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Moschonas NK (2000) Craniosynostosis and Related Limb Anomalies

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Moschonas NK (2000) Craniosynostosis and Related Limb Anomalies Chromosome 10 Mouse Genome Informatics (MGI 2.8). This site is a comprehensive SNP Consortium. This is the website of the SNP Consortium Ltd, a listing of mammalian homology and comparative maps that public/private collaboration that has to date discovered and allows you to search by gene name or map location, as well as characterized nearly 1.8 million SNPs view whole-genome maps http://snp.cshl.org http://www.informatics.jax.org/menus/homology_menu.shtml UCSC Genome Bioinformatics. The UCSC Genome Bioinformatics National Center for Biotechnology Information (NCBI) dbSNP. site contains working drafts for the human genome and the This site is the single nucleotide polymorphism database main- mouse genome. The Genome Browser and the data it displays are tained by the National Center for Biotechnology Information freely available for academic, nonpro®t and personal use http://www.ncbi.nlm.nih.gov/SNP/ http://genome.ucsc.edu Sanger Centre. This site is the human chromosome 9 sequencing Washington University Genome Center. The focus of the project overview page that reports the sequencing status of the Washington University Genome Center is sequencing human chromosome. The Sanger Centre is a genome research institute and microbial genomes and analysis of genetic variations among funded by the Wellcome Trust populations. This site describes the various sequencing projects http://www.sanger.ac.uk/HGP/Chr9/ and provides progress updates http://www.genome.washington.edu/UWGC/ Chromosome 10 Intermediate article Nicholas K Moschonas, University of Crete and Institute of Molecular Biology and Article contents Biotechnology (IMBB-FORTH), Crete, Greece Human Chromosome Characteristics Chromosome 10 is a medium sized submetacentric chromosome corresponding to about Structure and Statistics of Chromosome 10 Genetic Map and Polymorphisms 4.2% of the genetic material in the genome. Disease Gene Loci Cytogenetic Characteristics Human Chromosome Characteristics 1991). Similarly, HC10 length shown in the Ensembl Table 1 gives details of the characteristics of the human database (see Web Links), i.e. 144.7 Mb, is possibly an chromosome. overestimate and may include artifactual duplications/ overlaps, present in the draft sequence. Structure and Statistics of Genes Chromosome 10 Euchromatin covers 96.7%of chromosome 10. Based Chromosome size on draft sequence estimations as cited in the UCSC Genome Browser (Web Links), HC10 C G content is Human chromosome 10 (HC10) is a medium-sized about 41.8%. Investigation along the assembled submetacentric chromosome corresponding to about chromosome sequence using 50 kb windows indicated 4.2%of the total chromosomal length. An overview of a reasonably good correlation between gene density HC10 physical characteristics is shown in the Ensembl and G C content (Venter et al., 2001). More than genome server (see Web Links). HC10 size estimations 1050 genes have been assigned to HC10, that is 659 based on recent physical mapping and draft genomic protein-coding RefSeq gene entries (see Web Links) deoxyribonucleic acid (DNA) sequencing data give a and 398 `novel' Ensembl genes, resulting in an average total value of approximately 130±133 Mb with a short gene density of about 8 genes/Mb. In addition, 25 (p) arm of 37.0 Mb and a long (q) arm of 92.0 Mb pseudogenes have been assigned to HC10 (RefSeq). A (Bentley et al., 2001; Venter et al., 2001). This estimate higher density, i.e. * 10.5 genes/Mb, was estimated by differs signi®cantly from the 144 Mb value determined the IHGSC (2001) based on the HC10 GeneMap98 previously by less accurate physical methods, such as number of genes. The most gene-rich regions are autoradiography, ¯ow and image cytometry (Morton, 10q23.3±q25.1 and 10q22.1±q23.1. A preliminary 618 NATURE ENCYCLOPEDIA OF THE HUMAN GENOME / &2003 Macmillan Publishers Ltd, Nature Publishing Group / www.ehgonline.net Chromosome 10 Table 1 Characteristics of human chromosome 10. Characteristic Details Chromosome number 10 Chromosome type Submetacentric Physical size Overall 133.0 Mb Short arm 37.0 Mb Long arm 92.0 Mb Genetic size Overall average 181.7 cM Male average 146.1 cM Female average 209.7 cM Average recombination length 1.37 cM/Mb Physical characteristics Heterochromatic regions Distribution Pericentromeric Length 3.3±4.0 Mb Repetitive sequence content Nature Density (%) Distribution SINEs 12.34 Interspersed LINEs 21.30 Interspersed LTRs 7.50 Interspersed DNA transposons 2.0 Interspersed Variability SNP density 460 SNPs/Mb Microsatellite density 4.0 microsatellites/Mb Euchromatin G C content 42% CpG density 8.17 CpG islands/Mb Genes Gene density 8 genes/Mb (average) Gene number 1057 Con®rmed 