Update README.md

README.md

@@ -55,6 +55,164 @@ Additional documentations are avaialble [here](https://github.com/badozor/mgmtst
 
 ## Unexhaustive References ##
   * Bady, P., D. Sciuscio, A.-C. Diserens, J. Bloch, M. J. van den Bent, C. Marosi, P.-Y. Dietrich, M. Weller, L. Mariani, F. L. Heppner, D. R. McDonald, D. Lacombe, R. Stupp, M. Delorenzi, and M. E. Hegi. (2012). MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropathologica 124:547-560. PubMed:http://www.ncbi.nlm.nih.gov/pubmed/22810491
+  * van den Bent MJ, Erdem-Eraslan L, Idbaih A, de Rooi J, Eilers PHC, Spliet WGM, den Dunnen WFA, Tijssen C, Wesseling P, Sillevis Smitt PAEet al (2013) MGMT-STP27 Methylation Status as Predictive Marker for Response to PCV in Anaplastic Oligodendrogliomas and Oligoastrocytomas. A Report from EORTC Study 26951. Clinical Cancer Research 19: 5513-5522. PubMed: http://www.ncbi.nlm.nih.gov/pubmed/23948976
+  * 
+ 
+
+## References related to the model [2015-07-09 from pubmed] ##
+  *Wesseling P, van den Bent M, Perry A. Oligodendroglioma: pathology, molecular 
+mechanisms and markers. Acta Neuropathol. 2015 Jun;129(6):809-27. doi:
+10.1007/s00401-015-1424-1. Epub 2015 May 6. PubMed PMID: 25943885; PubMed Central
+PMCID: PMC4436696.
+
+  *Vigneswaran K, Neill S, Hadjipanayis CG. Beyond the World Health Organization 
+grading of infiltrating gliomas: advances in the molecular genetics of glioma
+classification. Ann Transl Med. 2015 May;3(7):95. doi:
+10.3978/j.issn.2305-5839.2015.03.57. Review. PubMed PMID: 26015937; PubMed
+Central PMCID: PMC4430738.
+
+  *van Thuijl HF, Mazor T, Johnson BE, Fouse SD, Aihara K, Hong C, Malmström A,
+Hallbeck M, Heimans JJ, Kloezeman JJ, Stenmark-Askmalm M, Lamfers ML, Saito N,
+Aburatani H, Mukasa A, Berger MS, Söderkvist P, Taylor BS, Molinaro AM, Wesseling
+P, Reijneveld JC, Chang SM, Ylstra B, Costello JF. Evolution of DNA repair
+defects during malignant progression of low-grade gliomas after temozolomide
+treatment. Acta Neuropathol. 2015 Apr;129(4):597-607. doi:
+10.1007/s00401-015-1403-6. Epub 2015 Feb 28. PubMed PMID: 25724300; PubMed
+Central PMCID: PMC4482618.
+
+  *Kurscheid S, Bady P, Sciuscio D, Samarzija I, Shay T, Vassallo I, Criekinge
+WV, Daniel RT, van den Bent MJ, Marosi C, Weller M, Mason WP, Domany E, Stupp R, 
+Delorenzi M, Hegi ME. Chromosome 7 gain and DNA hypermethylation at the HOXA10
+locus are associated with expression of a stem cell related HOX-signature in
+glioblastoma. Genome Biol. 2015 Jan 27;16:16. doi: 10.1186/s13059-015-0583-7.
+PubMed PMID: 25622821; PubMed Central PMCID: PMC4342872.
+
+  *Le Rhun E, Taillibert S, Chamberlain MC. The future of high-grade glioma:
+Where we are and where are we going. Surg Neurol Int. 2015 Feb 13;6(Suppl
+1):S9-S44. doi: 10.4103/2152-7806.151331. eCollection 2015. Erratum in: Surg
+Neurol Int. 2015 Mar 5;6:37. Rhun, Emilie Le [corrected to Le Rhun, Emilie].
+PubMed PMID: 25722939; PubMed Central PMCID: PMC4338495.
+
+  *Wiestler B, Capper D, Hovestadt V, Sill M, Jones DT, Hartmann C, Felsberg J,
+Platten M, Feiden W, Keyvani K, Pfister SM, Wiestler OD, Meyermann R,
+Reifenberger G, Pietsch T, von Deimling A, Weller M, Wick W. Assessing CpG island
+methylator phenotype, 1p/19q codeletion, and MGMT promoter methylation from
+epigenome-wide data in the biomarker cohort of the NOA-04 trial. Neuro Oncol.
