066697] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Marshfield comprehensive genetic maps are frequently used for linkage and association studies, however, for some regions of these maps the marker order has low level of likelihood ratio support. In order to investigate the level of statistical support and the accuracy of the genetic maps compared to sequence-based physical maps, two approximately 30 cM autosomal regions were selected. The first region was selected from chromosome 3 and consisted predominately of draft sequence. The second region was selected from chromosome 21 and consisted of finished sequence data. The physical order of these markers was based upon their position on Celera (CEL) and Human Genome Project-Santa Cruz (HGP-sc) sequence-based physical maps. The chromosome 3 and 21 regions contained 100 and 61 markers, respectively, on the Marshfield genetic map. The genetic and physical map order was consistent for 88.9 and 89.2% of the markers in the region on chromosome 3 and 21, respectively. Using a novel scoring criterion to assess inconsistent marker order between genetic and physical maps, it was determined that the physical order was likely the correct order for 3.3 and 7.1% of the markers in the chromosome 3 and 21 regions, respectively. To increase the accuracy of the order of markers selected for fine mapping a method is presented which combines information from genetic and sequence-based physical maps.
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Affiliation(s)
- Andrew T. DeWan
- The Laboratory of Statistical Genetics, The Rockefeller University, New York, N.Y
| | - Antonio R. Parrado
- The Laboratory of Statistical Genetics, The Rockefeller University, New York, N.Y
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, N.J
| | - Suzanne M. Leal
- The Laboratory of Statistical Genetics, The Rockefeller University, New York, N.Y
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex., USA
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