659 Predicted 398 Imprinted gene regions 1 Disease genes 53 Cytogenetic characteristics Chromosome breakpoints 46 Disease related 45 Cancer related 22 Fragile sites 7 Chromosome heteromorphisms 1 cM: centimorgan; DNA: deoxyribonucleic acid; LINEs: long interspersed nuclear elements; LTR: long terminal repeat; Mb: megabase; SINEs: short interspersed nuclear elements; SNP: single nucleotide polymorphism. analysis to classify the molecular function of the tissue-speci®c gene activity and imprinting. Based on current HC10 RefSeq list of genes by exploring HC10 draft sequence data, Venter et al. (2001) published data is presented in Figure 1. About 44.3% identi®ed 1087 CpG islands on HC10, resulting in an of genes (i.e. 292 out of 659) could be classi®ed into 11 average density of 8.17 CpGs/Mb, a value correlating established functional categories. well with the above-mentioned gene density. A slightly higher CpG density, *10.5 CpGs/Mb, was calculated CpG islands by the IHGSC (2001). Interestingly, according to this investigation, the longest CpG island of the human CpG islands in the human genome are considered to be genome (i.e. 36 619 bp) maps to HC10. DNA fragments larger than 200 base pairs (bp) with > 50%G C content and a ratio of observed versus Human chromosome 10±mouse synteny expected GC dinucleotide frequency of at least 60%. Many CpG islands are adjacent to the 50 end of genes. Comparative gene mapping combined with functional They are of particular importance because their analysis has facilitated the determination of HC10± cytosine methylation state has been correlated with mouse synteny (see NCBI Human±Mouse Homology NATURE ENCYCLOPEDIA OF THE HUMAN GENOME / &2003 Macmillan Publishers Ltd, Nature Publishing Group / www.ehgonline.net 619 Chromosome 10 25% resolution linkage map data, combined with chromo- some physical mapping and sequence data, provide 20% an ideal tool for effective positional cloning and identi®cation of disease candidate genes. About 524 15% microsatellite markers (i.e. 356 dinucleotide, a penta- 10% nucleotide, 132 tetranucleotide and 35 trinucleotide repeats) have been assigned to HC10. The most 5% informative microsatellite markers together with restriction fragment length polymorphisms (RFLPs) 0% and variant numbers of tandem repeats (VNTRs) have been used for the construction of several high- Signaling Transport Cell cycle resolution genetic maps (such as those on the Human Metabolism Cytoskeletal Genome Organisation (HUGO) website). Based on Cellular processes Defense/immunity the current estimates of the physical length of the Protein modification DNA/RNA modification chromosome and the size of the corresponding sex- Transcription/translationCell–cell communication average Ge ne thon linkage map (Dib et al., 1996), an Figure 1 Distribution of the molecular function of 292 overall recombination length of 1.37 cM/Mb was chromosome 10 RefSeq genes. calculated. However, a more informative estimation across 3 Mb contiguous chromosomal regions has Map in Web Links). Syntenic regions of genes mapped been made by Venter et al. (2001). This group placed to the 10p arm are mainly on mouse chromosome 2; the corresponding Ge ne thon markers on HC10 chromosomes 18, 13 and 6 are also represented. Genes compartmentalized shotgun assemblies and subse- mapped to the 10q arm have syntenic regions, quently calculated the relative physical distances and particularly on mouse chromosome 19 as well as on rates of recombination. Using this approach, the 14, 10 and 7. average value determined on the sex-average map was 1.29 cM/Mb with a minimum of 0.66 and a maximum Heterochromatin of 3.05 cM/Mb, elegantly con®rming the variability in recombination rates among various regions of the The chromosome 10 pericentromeric heterochromatic chromosome and the high recombination rates in the region is 3.3±4 Mb. Structural analysis of a more than telomeric regions. 1 Mb contiguous pericentromeric sequence, spanning The most frequent genetic variation is a single the transition from centric heterochromatin to euchro- nucleotide polymorphism (SNP) occurring once every matin at 10q11, revealed that the proximal 25%of its 100±300 bases. Most of the genome contains SNPs at length consists of satellite arrays and other tandem high density, relatively constant across the autosomes. repeats separated by tracts of complex sequence The use of SNPs in genetic analysis will accelerate evolved by pericentromeric-directed duplications, particularly the identi®cation of common disease genes whereas the rest contains few chromosome-speci®c by allowing a search for associations between a clinical tandem repeats (Guy et al., 2000). phenotype and speci®c molecular differences for a Chromosome 10 repeats given population group. More than 61 000 SNPs have been identi®ed on HC10 (see SNP Consortium Ltd in Interspersed
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