Inferring short tandem repeat variation from paired-end short reads

Nucleic Acids Research

Volumn 42, Issue 3, 2014, Pages

  Cao, Minh Duc ^a,b   Tasker, Edward ^c   Willadsen, Kai ^a   Imelfort, Michael ^a   Vishwanathan, Sailaja ^c   Sureshkumar, Sridevi ^c   Balasubramanian, Sureshkumar ^c   Boden, Mikael ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b MONASH UNIVERSITY   (Australia)

^c MONASH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS THALIANA; ARTICLE; BAYES THEOREM; CONTROLLED STUDY; GENE STRUCTURE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GENOMIC INSTABILITY; GENOTYPE; HIGH THROUGHPUT SEQUENCING; INDEL MUTATION; NONHUMAN; PAIRED END SHORT READ SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM;

ARABIDOPSIS; BAYES THEOREM; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA; SOFTWARE; TANDEM REPEAT SEQUENCES;

EID: 84896731172     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1313     Document Type: Article

References (45)

1. Verstrepen, K.J., Jansen, A., Lewitter, F. and Fink, G.R. (2005) Intragenic tandem repeats generate functional variability. Nat. Genet., 37, 986-990.
2. Pearson, C.E., Edamura, K.N. and Cleary, J.D. (2005) Repeat instability: mechanisms of dynamic mutations. Nat. Rev. Genet., 6, 729-742.
3. Castel, A.L., Cleary, J.D. and Pearson, C.E. (2010) Repeat instability as the basis for human diseases and as a potential target for therapy. Nat. Rev. Mol. Cell Biol., 11, 165-170.
4. MacDonald, M.E., Ambrose, C.M., Duyao, M.P., Myers, R.H., Lin, C., Srinidhi, L., Barnes, G., Taylor, S.A., James, M., Groot, N. et al. (1993) A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntingtons disease chromosomes. Cell, 72, 971-983.
5. Verkerk, A.J.M.H., Pieretti, M., Sutcliffe, J.S., Fu, Y.H., Kuhl, D.P.A., Pizzuti, A., Reiner, O., Richards, S., Victoria, M.F., Zhang, F. et al. (1991) Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in Fragile X syndrome. Cell, 65, 905-914.
6. Sureshkumar, S., Todesco, M., Schneeberger, K., Harilal, R., Balasubramanian, S. and Weigel, D. (2009) A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science, 323, 1060-1063.
7. Whan, V., Hobbs, M., McWilliam, S., Lynn, D., Lutzow, Y., Khatkar, M., Barendse, W., Raadsma, H. and Tellam, R. (2010) Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes. BMC Genomics, 11, 654.
8. 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.
9. Undurraga, S.F., Press, M.O., Legendre, M., Bujdoso, N., Bale, J., Wang, H., Davis, S.J., Verstrepen, K.J. and Queitsch, C. (2012) Background-dependent effects of polyglutamine variation in the Arabidopsis thaliana gene ELF3. Proc. Natl Acad. Sci. USA, 109, 19363-19367.
10. Liquori, C.L., Ricker, K., Moseley, M.L., Jacobsen, J.F., Kress, W., Naylor, S.L., Day, J.W. and Ranum, L.P.W. (2001) Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science, 293, 864-867.
11. Matsuura, T., Yamagata, T., Burgess, D.L., Rasmussen, A., Grewal, R.P., Watase, K., Khajavi, M., McCall, A.E., Davis, C.F., Zu, L. et al. (2000) Large expansion of the ATTCT pentanucleotide repeat in spinocerebellar ataxia type 10. Nat. Genet., 26, 191-194.
12. DeJesus-Hernandez, M., Mackenzie, I.R., Boeve, B.F., Boxer, A.L., Baker, M., Rutherford, N.J., Nicholson, A.M., Finch, N.A., Flynn, H., Adamson, J. et al. (2011) Expanded GGGGCC Hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron, 72, 245-256.
13. Renton, A.E., Majounie, E., Waite, A., Simo n-Sanche z, J., Rollinson, S., Gibbs, J.R., Schymick, J.C., Laaksovirta, H., van Swieten, J.C., Myllykangas, L. et al. (2011) A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-Linked ALS-FTD. Neuron, 72, 257-268.
14. Cao, M.D., Dix, T.I. and Allison, L. (2010) A genome alignment algorithm based on compression. BMC Bioinformatics, 11, 599.
15. Cao, M.D., Dix, T.I. and Allison, L. (2011) A biological compression model and its applications. In: Arabnia, H.R.R. and Tran, Q.N. (eds), Software Tools and Algorithms for Biological Systems, Vol. 696 of Advances in Experimental Medicine and Biology. Springer, New York, pp. 657-666.
16. Treangen, T.J. and Salzberg, S.L. (2012) Repetitive DNA and nextgeneration sequencing: computational challenges and solutions. Nat. Rev. Genet., 13, 36-46.
17. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics, 25, 1754-1760.
18. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
19. Lunter, G. and Goodson, M. (2011) Stampy: a statistical algorithm for sensitive and fast mapping of illumina sequence reads. Genome Res., 21, 936-939.
20. 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.
21. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. and Subgroup, G.P. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
22. Albers, C.A., Lunter, G., MacArthur, D.G., McVean, G., Ouwehand, W.H. and Durbin, R. (2011) Dindel: accurate indel calls from short-read data. Genome Res., 21, 961-973.
23. Gymrek, M., Golan, D., Rosset, S. and Erlich, Y. (2012) lobSTR: a short tandem repeat profiler for personal genomes. Genome Res., 22, 1154-1162.
24. Schneeberger, K., Ossowski, S., Ott, F., Klein, J.D., Wang, X., Lanz, C., Smith, L.M., Cao, J., Fitz, J., Warthmann, N. et al. (2011) Reference-guided assembly of four diverse Arabidopsis thaliana genomes. Proc. Natl Acad. Sci. USA, 108, 10249-10254.
25. Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
26. Lee, S., Hormozdiari, F., Alkan, C. and Brudno, M. (2009) MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat. Methods, 6, 473-474.
27. Gan, X., Stegle, O., Behr, J., Steffen, J.G., Drewe, P., Hildebrand, K.L., Lyngsoe, R., Schultheiss, S.J., Osborne, E.J., Sreedharan, V.T. et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature, 477, 419-423.
28. Highnam, G., Franck, C., Martin, A., Stephens, C., Puthige, A. and Mittelman, D. (2012) Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles. Nucleic Acids Res., 41, e32.
29. Neuman, J.A., Isakov, O. and Shomron, N. (2012) Analysis of insertion deletion from deep-sequencing data: software evaluation for optimal detection. Brief. Bioinform., 14, 46-55.
30. Mirkin, S.M. (2006) DNA structures, repeat expansions and human hereditary disorders. Curr. Opin. Struct. Biol., 16, 351-358.
31. McIvor, E.I., Polak, U. and Napierala, M. (2010) New insights into repeat instability: role of RNA.DNA hybrids. RNA Biol., 7, 551-558.
32. Dere, R., Napierala, M., Ranum, L.P.W. and Wells, R.D. (2004) Hairpin structure-forming propensity of the (CCTG.CAGG) tetranucleotide repeats contributes to the genetic instability associated with myotonic dystrophy type 2. J. Biol. Chem., 279, 41715-41726.
33. Edamura, K.N., Leonard, M.R. and Pearson, C.E. (2005) Role of replication and CpG methylation in fragile X syndrome CGG deletions in primate cells. Am. J. Hum. Genet., 76, 302-311.
34. Soragni, E., Herman, D., Dent, S.Y.R., Gottesfeld, J.M., Wells, R.D. and Napierala, M. (2008) Long intronic GAA.TTC repeats induce epigenetic changes and reporter gene silencing in a molecular model of Friedreich Ataxia. Nucleic Acids Res., 36, 6056-6065.
35. Costas, C., de la Paz Sanchez, M., Stroud, H., Yu, Y., Oliveros, J.C., Feng, S., Benguria, A., Lpez-Vidriero, I., Zhang, X., Solano, R. et al. (2011) Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks. Nat. Struct. Mol. Biol., 18, 395-400.
36. Kovtun, I.V. and McMurray, C.T. (2008) Features of trinucleotide repeat instability in vivo. Cell Res., 18, 198-213.
37. Cleary, J.D. and Pearson, C.E. (2003) The Contribution of cis-elements to disease-Associated repeat instability: clinical and experimental evidence. Cytogenet. Genome Res., 100, 25-55.
38. Xie, C. and Tammi, M. (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics, 10, 80.
39. Yoon, S., Xuan, Z., Makarov, V., Ye, K. and Sebat, J. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-1592.
40. Xi, R., Hadjipanayis, A.G., Luquette, L.J., Kim, T.M., Lee, E., Zhang, J., Johnson, M.D., Muzny, D.M., Wheeler, D.A., Gibbs, R.A. et al. (2011) Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc. Natl Acad. Sci. USA, 108, E1128-E1136.
41. Medvedev, P., Stanciu, M. and Brudno, M. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6, S13-S20.
42. Chen, K., Wallis, J.W., McLellan, M.D., Larson, D.E., Kalicki, J.M., Pohl, C.S., McGrath, S.D., Wendl, M.C., Zhang, Q., Locke, D.P. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
43. Payseur, B.A., Jing, P. and Haasl, R.J. (2011) A genomic portrait of human microsatellite variation. Mol. Biol. Evol., 28, 303-312.
44. 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.
45. 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.