In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

Nucleic Acids Research

Volumn 41, Issue 6, 2013, Pages

  Ivanov, Maxim ^a   Kals, Mart ^b   Kacevska, Marina ^a   Metspalu, Andres ^b,c   Ingelman Sundberg, Magnus ^a   Milani, Lili ^b  

^a KAROLINSKA INSTITUTE   (Sweden)

^b UNIVERSITY OF TARTU   (Estonia)

^c UNIVERSITY OF TARTU   (Estonia)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; DRUG ABSORPTION; DRUG DISTRIBUTION; DRUG EXCRETION; DRUG METABOLISM; GENE LIBRARY; GENE SEQUENCE; GENE TARGETING; GENETIC PROCEDURES; IN SOLUTION HYBRID CAPTURE; PRIORITY JOURNAL; PYROSEQUENCING; VALIDATION STUDY;

ALGORITHMS; DNA METHYLATION; ENZYMES; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PHARMACEUTICAL PREPARATIONS; SEQUENCE ANALYSIS, DNA; SULFITES;

EID: 84876042374     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1467     Document Type: Article

References (19)

1. Gopalakrishnan, S., Van Emburgh, B.O. and Robertson, K.D. (2008) DNA methylation in development and human disease. Mutat. Res., 647, 30-38.
2. Laird, P.W. (2010) Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
3. Metzker, M.L. (2010) Sequencing technologies-the next generation. Nat. Rev. Genet., 11, 31-46.
4. Fouse, S.D., Nagarajan, R.O. and Costello, J.F. (2010) Genome-scale DNA methylation analysis. Epigenomics, 2, 105-117.
5. Mamanova, L., Coffey, A.J., Scott, C.E., Kozarewa, I., Turner, E.H., Kumar, A., Howard, E., Shendure,J. and Turner, D.J. (2010) Target-enrichment strategies for next-generation sequencing. Nat. Methods, 7, 111-118.
6. Hodges, E., Smith, A.D., Kendall, J., Xuan, Z., Ravi, K., Rooks, M., Zhang, M.Q., Ye, K., Bhattacharjee, A., Brizuela, L. et al. (2009) High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res., 19, 1593-1605.
7. Ball, M.P., Li, J.B., Gao, Y., Lee, J.H., LeProust, E.M., Park, I.H., Xie, B., Daley, G.Q. and Church, G.M. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol., 27, 361-368.
8. Deng, J., Shoemaker, R., Xie, B., Gore, A., LeProust, E.M., Antosiewicz-Bourget, J., Egli, D., Maherali, N., Park, I.H., Yu, J. et al. (2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat. Biotechnol., 27, 353-360.
9. Nautiyal, S., Carlton, V.E., Lu, Y., Ireland, J.S., Flaucher, D., Moorhead, M., Gray, J.W., Spellman, P., Mindrinos, M., Berg, P. et al. (2010) High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proc. Natl Acad. Sci. USA, 107, 12587-12592.
10. Varley, K.E. and Mitra, R.D. (2010) Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. Genome Res., 20, 1279-1287.
11. Lee, E.J., Pei, L., Srivastava, G., Joshi, T., Kushwaha, G., Choi, J.H., Robertson, K.D., Wang, X., Colbourne, J.K., Zhang, L. et al. (2011) Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing. Nucleic Acids Res., 39, e127.
12. Komori, H.K., LaMere, S.A., Torkamani, A., Hart, G.T., Kotsopoulos, S., Warner, J., Samuels, M.L., Olson, J., Head, S.R., Ordoukhanian, P. et al. (2011) Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res., 21, 1738-1745.
13. Wang, J., Jiang, H., Ji, G., Gao, F., Wu, M., Sun, J., Luo, H., Wu, J., Wu,R. and Zhang, X. (2011) High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing. BMC Genomics, 12, 597.
14. Dedeurwaerder, S., Defrance, M., Calonne, E., Denis, H., Sotiriou,C. and Fuks, F. (2011) Evaluation of the Infinium Methylation 450K technology. Epigenomics, 3, 771-784.
15. Krueger,F. and Andrews, S.R. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-1572.
16. 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.
17. Newcombe, R.G. (1998) Two-sided confidence intervals for the single proportion: comparison of seven methods. Stat. Med., 17, 857-872.
18. Hughes, T.R., Mao, M., Jones, A.R., Burchard, J., Marton, M.J., Shannon, K.W., Lefkowitz, S.M., Ziman, M., Schelter, J.M., Meyer, M.R. et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol., 19, 342-347.
19. Irizarry, R.A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M. et al. (2009) The human colon cancer methylome shows similar hypoand hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.