MethyQA: A pipeline for bisulfite-treated methylation sequencing quality assessment

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Sun, Shuying ^a,b   Noviski, Aaron ^c   Yu, Xiaoqing ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b TEXAS STATE UNIVERSITY   (United States)

^c Case Western Reserve University   (United States)

Author keywords

Alignment; BRAT; DNA methylation; Next generation sequencing; Quality assessment

Indexed keywords

BRAT; DNA METHYLATION; EPIGENETIC MODIFICATION; NEXT-GENERATION SEQUENCING; OPEN-SOURCE SOFTWARES; PCR AMPLIFICATION BIAS; QUALITY ASSESSMENT; SEQUENCE STRUCTURE;

ALIGNMENT; GENE EXPRESSION; METHYLATION; PIPELINES; POLYMERASE CHAIN REACTION; SOFTWARE PACKAGES;

ALKYLATION;

DNA; HYDROGEN SULFITE; SULFITE;

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; DNA METHYLATION; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY; POLYMERASE CHAIN REACTION;

DNA; DNA METHYLATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SOFTWARE; SULFITES;

EID: 84882504928     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-259     Document Type: Article

References (43)

1. Chung W, Kwabi-Addo B, Ittmann M, Jelinek J, Shen L, Yu Y, Issa JP. Identification of novel tumor markers in prostate, colon and breast cancer by unbiased methylation profiling. PLoS One 2008, 3(4):e2079. 10.1371/journal.pone.0002079, 2323612, 18446232.
2. Fiegl H, Millinger S, Goebel G, Muller-Holzner E, Marth C, Laird PW, Widschwendter M. Breast cancer DNA methylation profiles in cancer cells and tumor stroma: association with HER-2/neu status in primary breast cancer. Cancer Res 2006, 66(1):29-33. 10.1158/0008-5472.CAN-05-2508, 16397211.
3. Huang TH, Perry MR, Laux DE. Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet 1999, 8(3):459-470. 10.1093/hmg/8.3.459, 9949205.
4. Khalili A, Potter D, Yan P, Li L, Gray J, Huang T, Lin S. Gamma-normal-gamma mixture model for detecting differentially methylated Loci in three breast cancer cell lines. Cancer Inform 2007, 3:43-54. 2675845, 19455234.
5. Lin HJ, Zuo T, Lin CH, Kuo CT, Liyanarachchi S, Sun S, Shen R, Deatherage DE, Potter D, Asamoto L, et al. Breast cancer-associated fibroblasts confer AKT1-mediated epigenetic silencing of Cystatin M in epithelial cells. Cancer Res 2008, 68(24):10257-10266. 10.1158/0008-5472.CAN-08-0288, 2821873, 19074894.
6. Tan LW, Bianco T, Dobrovic A. Variable promoter region CpG island methylation of the putative tumor suppressor gene Connexin 26 in breast cancer. Carcinogenesis 2002, 23(2):231-236. 10.1093/carcin/23.2.231, 11872627.
7. Widschwendter M, Jones PA. DNA methylation and breast carcinogenesis. Oncogene 2002, 21(35):5462-5482. 10.1038/sj.onc.1205606, 12154408.
8. Yan PS, Perry MR, Laux DE, Asare AL, Caldwell CW, Huang TH. CpG island arrays: an application toward deciphering epigenetic signatures of breast cancer. Clin Cancer Res 2000, 6(4):1432-1438.
9. Yang X, Yan L, Davidson NE. DNA methylation in breast cancer. Endocr Relat Cancer 2001, 8(2):115-127. 10.1677/erc.0.0080115, 11446343.
10. Zhu W, Qin W, Hewett JE, Sauter ER. Quantitative evaluation of DNA hypermethylation in malignant and benign breast tissue and fluids. Int J Cancer 2010, 126(2):474-482. 10.1002/ijc.24728, 3398695, 19618401.
11. Kim MS, Lee J, Sidransky D. DNA methylation markers in colorectal cancer. Cancer Metastasis Rev 2010, 29(1):181-206. 10.1007/s10555-010-9207-6, 20135198.
12. Lin J, Lai M, Huang Q, Ma Y, Cui J, Ruan W. Methylation patterns of IGFBP7 in colon cancer cell lines are associated with levels of gene expression. J Pathol 2007, 212(1):83-90. 10.1002/path.2144, 17334979.
13. Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP. CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A 1999, 96(15):8681-8686. 10.1073/pnas.96.15.8681, 17576, 10411935.
14. Zitt M, Muller HM. DNA methylation in colorectal cancer-impact on screening and therapy monitoring modalities?. Dis Markers 2007, 23(1-2):51-71.
