Meyers PA, Gorlick R. Osteosarcoma. Pediatr Clin N Am. 1997;44(4):973–89.
Article
CAS
Google Scholar
Link MP, Goorin AM, Miser AW, Green AA, Pratt CB, Belasco JB, Pritchard J, Malpas JS, Baker AR, Kirkpatrick JA, et al. The effect of adjuvant chemotherapy on relapse-free survival in patients with osteosarcoma of the extremity. N Engl J Med. 1986;314(25):1600–6.
Article
CAS
PubMed
Google Scholar
Meyers PA, Heller G, Healey J, Huvos A, Lane J, Marcove R, Applewhite A, Vlamis V, Rosen G. Chemotherapy for nonmetastatic osteogenic sarcoma: the memorial Sloan-Kettering experience. J Clin Oncol. 1992;10(1):5–15.
Article
CAS
PubMed
Google Scholar
Provisor AJ, Ettinger LJ, Nachman JB, Krailo MD, Makley JT, Yunis EJ, Huvos AG, Betcher DL, Baum ES, Kisker CT, et al. Treatment of nonmetastatic osteosarcoma of the extremity with preoperative and postoperative chemotherapy: a report from the Children's Cancer group. J Clin Oncol. 1997;15(1):76–84.
Article
CAS
PubMed
Google Scholar
Bielack SS, Kempf-Bielack B, Delling G, Exner GU, Flege S, Helmke K, Kotz R, Salzer-Kuntschik M, Werner M, Winkelmann W, et al. Prognostic factors in high-grade osteosarcoma of the extremities or trunk: an analysis of 1,702 patients treated on neoadjuvant cooperative osteosarcoma study group protocols. J Clin Oncol. 2002;20(3):776–90.
Article
PubMed
Google Scholar
Whelan JS, Jinks RC, McTiernan A, Sydes MR, Hook JM, Trani L, Uscinska B, Bramwell V, Lewis IJ, Nooij MA, et al. Survival from high-grade localised extremity osteosarcoma: combined results and prognostic factors from three European osteosarcoma intergroup randomised controlled trials. Ann Oncol. 2012;23(6):1607–16.
Article
CAS
PubMed
Google Scholar
Meyers PA, Schwartz CL, Krailo MD, Healey JH, Bernstein ML, Betcher D, Ferguson WS, Gebhardt MC, Goorin AM, Harris M, et al. Osteosarcoma: the addition of muramyl tripeptide to chemotherapy improves overall survival--a report from the Children's oncology group. J Clin Oncol. 2008;26(4):633–8.
Article
CAS
PubMed
Google Scholar
Kung FH, Pratt CB, Vega RA, Jaffe N, Strother D, Schwenn M, Nitschke R, Homans AC, Holbrook CT, Golembe B, et al. Ifosfamide/etoposide combination in the treatment of recurrent malignant solid tumors of childhood. A pediatric oncology group phase II study. Cancer. 1993;71(5):1898–903.
Article
CAS
PubMed
Google Scholar
Miser JS, Kinsella TJ, Triche TJ, Tsokos M, Jarosinski P, Forquer R, Wesley R, Magrath I. Ifosfamide with mesna uroprotection and etoposide: an effective regimen in the treatment of recurrent sarcomas and other tumors of children and young adults. J Clin Oncol. 1987;5(8):1191–8.
Article
CAS
PubMed
Google Scholar
Fuchs N, Bielack SS, Epler D, Bieling P, Delling G, Korholz D, Graf N, Heise U, Jurgens H, Kotz R, et al. Long-term results of the co-operative German-Austrian-Swiss osteosarcoma study group's protocol COSS-86 of intensive multidrug chemotherapy and surgery for osteosarcoma of the limbs. Ann Oncol. 1998;9(8):893–9.
Article
CAS
PubMed
Google Scholar
International HapMap C. A haplotype map of the human genome. Nature. 2005;437(7063):1299–320.
Article
CAS
Google Scholar
Deeken J. The Affymetrix DMET platform and pharmacogenetics in drug development. Curr Opin Mol Ther. 2009;11(3):260–8.
