Short tandem repeats in human exons: A target for disease mutations

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Madsen, Bo Eskerod ^a   Villesen, Palle ^a   Wiuf, Carsten ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DISEASE ASSOCIATION; EXON; GENETIC SCREENING; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; MOUSE; MUTATIONAL ANALYSIS; NONHUMAN; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SHORT TANDEM REPEAT; ALGORITHM; ANIMAL; BIOLOGY; GENETIC PREDISPOSITION; GENETIC VARIABILITY; GENOME; INSERTION DELETION MUTATION; NUCLEIC ACID DATABASE;

MICROSATELLITE DNA;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; EXONS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; HUMANS; INDEL MUTATION; MICE; MICROSATELLITE REPEATS; VARIATION (GENETICS);

EID: 52449094233     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-410     Document Type: Article

References (33)

1. Levy S Sutton G Ng PC Feuk L Halpern AL Walenz BP Axelrod N Huang J Kirkness EF Denisov G et al. The Diploid Genome Sequence of an Individual Human PLoS Biology 2007, 5(10):e254. 1964779 17803354 10.1371/ journal.pbio.0050254
2. Freeman JL Perry GH Feuk L Redon R McCarroll SA Altshuler DM Aburatani H Jones KW Tyler-Smith C Hurles ME et al. Copy number variation: New insights in genome diversity Genome Res 2006, 16(8):949-961. 10.1101/ gr.3677206 16809666
3. Tuzun E Sharp AJ Bailey JA Kaul R Morrison VA Pertz LM Haugen E Hayden H Albertson D Pinkel D Fine-scale structural variation of the human genome Nat Genet 2005, 37(7):727-732. 10.1038/ng1562 15895083
4. Conrad DF Andrews TD Carter NP Hurles ME Pritchard JK et al. A high-resolution survey of deletion polymorphism in the human genome Nat Genet 2006, 38(1):75-81. 10.1038/ng1697 16327808
5. Redon R Ishikawa S Fitch KR Feuk L Perry GH Andrews TD Fiegler H Shapero MH Carson AR Chen W Global variation in copy number in the human genome Nature 2006, 444(7118):444-454. 10.1038/nature05329 17122850
6. Khaja R Zhang J MacDonald JR He Y Joseph-George AM Wei J Rafiq MA Qian C Shago M Pantano L et al. Genome assembly comparison identifies structural variants in the human genome Nat Genet 2006, 38(12):1413-1418. 10.1038/ng1921 17115057
7. Madsen BE Villesen P Wiuf C A periodic pattern of SNPs in the human genome Genome Res 2007, 17(10):1414-1419. 1987342 17673700 10.1101/ gr.6223207
8. Boby T Patch AM Aves SJ TRbase: A database relating tandem repeats to disease genes for the human genome Bioinformatics 2005, 21(6):811-816. 10.1093/bioinformatics/bti059 15479712
9. Borstnik B Pumpernik D Tandem Repeats in Protein Coding Regions of Primate Genes Genome Res 2002, 12(6):909-915. 1383732 12045144 10.1101/ gr.138802
10. O'Dushlaine C Edwards R Park S Shields D Tandem repeat copy-number variation in protein-coding regions of human genes Genome Biology 2005, 6(8):R69. 1273636 16086851 10.1186/gb-2005-6-8-r69
11. Hancock JM Simon M Simple sequence repeats in proteins and their significance for network evolution Gene 2005, 345(1):113-118. 10.1016/ j.gene.2004.11.023 15716087
12. Alba MM Guigo R Comparative analysis of amino acid repeats in rodents and humans Genome Res 2004, 14(4):549-554. 383298 15059995 10.1101/ gr.1925704
13. Kashi Y King DG Simple sequence repeats as advantageous mutators in evolution Trends in Genetics 2006, 22(5):253-259. 10.1016/ j.tig.2006.03.005 16567018
14. Kelkar YD Tyekucheva S Chiaromonte F Makova KD The genome-wide determinants of human and chimpanzee microsatellite evolution Genome Res 2007. gr.7113408 2134767 18032720
15. Mirkin SM Expandable DNA repeats and human disease Nature 2007, 447(7147):932-940. 10.1038/nature05977 17581576
16. Levinson G Gutman GA Slipped-strand mispairing: A major mechanism for DNA sequence evolution Mol Biol Evol 1987, 4(3):203-221. 3328815
17. Eppig JT Blake JA Bult CJ Kadin JA Richardson JE The mouse genome database (MGD): New features facilitating a model system Nucleic Acids Res 2007, 35: Database D630-637. 1751527 17135206 10.1093/nar/gkl940
18. Cohen J GENOMICS: DNA Duplications and Deletions Help Determine Health Science 2007, 317(5843):1315-1317. 10.1126/science.317.5843.1315 17823326
19. Lupski JR Genome structural variation and sporadic disease traits Nat Genet 2006, 38(9):974-976. 10.1038/ng0906-974 16941003
20. Lai Y Sun F The Relationship Between Microsatellite Slippage Mutation Rate and the Number of Repeat Units Mol Biol Evol 2003, 20(12):2123-2131. 10.1093/molbev/msg228 12949124
21. Pumpernik D Oblak B Borštnik B Replication slippage versus point mutation rates in short tandem repeats of the human genome Molecular Genetics and Genomics 2008, 279(1):53-61. 10.1007/s00438-007-0294-1
22. Leclercq S Rivals E Jarne P Detecting microsatellites within genomes: significant variation among algorithms BMC Bioinformatics 2007, 8(1):125. 1876248 17442102 10.1186/1471-2105-8-125
23. Hodges E Xuan Z Balija V Kramer M Molla MN Smith SW Middle CM Rodesch MJ Albert TJ Hannon GJ Genome-wide in situ exon capture for selective resequencing Nat Genet 2007, 39(12):1522-1527. 10.1038/ng.2007.42 17982454
24. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome Nature 2001 409 6822 860 921 10.1038/ 35057062 11237011
25. Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome Nature 2002, 420(6915):520-562. 10.1038/ nature01262 12466850
26. Sherry ST Ward MH Kholodov M Baker J Phan L Smigielski EM Sirotkin K dbSNP: The NCBI database of genetic variation Nucl Acids Res 2001, 29(1):308-311. 29783 11125122 10.1093/nar/29.1.308
27. Durinck S Moreau Y Kasprzyk A Davis S De Moor B Brazma A Huber W BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis Bioinformatics 2005, 21(16):3439-3440. 10.1093/ bioinformatics/bti525 16082012
28. Hamosh A Scott AF Amberger JS Bocchini CA McKusick VA Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders Nucl Acids Res 2005, 33(suppl_1):D514-517.
29. Bult CJ Blake JA Richardson JE Kadin JA Eppig JT the Mouse Genome Database G The Mouse Genome Database (MGD): Integrating biology with the genome Nucl Acids Res 2004, 32(suppl_1):D476-481. 10.1093/nar/gkh125
30. Karolchik D Hinrichs AS Furey TS Roskin KM Sugnet CW Haussler D Kent WJ The UCSC Table Browser data retrieval tool Nucl Acids Res 2004, 32(suppl_1):D493-496. 10.1093/nar/gkh103
31. Benson G Tandem repeats finder: A program to analyze DNA sequences Nucl Acids Res 1999, 27(2):573-580. 148217 9862982 10.1093/nar/27.2.573
32. Wilcoxon F Individual Comparisons by Ranking Methods Biometrics Bulletin 1945, 1(6):80-83. 10.2307/3001968
33. R Development Core Team R: A Language and Environment for Statistical Computing Vienna, Austria: R Foundation for Statistical Computing 2006.