Large-scale analysis of tandem repeat variability in the human genome

Nucleic Acids Research

Volumn 42, Issue 9, 2014, Pages 5728-5741

  Duitama, Jorge ^a,b   Zablotskaya, Alena ^a,c   Gemayel, Rita ^a   Jansen, An ^a,c   Belet, Stefanie ^a,c   Vermeesch, Joris R ^d   Verstrepen, Kevin J ^a   Froyen, Guy ^a,c  

^a UNIVERSITY OF LEUVEN   (Belgium)

^b INTERNATIONAL CENTER FOR TROPICAL AGRICULTURE CIAT   (Colombia)

^c DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^d UNIVERSITY HOSPITALS LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ACCURACY; ARTICLE; BIOINFORMATICS; CAPILLARY ELECTROPHORESIS; GENE EXPRESSION; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN GENOME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; TANDEM REPEAT; TANDEM REPEAT VARIABILITY;

BASE SEQUENCE; FEMALE; GENE COMPONENTS; GENOME, HUMAN; HUMANS; MALE; MOLECULAR SEQUENCE DATA; PEDIGREE; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; TANDEM REPEAT SEQUENCES;

EID: 84901298048     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku212     Document Type: Article

References (45)

1. Jelinek, W.R., Toomey, T.P., Leinwand, L., Duncan, C.H., Biro, P.A., Choudary, P.V., Weissman, S.M., Rubin, C.M., Houck, C.M., Deininger, P.L. et al. (1980) Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc. Natl. Acad. Sci. U.S.A, 77, 1398-1402.
2. Verstrepen, K.J., Jansen, A., Lewitter, F. and Fink, G.R. (2005) Intragenic tandem repeats generate functional variability. Nat. Genet., 37, 986-990.
3. Ohno, S. (1972) So much "junk" DNA in our genome. Brookhaven. Symp. Biol., 23, 366-370.
4. Gulcher, J. (2012) Microsatellite markers for linkage and association studies. Cold Spring Harb. Protoc., 2012, 425-432.
5. Kim, T.M., Laird, P.W. and Park, P.J. (2013) The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell, 155, 858-868.
6. Kashi, Y. and King, D.G. (2006) Simple sequence repeats as advantageous mutators in evolution. Trends Genet., 22, 253-259.
7. Vinces, M.D., Legendre, M., Caldara, M., Hagihara, M. and Verstrepen, K.J. (2009) Unstable tandem repeats in promoters confer transcriptional evolvability. Science, 324, 1213-1216.
8. Gemayel, R., Vinces, M.D., Legendre, M. and Verstrepen, K.J. (2010) Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu. Rev. Genet., 44, 445-477.
9. Jansen, A., Gemayel, R. and Verstrepen, K.J. (2012) Unstable microsatellite repeats facilitate rapid evolution of coding and regulatory sequences. Genome Dyn., 7, 108-125.
10. Fondon, J.W. III and Garner, H.R. (2004) Molecular origins of rapid and continuous morphological evolution. Proc. Natl. Acad. Sci. U.S.A, 101, 18058-18063.
11. La Spada, A.R. and Taylor, J.P. (2010) Repeat expansion disease: Progress and puzzles in disease pathogenesis. Nat. Rev. Genet., 11, 247-258.
12. Gatchel, J.R. and Zoghbi, H.Y. (2005) Diseases of unstable repeat expansion: Mechanisms and common principles. Nat. Rev. Genet., 6, 743-755.
13. Brouwer, J.R., Willemsen, R. and Oostra, B.A. (2009) Microsatellite repeat instability and neurological disease. Bioessays, 31, 71-83.
14. Law, M.J., Lower, K.M., Voon, H.P., Hughes, J.R., Garrick, D., Viprakasit, V., Mitson, M., De Gobbi, M., Marra, M., Morris, A. et al. (2010) ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner. Cell, 143, 367-378.
15. Biason, P., Visentin, M., Talamini, R., Stopar, A., Giorda, G., Lucia, E., Campagnutta, E. and Toffoli, G. (2012) Polymorphic thymidylate synthase gene impacts on overall survival of patients with epithelial ovarian cancer after platinum-based chemotherapy. Pharmacogenomics., 13, 1609-1619.
16. Lecomte, T., Ferraz, J.M., Zinzindohoue, F., Loriot, M.A., Tregouet, D.A., Landi, B., Berger, A., Cugnenc, P.H., Jian, R., Beaune, P. et al. (2004) Thymidylate synthase gene polymorphism predicts toxicity in colorectal cancer patients receiving 5-fluorouracil-based chemotherapy. Clin. Cancer Res., 10, 5880-5888.
17. Legendre, M., Pochet, N., Pak, T. and Verstrepen, K.J. (2007) Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res., 17, 1787-1796. (Pubitemid 351360003
18. Rockman, M.V. and Wray, G.A. (2002) Abundant raw material for cis-regulatory evolution in humans. Mol. Biol. Evol., 19, 1991-2004.
19. Hammock, E.A. and Young, L.J. (2005) Microsatellite instability generates diversity in brain and sociobehavioral traits. Science, 308, 1630-1634. (Pubitemid 40807513
20. Rockman, M.V., Hahn, M.W., Soranzo, N., Loisel, D.A., Goldstein, D.B. and Wray, G.A. (2004) Positive selection on MMP3 regulation has shaped heart disease risk. Curr. Biol., 14, 1531-1539.