CAS
PubMed
Google Scholar
Iyer L, Das S, Janisch L, Wen M, Ramirez J, Karrison T, Fleming GF, Vokes EE, Schilsky RL, Ratain MJ. UGT1A1*28 polymorphism as a determinant of irinotecan disposition and toxicity. Pharmacogenomics J. 2002;2(1):43–7.
Article
CAS
PubMed
Google Scholar
Evans WE, Hon YY, Bomgaars L, Coutre S, Holdsworth M, Janco R, Kalwinsky D, Keller F, Khatib Z, Margolin J, et al. Preponderance of thiopurine S-methyltransferase deficiency and heterozygosity among patients intolerant to mercaptopurine or azathioprine. J Clin Oncol. 2001;19(8):2293–301.
Article
CAS
PubMed
Google Scholar
Pullarkat ST, Stoehlmacher J, Ghaderi V, Xiong YP, Ingles SA, Sherrod A, Warren R, Tsao-Wei D, Groshen S, Lenz HJ. Thymidylate synthase gene polymorphism determines response and toxicity of 5-FU chemotherapy. Pharmacogenomics J. 2001;1(1):65–70.
Article
CAS
PubMed
Google Scholar
Dehal SS, Kupfer D. CYP2D6 catalyzes tamoxifen 4-hydroxylation in human liver. Cancer Res. 1997;57(16):3402–6.
CAS
PubMed
Google Scholar
Deeken JF, Figg WD, Bates SE, Sparreboom A. Toward individualized treatment: prediction of anticancer drug disposition and toxicity with pharmacogenetics. Anti-Cancer Drugs. 2007;18(2):111–26.
Article
CAS
PubMed
Google Scholar
Hattinger CM, Tavanti E, Fanelli M, Vella S, Picci P, Serra M. Pharmacogenomics of genes involved in antifolate drug response and toxicity in osteosarcoma. Expert Opin Drug Metab Toxicol. 2017;13(3):245–57.
Article
CAS
PubMed
Google Scholar
Horton I, Lin Y, Reed G, Wiepert M, Hart S. Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing. J Pers Med. 2017;7(3):E7. https://doi.org/10.3390/jpm7030007.
Article
PubMed Central
Google Scholar
Harris M, Bhuvaneshwar K, Natarajan T, Sheahan L, Wang D, Tadesse MG, Shoulson I, Filice R, Steadman K, Pishvaian MJ, et al. Pharmacogenomic characterization of gemcitabine response--a framework for data integration to enable personalized medicine. Pharmacogenet Genomics. 2014;24(2):81–93.
Article
CAS
PubMed
Google Scholar
Horak P, Frohling S, Glimm H. Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls. ESMO Open. 2016;1(5):e000094.
Article
PubMed
PubMed Central
Google Scholar
FASTQ format. https://en.wikipedia.org/wiki/FASTQ_format. Accessed 11 Aug 2017.
Osteosarcoma [https://ocg.cancer.gov/programs/target/projects/osteosarcoma] Last Accessed 11 Aug 2017.
Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, et al. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature. 2018;555(7696):371–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
TARGET: Osteosarcoma (OS). https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000468.v14.p6. Accessed 11 Aug 2017.
Sequence Alignment Map. https://samtools.github.io/hts-specs/SAMv1.pdf. Accessed 11 Aug 2017.
Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files [https://github.com/najoshi/sickle] Last Accessed 26 June 2017.
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome project data processing S: the sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Picard. http://broadinstitute.github.io/picard. Accessed 26 June 2017.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davis AM, Bell RS, Goodwin PJ. Prognostic factors in osteosarcoma: a critical review. J Clin Oncol. 1994;12(2):423–31.
Article
CAS
PubMed
Google Scholar
Hey J. What's so hot about recombination hotspots? PLoS Biol. 2004;2(6):e190.
Article
PubMed
PubMed Central
CAS
Google Scholar
Haplotype. https://en.wikipedia.org/wiki/Haplotype. Accessed 26 June 2017.
Tan Q, Christiansen L, Bathum L, Zhao JH, Yashin AI, Vaupel JW, Christensen K, Kruse TA. Estimating haplotype relative risks on human survival in population-based association studies. Hum Hered. 2005;59(2):88–97.
