Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles

Nucleic Acids Research

Volumn 41, Issue 1, 2013, Pages

  Highnam, Gareth ^a   Franck, Christopher ^a,b   Martin, Andy ^a   Stephens, Calvin ^a   Puthige, Ashwin ^a   Mittelman, David ^a,b  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL ERROR; ARTICLE; BAYES THEOREM; COMPUTER LANGUAGE; COMPUTER PROGRAM; GENOME ANALYSIS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; INTERNET; MICROSATELLITE MARKER; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

BAYES THEOREM; GENOME, HUMAN; GENOMICS; GENOTYPE; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICROSATELLITE REPEATS; SOFTWARE;

EID: 84871774158     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks981     Document Type: Article

References (23)

1. Mirkin, S.M. (2007) Expandable DNA repeats and human disease. Nature, 447, 932-940.
2. Lopez Castel, A., 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.
3. Orr, H.T. (2009) Unstable nucleotide repeat minireview series: a molecular biography of unstable repeat disorders. J. Biol. Chem., 284, 7405.
4. Albrecht, A. and Mundlos, S. (2005) The other trinucleotide repeat: polyalanine expansion disorders. Curr. Opin. Genet. Dev., 15, 285-293.
5. 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.
6. Fonville, N.C., Ward, R.M. and Mittelman, D. (2011) Stress-induced modulators of repeat instability and genome evolution. J. Mol. Microbiol. Biotechnol., 21, 36-44.
7. Glen, C.D. and Dubrova, Y.E. (2012) Exposure to anticancer drugs can result in transgenerational genomic instability in mice. Proc. Natl. Acad. Sci. USA, 109, 2984-2988.
8. Loeb, L.A., Loeb, K.R. and Anderson, J.P. (2003) Multiple mutations and cancer. Proc. Natl. Acad. Sci. USA, 100, 776-781.
9. Ge, J., Eisenberg, A. and Budowle, B. (2012) Developing criteria and data to determine best options for expanding the core CODIS loci. Investig. Genet., 3, 1.
10. Gymrek, M., Golan, D., Rosset, S. and Erlich, Y. (2012) lobSTR: a short tandem repeat profiler for personal genomes. Genome Res., 22, 1154-1162.
11. 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.
12. Mackay, T.F.C., Richards, S., Stone, E.A., Barbadilla, A., Ayroles, J.F., Zhu, D., Casillas, S., Han, Y., Magwire, M.M., Cridland, J.M. et al. (2012) The Drosophila melanogaster Genetic Reference Panel. Nature, 482, 173-178.
13. DePristo, M.A., Banks, E., Poplin, R., Garimella, K.V., Maguire, J.R., Hartl, C., Philippakis, A.A., del Angel, G., Rivas, M.A., Hanna, M. et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491-498.
14. Challis, D., Yu, J., Evani, U.S., Jackson, A.R., Paithankar, S., Coarfa, C., Milosavljevic, A., Gibbs, R.A. and Yu, F. (2012) An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics, 13, 8.
15. 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.
16. 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
17. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
18. Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T. et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.
19. Li, H. and Homer, N. (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform., 11, 473-483.
20. Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods., 9, 357-359.
21. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
22. Lunter, G. and Goodson, M. (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res., 21, 936-939.
23. Douglas, J.A., Skol, A.D. and Boehnke, M. (2002) Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear-family data. Am. J. Hum. Genet., 70, 487-495.