21. Gymrek, M., Golan, D., Rosset, S. and Erlich, Y. (2012) lobSTR: A short tandem repeat profiler for personal genomes. Genome Res., 22, 1154-1162.
22. McIver, L.J., Fondon, J.W. III, Skinner, M.A. and Garner, H.R. (2011) Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments. Genomics, 97, 193-199.
23. Highnam, G., Franck, C., Martin, A., Stephens, C., Puthige, A. and Mittelman, D. (2013) Accurate human microsatellite genotypes from high-Throughput resequencing data using informed error profiles. Nucleic Acids Res., 41, e32.
24. Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A. et al. (2011) The UCSC Genome Browser database: Update 2011. Nucleic Acids Res., 39, D876-D882.
25. Benson, G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
26. Matsumoto, C., Shinkai, T., Hori, H., Ohmori, O. and Nakamura, J. (2004) Polymorphisms of dopamine degradation enzyme (COMT and MAO) genes and tardive dyskinesia in patients with schizophrenia. Psychiatry Res., 127, 1-7. (Pubitemid 38916861
27. Griffith, O.L., Montgomery, S.B., Bernier, B., Chu, B., Kasaian, K., Aerts, S., Mahony, S., Sleumer, M.C., Bilenky, M., Haeussler, M. et al. (2008) ORegAnno: An open-Access community-driven resource for regulatory annotation. Nucleic Acids Res., 36, D107-D113. (Pubitemid 351149705
28. Meyer, L.R., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Kuhn, R.M., Wong, M., Sloan, C.A., Rosenbloom, K.R., Roe, G., Rhead, B. et al. (2013) The UCSC Genome Browser database: Extensions and updates 2013. Nucleic Acids Res., 41, D64-D69.
29. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
30. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics., 26, 589-595.
31. Choi, Y., Sims, G.E., Murphy, S., Miller, J.R. and Chan, A.P. (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS ONE., 7, e46688.
32. Shinde, D., Lai, Y., Sun, F. and Arnheim, N. (2003) Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites. Nucleic Acids Res., 31, 974-980. (Pubitemid 36240435
33. Walsh, P.S., Fildes, N.J. and Reynolds, R. (1996) Sequence analysis and characterization of stutter products at the tetranucleotide repeat locus vWA. Nucleic Acids Res., 24, 2807-2812. (Pubitemid 26239753
34. Hauge, X.Y. and Litt, M. (1993) A study of the origin of 'shadow bands' seen when typing dinucleotide repeat polymorphisms by the PCR. Hum. Mol. Genet., 2, 411-415.
35. McIver, L.J., McCormick, J.F., Martin, A., Fondon, J.W. III and Garner, H.R. (2013) Population-scale analysis of human microsatellites reveals novel sources of exonic variation. Gene, 516, 328-334.
36. Fondon, J.W. III, Martin, A., Richards, S., Gibbs, R.A. and Mittelman, D. (2012) Analysis of microsatellite variation in Drosophila melanogaster with population-scale genome sequencing. PLoS ONE., 7, e33036.
37. Yoon, K., Lee, S., Han, T.S., Moon, S.Y., Yun, S.M., Kong, S.H., Jho, S., Choe, J., Yu, J., Lee, H.J. et al. (2013) Comprehensive genome-And transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers. Genome Res., 23, 1109-1117.
38. Guilmatre, A., Highnam, G., Borel, C., Mittelman, D. and Sharp, A.J. (2013) Rapid multiplexed genotyping of simple tandem repeats using capture and high-Throughput sequencing. Hum. Mutat., 34, 1304-1311.
39. Legendre, M. and Verstrepen, K.J. (2008) Using the SERV applet to detect tandem repeats in DNA sequences and to predict their variability. CSH. Protoc., 2, pdb.ip50.
40. Ellegren, H. (2004) Microsatellites: Simple sequences with complex evolution. Nat. Rev. Genet., 5, 435-445.
41. Fordyce, S.L., Avila-Arcos, M.C., Rockenbauer, E., Borsting, C., Frank-Hansen, R., Petersen, F.T., Willerslev, E., Hansen, A.J., Morling, N. and Gilbert, M.T. (2011) High-Throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform. BioTechniques, 51, 127-133.
42. Malausa, T., Gilles, A., Meglecz, E., Blanquart, H., Duthoy, S., Costedoat, C., Dubut, V., Pech, N., Castagnone-Sereno, P., Delye, C. et al. (2011) High-Throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Mol. Ecol. Resour., 11, 638-644.
43. Abecasis, G.R., Auton, A., Brooks, L.D., DePristo, M.A., Durbin, R.M., Handsaker, R.E., Kang, H.M., Marth, G.T. and McVean, G.A. (2012) An integrated map of genetic variation from 1092 human genomes. Nature, 491, 56-65.
44. O'Dushlaine, C.T., Edwards, R.J., Park, S.D. and Shields, D.C. (2005) Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biol., 6, R69.
45. Vogler, A.J., Keys, C., Nemoto, Y., Colman, R.E., Jay, Z. and Keim, P. (2006) Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7. J. Bacteriol., 188, 4253-4263.