Article
PubMed
Google Scholar
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4:7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Caret. https://cran.r-project.org/web/packages/caret/caret.pdf. Accessed 11 Aug 2017.
Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Roy Stat Soc B Met. 1995;57(1):289–300.
Google Scholar
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6(2):80–92.
Article
CAS
Google Scholar
Survival: Survival Analysis. https://cran.r-project.org/package=survival. Accessed 23 June 2017.
Goel MK, Khanna P, Kishore J. Understanding survival analysis: Kaplan-Meier estimate. Int J Ayurveda Res. 2010;1(4):274–8.
Article
PubMed
PubMed Central
Google Scholar
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2016;44(D1):D481–7.
Article
CAS
PubMed
Google Scholar
Understanding Cancer Genomics. http://www.ubooks.pub/Books/ON/B0/E10R1010/TOC.html. Accessed 29 Nov 2018.
Chaudhry AS, Thirumaran RK, Yasuda K, Yang X, Fan Y, Strom SC, Schuetz EG. Genetic variation in aldo-keto reductase 1D1 (AKR1D1) affects the expression and activity of multiple cytochrome P450s. Drug Metab Dispos. 2013;41(8):1538–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cell adhesion. https://en.wikipedia.org/wiki/Cell_adhesion. Accessed 26 June 2017.
Cheng SL, Lecanda F, Davidson MK, Warlow PM, Zhang SF, Zhang L, Suzuki S, St John T, Civitelli R. Human osteoblasts express a repertoire of cadherins, which are critical for BMP-2-induced osteogenic differentiation. J Bone Miner Res. 1998;13(4):633–44.
Article
CAS
PubMed
Google Scholar
Perbal B, Zuntini M, Zambelli D, Serra M, Sciandra M, Cantiani L, Lucarelli E, Picci P, Scotlandi K. Prognostic value of CCN3 in osteosarcoma. Clin Cancer Res. 2008;14(3):701–9.
Article
CAS
PubMed
Google Scholar
Chae B, Yang KM, Kim TI, Kim WH. Adherens junction-dependent PI3K/Akt activation induces resistance to genotoxin-induced cell death in differentiated intestinal epithelial cells. Biochem Biophys Res Commun. 2009;378(4):738–43.
Article
CAS
PubMed
Google Scholar
Luizon MR, Ahituv N. Uncovering drug-responsive regulatory elements. Pharmacogenomics. 2015;16(16):1829–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Piwi-interacting RNA (piRNA). https://en.wikipedia.org/wiki/Piwi-interacting_RNA. Accessed 12 June 2017.
PIR61811. http://www.genecards.org/cgi-bin/carddisp.pl?gene=PIR61811. Accessed 12 June 2017.
Ng KW, Anderson C, Marshall EA, Minatel BC, Enfield KS, Saprunoff HL, Lam WL, Martinez VD. Piwi-interacting RNAs in cancer: emerging functions and clinical utility. Mol Cancer. 2016;15:5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ortogero N, Schuster AS, Oliver DK, Riordan CR, Hong AS, Hennig GW, Luong D, Bao J, Bhetwal BP, Ro S, et al. A novel class of somatic small RNAs similar to germ cell pachytene PIWI-interacting small RNAs. J Biol Chem. 2014;289(47):32824–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mei Y, Wang Y, Kumari P, Shetty AC, Clark D, Gable T, MacKerell AD, Ma MZ, Weber DJ, Yang AJ, et al. A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells. Nat Commun. 2015;6:7316.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Gable T, Ma MZ, Clark D, Zhao J, Zhang Y, Liu W, Mao L, Mei Y. A piRNA-like small RNA induces Chemoresistance to cisplatin-based therapy by inhibiting apoptosis in lung squamous cell carcinoma. Mol Ther Nucleic Acids. 2017;6:269–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
DGCR6. http://www.genecards.org/cgi-bin/carddisp.pl?gene=DGCR6. Accessed 30 June 2017.
DIGEORGE SYNDROME CRITICAL REGION GENE 6; DGCR6. https://www.omim.org/entry/601279. Accessed 30 June 2017.
