TSSV: A tool for characterization of complex allelic variants in pure and mixed genomes

Bioinformatics

Volumn 30, Issue 12, 2014, Pages 1651-1659

  Anvar, Seyed Yahya ^a   Van Der Gaag, Kristiaan J ^a   Van Der Heijden, Jaap W F ^a   Veltrop, Marcel H A M ^a   Vossen, Rolf H A M ^a   De Leeuw, Rick H ^a   Breukel, Cor ^a   Buermans, Henk P J ^a   Verbeek, J Sjef ^a   De Knijff, Peter ^a   Den Dunnen, Johan T ^a   Laros, Jeroen F J ^a,b  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b Netherlands Bioinformatics Centre   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; DMD PROTEIN, HUMAN; DYSTROPHIN; MICROSATELLITE DNA;

ALGORITHM; ALLELE; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; FEMALE; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; MALE; METABOLISM; METHODOLOGY; MUTATION;

ALGORITHMS; ALLELES; DEOXYRIBONUCLEASES; DYSTROPHIN; FEMALE; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MICROSATELLITE REPEATS; MUTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84896970956     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu068     Document Type: Article

References (59)

1. Alkan, C. et al. (2011) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363-376.
2. Anvar, S.Y. (2013a) Allele-specific characterization of STR structures in pure and mixed forensic samples using TSSV, http://dx.doi.org/10.6084/m9. figshare.757791.
3. Anvar, S.Y. (2013b) Characterization of DeNovo structural variations induced by TALENs targeting hDMD in mouse ES cells using TSSV, http://dx.doi.org/10.6084/m9.figshare.757790.
4. Anvar, S.Y. (2013c) Characterizing IonTorrent PGM Error Profiles using TSSV, http://dx.doi.org/10.6084/m9.figshare.757792.
5. Boch, J. (2011) TALEs of genome targeting. Nat. Biotechnol., 29, 135-136.
6. Brook, J.D. et al. (1992) Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3′ end of a transcript encoding a protein kinase family member. Cell, 69, 385.
7. Cermak, T. et al. (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res., 39, e82.
8. Chen, K. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
9. Conrad, D.F. et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature, 464, 704-712.
10. Costello, M. et al. (2013) Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res., 41, e67.
11. de Cid, R. et al. (2009) Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat. Genet., 41, 211-215.
12. DePristo, M.A. et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491-498.
13. Dere, R. et al. (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.
14. Ellegren, H. (2004) Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet., 5, 435-445.
15. Girirajan, S. et al. (2011) Relative burden of large CNVs on a range of neurodeve-lopmental phenotypes. PLoS Genet., 7, e1002334.
16. Goya, R. et al. (2010) SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics, 26, 730-736.
17. Gymrek, M. et al. (2012) lobSTR: A short tandem repeat profiler for personal genomes. Genome Res., 22, 1154-1162.
18. 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.
19. Highnam, G. et al. (2013) Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles. Nucleic Acids Res., 41, e32.
20. Hinds, D.A. et al. (2006) Common deletions and SNPs are in linkage disequilibrium in the human genome. Nat. Genet., 38, 82-85.
21. Hollox, E.J. et al. (2008) Psoriasis is associated with increased beta-defensin genomic copy number. Nat. Genet., 40, 23-25.
22. Iafrate, A.J. et al. (2004) Detection of large-scale variation in the human genome. Nat. Genet., 36, 949-951.
23. Kayser, M. and de Knijff, P. (2011) Improving human forensics through advances in genetics, genomics and molecular biology. Nat. Rev. Genet., 12, 179-192.
24. Kidd, J.M. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56-64.
25. Kim, Y. et al. (2013) TALENs and ZFNs are associated with different mutation signatures. Nat. Methods, 10, 185.
26. Kimura, M. et al. (2009) Rapid variable-number tandem-repeat genotyping for Mycobacterium leprae clinical specimens. J. Clin. Microbiol., 47, 1757-1766.
27. Koboldt, D.C. et al. (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics, 25, 2283-2285.
28. Kremer, E.J. et al. (1991) Mapping of DNA instability at the fragile X to a trinu-cleotide repeat sequence p(CCG)n. Science, 252, 1711-1714.
29. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357-359.
30. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics, 25, 1754-1760.
31. Li, H. and Homer, N. (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform., 11, 473-483.
32. Mahadevan, M. et al. (1992) Myotonic dystrophy mutation: an unstable CTG repeat in the 3' untranslated region of the gene. Science, 255, 1253-1255.
33. McCarroll, S.A. et al. (2009) Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease. Nat. Genet., 41, 1341-1344.
34. McKenna, A. et al. (2010) The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res, 20, 1297-1303.
35. Medvedev, P. et al. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6, S13-S20.
36. Miller, J.C. et al. (2011) A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol., 29, 143-148.
37. Mills, R.E. et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-65.
38. Mirkin, S.M. (2007) Expandable DNA repeats and human disease. Nature, 447, 932-940.
39. Moretti, T.R. et al. (2001) Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples. J. Forensic Sci., 46, 647-660.
40. Pearson, C.E. et al. (2002) Slipped-strand DNAs formed by long (CAG)*(CTG) repeats: slipped-out repeats and slip-out junctions. Nucleic Acids Res., 30, 4534-4547.
41. Pearson, C.E. et al. (2005) Repeat instability: mechanisms of dynamic mutations. Nat. Rev. Genet., 6, 729-742.
42. Pinto, D. et al. (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature, 466, 368-372.
43. Redon, R. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454.
44. Sebat, J. et al. (2004) Large-scale copy number polymorphism in the human genome. Science, 305, 525-528.
45. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
46. Stephens, P.J. et al. (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell, 144, 27-40.
47. Sudmant, P.H. et al. (2010) Diversity of human copy number variation and multicopy genes. Science, 330, 641-646.
48. Sutherland, G.R. and Richards, R.I. (1995) Simple tandem DNA repeats and human genetic disease. Proc. Natl Acad. Sci. USA, 92, 3636-3641.
49. t Hoen, P.A. et al. (2008) Generation and characterization of transgenic mice with the full-length human DMD gene. J. Biol. Chem., 283, 5899-5907.
50. Treangen, T.J. and Salzberg, S.L. (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet., 13, 36-46.
51. Tuzun, E. et al. (2005) Fine-scale structural variation of the human genome. Nat. Genet., 37, 727-732.
52. Veltrop, M.H.A.M. et al. (2013) Generation of embryonic stem cells and mice for duchenne research. PLoS Currents Muscular Dystrophy, 1.
53. Verkerk, A.J. 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.
54. Warshauer, D.H. et al. (2013) STRait Razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data. Forensic Sci. Int. Genet., 7, 409-417.
55. Weber, J.L. and May, P.E. (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet., 44, 388-396.
56. Weischenfeldt, J. et al. (2013) Phenotypic impact of genomic structural variation: insights from and for human disease. Nat. Rev. Genet., 14, 125-138.
57. Wildeman, M. et al. (2008) Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum. Mutat., 29, 6-13.
58. Ye, K. et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.
59. Zhang, F. et al. (2011) Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat. Biotechnol., 29, 149-153.