+2014 Dec;16(12):1630-8. doi: 10.1093/neuonc/nou138. Epub 2014 Jul 15. PubMed
+PMID: 25028501; PubMed Central PMCID: PMC4232086.
+
+  *Paulsson AK, Holmes JA, Peiffer AM, Miller LD, Liu W, Xu J, Hinson WH, Lesser 
+GJ, Laxton AW, Tatter SB, Debinski W, Chan MD. Comparison of clinical outcomes
+and genomic characteristics of single focus and multifocal glioblastoma. J
+Neurooncol. 2014 Sep;119(2):429-35. doi: 10.1007/s11060-014-1515-1. Epub 2014 Jul
+3. PubMed PMID: 24990827; PubMed Central PMCID: PMC4146694.
+
+  *Molenaar RJ, Verbaan D, Lamba S, Zanon C, Jeuken JW, Boots-Sprenger SH,
+Wesseling P, Hulsebos TJ, Troost D, van Tilborg AA, Leenstra S, Vandertop WP,
+Bardelli A, van Noorden CJ, Bleeker FE. The combination of IDH1 mutations and
+MGMT methylation status predicts survival in glioblastoma better than either IDH1
+or MGMT alone. Neuro Oncol. 2014 Sep;16(9):1263-73. doi: 10.1093/neuonc/nou005.
+Epub 2014 Feb 6. PubMed PMID: 24510240; PubMed Central PMCID: PMC4136888.
+
+  *Kanemoto M, Shirahata M, Nakauma A, Nakanishi K, Taniguchi K, Kukita Y,
+Arakawa Y, Miyamoto S, Kato K. Prognostic prediction of glioblastoma by
+quantitative assessment of the methylation status of the entire MGMT promoter
+region. BMC Cancer. 2014 Aug 30;14:641. doi: 10.1186/1471-2407-14-641. PubMed
+PMID: 25175833; PubMed Central PMCID: PMC4161852.
+
+  *Collins VP, Ichimura K, Di Y, Pearson D, Chan R, Thompson LC, Gabe R, Brada
+M, Stenning SP; BR12 Collaborators. Prognostic and predictive markers in
+recurrent high grade glioma; results from the BR12 randomised trial. Acta
+Neuropathol Commun. 2014 Jun 20;2:68. doi: 10.1186/2051-5960-2-68. PubMed PMID:
+24952577; PubMed Central PMCID: PMC4229733.
+
+  *Xu M, Nekhayeva I, Cross CE, Rondelli CM, Wickliffe JK, Abdel-Rahman SZ.
+Influence of promoter/enhancer region haplotypes on MGMT transcriptional
+regulation: a potential biomarker for human sensitivity to alkylating agents.
+Carcinogenesis. 2014 Mar;35(3):564-71. doi: 10.1093/carcin/bgt355. Epub 2013 Oct 
+25. PubMed PMID: 24163400; PubMed Central PMCID: PMC3941746.
+
+  *Quillien V, Lavenu A, Sanson M, Legrain M, Dubus P, Karayan-Tapon L, Mosser
+J, Ichimura K, Figarella-Branger D. Outcome-based determination of optimal
+pyrosequencing assay for MGMT methylation detection in glioblastoma patients. J
+Neurooncol. 2014 Feb;116(3):487-96. doi: 10.1007/s11060-013-1332-y. Epub 2014 Jan
+14. PubMed PMID: 24420923; PubMed Central PMCID: PMC3905192.
+
+  *Hiddingh L, Tannous BA, Teng J, Tops B, Jeuken J, Hulleman E, Boots-Sprenger 
+SH, Vandertop WP, Noske DP, Kaspers GJ, Wesseling P, Wurdinger T. EFEMP1 induces 
+γ-secretase/Notch-mediated temozolomide resistance in glioblastoma. Oncotarget.
+2014 Jan 30;5(2):363-74. PubMed PMID: 24495907; PubMed Central PMCID: PMC3964213.
+
+  *Shen D, Liu T, Lin Q, Lu X, Wang Q, Lin F, Mao W. MGMT promoter methylation
+correlates with an overall survival benefit in Chinese high-grade glioblastoma
+patients treated with radiotherapy and alkylating agent-based chemotherapy: a
+single-institution study. PLoS One. 2014 Sep 11;9(9):e107558. doi:
+10.1371/journal.pone.0107558. eCollection 2014. PubMed PMID: 25211033; PubMed
+Central PMCID: PMC4161443.