GenBank: DQ786190.1. https://www.ncbi.nlm.nih.gov/nuccore/DQ786190. Accessed 30 June 2017.
Savinkova LK, Ponomarenko MP, Ponomarenko PM, Drachkova IA, Lysova MV, Arshinova TV, Kolchanov NA. TATA box polymorphisms in human gene promoters and associated hereditary pathologies. Biochemistry (Mosc). 2009;74(2):117–29.
Article
CAS
Google Scholar
Fenger JM, Roberts RD, Iwenofu OH, Bear MD, Zhang X, Couto JI, Modiano JF, Kisseberth WC, London CA. MiR-9 is overexpressed in spontaneous canine osteosarcoma and promotes a metastatic phenotype including invasion and migration in osteoblasts and osteosarcoma cell lines. BMC Cancer. 2016;16(1):784.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sarkar FH, Li Y, Wang Z, Kong D, Ali S. Implication of microRNAs in drug resistance for designing novel cancer therapy. Drug Resist Updat. 2010;13(3):57–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
SLC13A2 Gene. http://www.genecards.org/cgi-bin/carddisp.pl?gene=SLC13A2. Accessed 9 June 2017.
Fenger JM. Investigating the biological and molecular consequences of MiR-9 dysregulation in canine mast cell tumors and osteosarcoma. The Ohio State University; 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1429761923.
Sowers R, Wenzel BD, Richardson C, Meyers PA, Healey JH, Levy AS, Gorlick R. Impairment of methotrexate transport is common in osteosarcoma tumor samples. Sarcoma. 2011;2011:834170.
Article
PubMed
CAS
Google Scholar
Pletscher-Frankild S, Palleja A, Tsafou K, Binder JX, Jensen LJ. DISEASES: text mining and data integration of disease-gene associations. Methods. 2015;74:83–9.
Article
CAS
PubMed
Google Scholar
Park JA, Shin HY. Influence of genetic polymorphisms in the folate pathway on toxicity after high-dose methotrexate treatment in pediatric osteosarcoma. Blood Res. 2016;51(1):50–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Park JA, Shin HY. ATIC gene polymorphism and histologic response to chemotherapy in pediatric osteosarcoma. J Pediatr Hematol Oncol. 2017;39(5):e270–4.
Article
CAS
PubMed
Google Scholar
Lin L, Yee SW, Kim RB, Giacomini KM. SLC transporters as therapeutic targets: emerging opportunities. Nat Rev Drug Discov. 2015;14(8):543–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li Q, Shu Y. Role of solute carriers in response to anticancer drugs. Mol Cell Ther. 2014;2:15.
Article
PubMed
PubMed Central
Google Scholar
PIK3R1 [http://www.genecards.org/cgi-bin/carddisp.pl?gene=PIK3R1] Last Accessed 9 June 2017.
Weigelt B, Downward J. Genomic determinants of PI3K pathway inhibitor response in Cancer. Front Oncol. 2012;2:109.
Article
PubMed
PubMed Central
Google Scholar
Chang MT, Asthana S, Gao SP, Lee BH, Chapman JS, Kandoth C, Gao J, Socci ND, Solit DB, Olshen AB, et al. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat Biotechnol. 2016;34(2):155–63.
Article
CAS
PubMed
Google Scholar
Zhao J, Cheng L. Long non-coding RNA CCAT1/miR-148a axis promotes osteosarcoma proliferation and migration through regulating PIK3IP1. Acta Biochim Biophys Sin Shanghai. 2017;49(6):503–12.
Article
CAS
PubMed
Google Scholar
Lee TI, Young RA. Transcriptional regulation and its misregulation in disease. Cell. 2013;152(6):1237–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fasching PA, Heusinger K, Haeberle L, Niklos M, Hein A, Bayer CM, Rauh C, Schulz-Wendtland R, Bani MR, Schrauder M, et al. Ki67, chemotherapy response, and prognosis in breast cancer patients receiving neoadjuvant treatment. BMC Cancer. 2011;11:486.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim KI, Lee KH, Kim TR, Chun YS, Lee TH, Park HK. Ki-67 as a predictor of response to neoadjuvant chemotherapy in breast cancer patients. J Breast Cancer. 2014;17(1):40–6.