15. Sun S, Chen Z, Yan PS, Huang YW, Huang TH, Lin S. Identifying hypermethylated CpG islands using a quantile regression model. BMC Bioinforma 2011, 12:54.
16. Esteller M, Corn PG, Baylin SB, Herman JG. A gene hypermethylation profile of human cancer. Cancer Res 2001, 61(8):3225-3229.
17. Suijkerbuijk KP, van Diest PJ, van der Wall E. Improving early breast cancer detection: focus on methylation. Ann Oncol 2011, 22(1):24-29. 10.1093/annonc/mdq305, 20591821.
18. Strathdee G, Brown R. Aberrant DNA methylation in cancer: potential clinical interventions. Expert Rev Mol Med 2002, 4(4):1-17.
19. Wei SH, Brown R, Huang TH. Aberrant DNA methylation in ovarian cancer: is there an epigenetic predisposition to drug response?. Ann N Y Acad Sci 2003, 983:243-250. 10.1111/j.1749-6632.2003.tb05979.x, 12724229.
20. Widschwendter M, Menon U. Circulating methylated DNA: a new generation of tumor markers. Clin Cancer Res 2006, 12(24):7205-7208. 10.1158/1078-0432.CCR-06-2531, 17189390.
21. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008, 452(7184):215-219. 10.1038/nature06745, 2377394, 18278030.
22. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2008, 133(3):523-536. 10.1016/j.cell.2008.03.029, 2723732, 18423832.
23. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454(7205):766-770. 2896277, 18600261.
24. Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 2011, 471(7336):68-73. 10.1038/nature09798, 3100360, 21289626.
25. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462(7271):315-322. 10.1038/nature08514, 2857523, 19829295.
26. Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, Carr JM, Khrebtukova I, Luo S, Zhang L, et al. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One 2011, 6(2):e17490. 10.1371/journal.pone.0017490, 3045451, 21364760.
27. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011, 43(8):768-775. 10.1038/ng.865, 3145050, 21706001.
28. Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res 2009, 19(6):1044-1056. 10.1101/gr.088773.108, 2694474, 19273619.
29. Chen PY, Cokus SJ, Pellegrini M. BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinforma 2010, 11:203.
30. Harris EY, Ponts N, Levchuk A, Roch KL, Lonardi S. BRAT: bisulfite-treated reads analysis tool. Bioinformatics 2010, 26(4):572-573. 10.1093/bioinformatics/btp706, 3716225, 20031974.
31. Xi Y, Li W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinforma 2009, 10:232.
32. Pedersen B, Hsieh TF, Ibarra C, Fischer RL. MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics 2011, 27(17):2435-2436. 10.1093/bioinformatics/btr394, 3157921, 21724594.
33. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, et al. SAAP-RRBS: Streamlined Analysis and Annotation Pipeline for Reduced Representation Bisulfite Sequencing. Bioinformatics 2012, 28(16):2180-2181. 10.1093/bioinformatics/bts337, 3413387, 22689387.
34. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 2011, 6(4):468-481. 10.1038/nprot.2010.190, 21412275.
35. Ecker JR. Zeroing in on DNA methylomes with no BS. Nat Methods 2010, 7:435-437. 10.1038/nmeth0610-435, 20508637.
36. Andrews S. FastQC 2010, http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/.
37. Yu X, Guda K, Willis J, Veigl M, Wang Z, Markowitz S, Adams M, Sun S. How well do alignment programs perform on sequencing data with varying qualities and from repetitive regions?. BioData Min 2012, 5:6. 10.1186/1756-0381-5-6, 3414812, 22709551.
38. Hannon GJ. FASTX-Toolkit 2009, http://hannonlab.cshl.edu/fastx_toolkit/.
39. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 2011, 17(1):10-12.
40. Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011, 27(11):1571-1572. 10.1093/bioinformatics/btr167, 3102221, 21493656.
41. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
42. Wu TD, Nacu S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 2010, 26(7):873-881. 10.1093/bioinformatics/btq057, 2844994, 20147302.
43. Harris EY, Ponts N, Le Roch KG, Lonardi S. BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinformatics 2012, 28(13):1795-1796. 10.1093/bioinformatics/bts264, 3381974, 22563065.