+
+  *Lai RK, Chen Y, Guan X, Nousome D, Sharma C, Canoll P, Bruce J, Sloan AE,
+Cortes E, Vonsattel JP, Su T, Delgado-Cruzata L, Gurvich I, Santella RM, Ostrom
+Q, Lee A, Gregersen P, Barnholtz-Sloan J. Genome-wide methylation analyses in
+glioblastoma multiforme. PLoS One. 2014 Feb 21;9(2):e89376. doi:
+10.1371/journal.pone.0089376. eCollection 2014. PubMed PMID: 24586730; PubMed
+Central PMCID: PMC3931727.
+
+  *Oberstadt MC, Bien-Möller S, Weitmann K, Herzog S, Hentschel K, Rimmbach C,
+Vogelgesang S, Balz E, Fink M, Michael H, Zeden JP, Bruckmüller H, Werk AN,
+Cascorbi I, Hoffmann W, Rosskopf D, Schroeder HW, Kroemer HK. Epigenetic
+modulation of the drug resistance genes MGMT, ABCB1 and ABCG2 in glioblastoma
+multiforme. BMC Cancer. 2013 Dec 31;13:617. doi: 10.1186/1471-2407-13-617. PubMed
+PMID: 24380367; PubMed Central PMCID: PMC3890604.
+
+  *Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S,
+Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, 
+Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung
+WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, 
+Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A,
+Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati
+R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson
+R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G,
+Chin L; TCGA Research Network. The somatic genomic landscape of glioblastoma.
+Cell. 2013 Oct 10;155(2):462-77. doi: 10.1016/j.cell.2013.09.034. Erratum in:
+Cell. 2014 Apr 24;157(3):753. PubMed PMID: 24120142; PubMed Central PMCID:
+PMC3910500.
+
+  *Thon N, Kreth S, Kreth FW. Personalized treatment strategies in glioblastoma:
+MGMT promoter methylation status. Onco Targets Ther. 2013 Sep 27;6:1363-72. doi: 
+10.2147/OTT.S50208. Review. PubMed PMID: 24109190; PubMed Central PMCID:
+PMC3792931.
+
+  *Wiestler B, Claus R, Hartlieb SA, Schliesser MG, Weiss EK, Hielscher T,
+Platten M, Dittmann LM, Meisner C, Felsberg J, Happold C, Simon M, Nikkhah G,
+Papsdorf K, Steinbach JP, Sabel M, Grimm C, Weichenhan D, Tews B, Reifenberger G,
+Capper D, Müller W, Plass C, Weller M, Wick W; Neuro-oncology Working Group (NOA)
+of the German Cancer Society. Malignant astrocytomas of elderly patients lack
+favorable molecular markers: an analysis of the NOA-08 study collective. Neuro
+Oncol. 2013 Aug;15(8):1017-26. doi: 10.1093/neuonc/not043. Epub 2013 Apr 17.
+PubMed PMID: 23595628; PubMed Central PMCID: PMC3714152.
+
+  *Qiu S, Lin S, Hu D, Feng Y, Tan Y, Peng Y. Interactions of
+miR-323/miR-326/miR-329 and miR-130a/miR-155/miR-210 as prognostic indicators for
+clinical outcome of glioblastoma patients. J Transl Med. 2013 Jan 9;11:10. doi:
+10.1186/1479-5876-11-10. PubMed PMID: 23302469; PubMed Central PMCID: PMC3551827.
+
+  *Weller M, Stupp R, Hegi ME, van den Bent M, Tonn JC, Sanson M, Wick W,
+Reifenberger G. Personalized care in neuro-oncology coming of age: why we need
+MGMT and 1p/19q testing for malignant glioma patients in clinical practice. Neuro
+Oncol. 2012 Sep;14 Suppl 4:iv100-8. doi: 10.1093/neuonc/nos206. Review. PubMed
+PMID: 23095825; PubMed Central PMCID: PMC3480248.
+
+  *McDonald KL, Aw G, Kleihues P. Role of Biomarkers in the Clinical Management 
+of Glioblastomas: What are the Barriers and How Can We Overcome Them? Front
+Neurol. 2013 Jan 18;3:188. doi: 10.3389/fneur.2012.00188. eCollection 2012.
+PubMed PMID: 23346075; PubMed Central PMCID: PMC3548232.
+
+  *Zinn PO, Sathyan P, Mahajan B, Bruyere J, Hegi M, Majumder S, Colen RR. A
+novel volume-age-KPS (VAK) glioblastoma classification identifies a prognostic
+cognate microRNA-gene signature. PLoS One. 2012;7(8):e41522. doi:
+10.1371/journal.pone.0041522. Epub 2012 Aug 3. PubMed PMID: 22870228; PubMed
+Central PMCID: PMC3411674.
+
 
 ## Depends ##
 R (>= 3.1.2), minfi, lumi, ade4,methylumi,MASS