Article
PubMed
PubMed Central
Google Scholar
Jabeen S, Holmboe L, Alnaes GI, Andersen AM, Hall KS, Kristensen VN. Impact of genetic variants of RFC1, DHFR and MTHFR in osteosarcoma patients treated with high-dose methotrexate. Pharmacogenomics J. 2015;15(5):385–90.
Article
CAS
PubMed
Google Scholar
Passetti F, Ferreira CG, Costa FF. The impact of microRNAs and alternative splicing in pharmacogenomics. Pharmacogenomics J. 2009;9(1):1–13.
Article
CAS
PubMed
Google Scholar
Chhibber A, French CE, Yee SW, Gamazon ER, Theusch E, Qin X, Webb A, Papp AC, Wang A, Simmons CQ, et al. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. Pharmacogenomics J. 2017;17(2):137–45.
Article
CAS
PubMed
Google Scholar
Moitra K, Scally M, McGee K, Lancaster G, Gold B, Dean M. Molecular evolutionary analysis of ABCB5: the ancestral gene is a full transporter with potentially deleterious single nucleotide polymorphisms. PLoS One. 2011;6(1):e16318.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shihab HA, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Hum Genomics. 2014;8:11.
Article
PubMed
PubMed Central
Google Scholar
Pinto N, Dolan ME. Clinically relevant genetic variations in drug metabolizing enzymes. Curr Drug Metab. 2011;12(5):487–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sim SC, Kacevska M, Ingelman-Sundberg M. Pharmacogenomics of drug-metabolizing enzymes: a recent update on clinical implications and endogenous effects. Pharmacogenomics J. 2013;13(1):1–11.
Article
CAS
PubMed
Google Scholar
Jacob AG, Smith CWJ. Intron retention as a component of regulated gene expression programs. Hum Genet. 2017;136(9):1043–57.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 2015;7(1):45.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sailaja K, Rao VR, Yadav S, Reddy RR, Surekha D, Rao DN, Raghunadharao D, Vishnupriya S. Intronic SNPs of TP53 gene in chronic myeloid leukemia: impact on drug response. J Nat Sci Biol Med. 2012;3(2):182–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang D, Guo Y, Wrighton SA, Cooke GE, Sadee W. Intronic polymorphism in CYP3A4 affects hepatic expression and response to statin drugs. Pharmacogenomics J. 2011;11(4):274–86.
Article
PubMed
CAS
Google Scholar
Elens L, Becker ML, Haufroid V, Hofman A, Visser LE, Uitterlinden AG, Stricker B, van Schaik RH. Novel CYP3A4 intron 6 single nucleotide polymorphism is associated with simvastatin-mediated cholesterol reduction in the Rotterdam study. Pharmacogenet Genomics. 2011;21(12):861–6.
Article
CAS
PubMed
Google Scholar
Elens L, Bouamar R, Hesselink DA, Haufroid V, van der Heiden IP, van Gelder T, van Schaik RH. A new functional CYP3A4 intron 6 polymorphism significantly affects tacrolimus pharmacokinetics in kidney transplant recipients. Clin Chem. 2011;57(11):1574–83.
Article
CAS
PubMed
Google Scholar
Elens L, Bouamar R, Hesselink DA, Haufroid V, van Gelder T, van Schaik RH. The new CYP3A4 intron 6 C>T polymorphism (CYP3A4*22) is associated with an increased risk of delayed graft function and worse renal function in cyclosporine-treated kidney transplant patients. Pharmacogenet Genomics. 2012;22(5):373–80.
CAS
PubMed
Google Scholar
Matsui M, Corey DR. Non-coding RNAs as drug targets. Nat Rev Drug Discov. 2017;16(3):167–79.
Article
CAS
PubMed
Google Scholar
Sur I, Taipale J. The role of enhancers in cancer. Nat Rev Cancer. 2016;16(8):483–93.
Article
CAS
PubMed
Google Scholar
Chen T, Wang Z, Zhou W, Chong Z, Meric-Bernstam F, Mills GB, Chen K. Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types. BMC Genomics. 2016;17 Suppl 2:394.
Article
PubMed
CAS
Google Scholar