The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process

Nucleic Acids Research

Volumn 40, Issue 6, 2012, Pages 2426-2431

  Heinrich, Verena ^a   Stange, Jens ^b   Dickhaus, Thorsten ^b   Imkeller, Peter ^b   Krüger, Ulrike ^a   Bauer, Sebastian ^a   Mundlos, Stefan ^a   Robinson, Peter N ^a   Hecht, Jochen ^a   Krawitz, Peter M ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b HUMBOLDT UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANALYTICAL ERROR; ARTICLE; GENE AMPLIFICATION; GENE FREQUENCY; GENE LOCUS; GENE TECHNOLOGY; GENETIC VARIABILITY; HETEROZYGOSITY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STOCHASTIC MODEL;

ALLELES; EXOME; GENE FREQUENCY; HETEROZYGOTE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA; STOCHASTIC PROCESSES;

EID: 84859341137     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1073     Document Type: Article

References (19)

1. Ng, S.B., Buckingham, K.J., Lee, C., Bigham, A.W., Tabor, H.K., Dent, K.M., Huff, C.D., Shannon, P.T., Jabs, E.W., Nickerson, D.A. et al. (2010) Exome sequencing identifies the cause of a Mendelian disorder. Nat. Genet., 42, 30-35
2. Robinson, P.N., Krawitz, P. and Mundlos, S. (2011) Strategies for exome and genome sequence data analysis in disease gene discovery projects. Clin. Genet., 80, 127-132
3. Choi, M., Scholl, U.I., Ji, W., Liu, T., Tikhonova, I.R., Zumbo, P., Nayir, A., Bakkalolu, A., zen, S., Sanjad, S. et al. (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Pro. Natl Acad. Sci. USA, 106, 19096-19101
4. Nothnagel, M., Herrmann, A., Wolf, A., Schreiber, S., Platzer, M., Siebert, R., Krawczak, M. and Hampe, J. (2010) Technology specific error signatures in the 1000 Genomes Project data. Hum. Genet., 130, 505-516
5. Harismendy, O., Ng, P.C., Strausberg, R.L., Wang, X., Stockwell, T.B., Beeson, K.Y., Schork, N.J., Murray, S.S., Topol, E.J., Levy, S. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Bio., 10, R32
6. Li, H., Ruan, J. and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genomes Res., 18, 1851-1858
7. Li, R., Li, Y., Kristiansen, K. and Wang, J. (2008) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713-714 (Pubitemid 351321217)
8. Goya, R., Sun, M.G.F., Morin, R.D., Leung, G., Ha, G., Wiegand, K.C., Senz, J., Crisan, A., Marra, M.A., Hirst, M. et al. (2010) SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics, 26, 730-736
9. Athreya, K.B. and Ney, P.E. (1972) Branching Processes. Springer, Berlin
10. Yakovlev, A.Y. and Yanev, N.M. (2009) Relative frequencies in multitype branching processes. Ann. Appl. Probab., 19, 1-14
11. Polya, G. and Szegö , G. (1970) Problems and Theorems in Analysis I. Springer, Berlin
12. Pruitt, K.D., Harrow, J., Harte, R.A., Wallin, C., Diekhans, M., Maglott, D.R., Searle, S., Farrell, C.M., Loveland, J.E., Ruef, B.J. et al. (2009) The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes. Genome Res., 19, 1316-1323
13. Hercus, C. (2011) Novoalign V2.07. www.novocraft.com (3 August 2011, date last accessed)
14. Bell, C.J., Dinwiddie, D.L., Miller, N.A., Hateley, S.L., Ganusova, E.E., Mudge, J., Langley, R.J., Zhang, L., Lee, C.C., Schilkey, F.D. et al. (2011) Carrier testing for severe childhood recessive disease by next generation sequencing. Sci. Trans. Med., 3, 64-69
15. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2010) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079
16. Degner, J.F., Marioni, J.C., Pai, A., Pickrell, J.K., Nkadori, E., Gilad, Y. and Pritchard, J.K. (2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics, 25, 3207-3212
17. Krawitz, P., Rdelsperger, C., JĹger, M., Jostins, L., Bauer, S. and Robinson, P.N. (2010) Microindel detection in short-read sequence data. Bioinformatics, 26, 722-729
18. Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., Hall, K.P., Evers, D.J., Barnes, C.L., Bignell, H.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59
19. Timp, W., Mirsaidov, U.M., Wang, D., Comer, J., Aksimentiev, A. and Timp, G. (2010) Nanopore sequencing: electrical measurements of the code of life. IEEE Trans. Nanotechnol., 9, 281-294.