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2. Somatic Mutation Profile as a Predictor of Treatment Response and Survival in Unresectable Pancreatic Ductal Adenocarcinoma Treated with FOLFIRINOX and Gemcitabine Nab-Paclitaxel.

Author

Paredes de la Fuente, Rodrigo, Sucre, Santiago, Ponce, Cristina, Rattani, Ahmed Anwer Ali, and Peters, Mary Linton B.

Subjects
THERAPEUTIC use of antineoplastic agents, RESEARCH funding, GENOMICS, TREATMENT effectiveness, RETROSPECTIVE studies, DECISION making in clinical medicine, CANCER patients, DESCRIPTIVE statistics, PANCREATIC tumors, CANCER chemotherapy, KAPLAN-Meier estimator, GEMCITABINE, DUCTAL carcinoma, QUALITY of life, GENETIC mutation, PACLITAXEL, SURVIVAL analysis (Biometry), OVERALL survival, PROPORTIONAL hazards models, REGRESSION analysis
Abstract

Simple Summary: This study explored how genetic changes influence treatment effectiveness and survival in patients with advanced pancreatic cancer. By examining tumors from 142 patients, researchers identified specific genetic mutations that can predict how well a patient responds to chemotherapy. Findings showed that mutations in certain genetic pathways are associated with longer survival and better treatment outcomes. This research highlights the importance of tailoring cancer treatment based on individual genetic profiles, potentially leading to more personalized and effective therapies for pancreatic cancer patients. (1) Background: Pancreatic ductal adenocarcinoma (PDAC) has low survival rates despite treatment advancements. Aim: This study aims to show how molecular profiling could possibly guide personalized treatment strategies, which may help improve survival outcomes in patients with PDAC. (2) Materials and Methods: A retrospective analysis of 142 PDAC patients from a single academic center was conducted. Patients underwent chemotherapy and next-generation sequencing for molecular profiling. Key oncogenic pathways were identified using the Reactome pathway database. Survival analysis was performed using Kaplan–Meier curves and Cox Proportional Hazards Regression. (3) Results: Patients mainly received FOLFIRINOX (n = 62) or gemcitabine nab-paclitaxel (n = 62) as initial chemotherapy. The median OS was 13.6 months. Longer median OS was noted in patients with NOTCH (15 vs. 12.3 months, p = 0.007) and KIT pathway mutations (21.3 vs. 12.12 months, p = 0.04). Combinatorial pathway analysis indicated potential synergistic effects on survival. In the PFS, PI3K pathway (6.6 vs. 5.7 months, p = 0.03) and KIT pathway (10.3 vs. 6.2 months, p = 0.03) mutations correlated with improved PFS within the gemcitabine nab-paclitaxel subgroup. (4) Conclusions: Molecular profiling could play a role in PDAC for predicting outcomes and responses to therapies like FOLFIRINOX and gemcitabine nab-paclitaxel. Integrating genomic data into clinical decision-making can benefit PDAC treatment, though further validation is needed to fully utilize precision oncology in PDAC management. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Regulation of anaphase in mammalian meiosis

Author

Rattani, Ahmed Anwer Ali, Novak, Bela, and Nasmyth, Kim

Subjects
571.8, Biochemistry, Cell Biology
Abstract

Missegregation of chromosomes during meiosis leads to formation of aneuploid eggs. Estimates suggest that in humans, about 10-30% of fertilised eggs and one-third of all miscarriages are aneuploid. Accurate chromosome segregation depends on the coordination between stepwise cohesion resolution and attachments of homologous chromosomes through kinetochores to microtubules, emanating from opposite poles of the cell. The Spindle Assembly Checkpoint (SAC) monitors microtubule-kinetochore attachments and prevents resolution of cohesin complexes by inhibiting the ubiquitin ligase APC/CCdc20 until all aberrant microtubule-kinetochore attachments have been rectified by an Aurora Kinase-dependent error correction machinery. During meiosis, these pathways work in seamless coordination to achieve balanced segregation of the genome at the first meiotic division. The cross-talk between different cell cycle pathways requires members with shared affiliations. During my DPhil studies, I worked on understanding the role of two such proteins, namely Bub1 (budding uninhibited by benzimidazoles 1) and Sgol2 (Shugoshin-like protein 2) in mouse oocytes. During the first meiotic division, Bub1 maintains the SAC, and through its kinase activity, Bub1 recruits Sgol2 to kinetochores to protect centromeric cohesion. This recruitment is essential for two rounds of chromosomes segregation in meiosis. Thus, Bub1 localisation at kinetochores can coordinate the timing of anaphase with the centromeric cohesion protection. During the first meiotic division, Sgol2 protects centromeric cohesion by recruiting PP2A to kinetochores, accelerates cohesin resolution by silencing the SAC through its interaction with PP2A and Mad2, and also promotes biorientation and congression of homologous chromosomes by its interaction with MCAK and through dephosphorylation of Aurora B/C kinase substrates at kinetochores. This research revealed that Bub1 and Sgol2 can regulate anaphase by linking multiple cell cycle pathways that work together to achieve faithful chromosomes segregation in mammalian meiosis.

Published
2012

4. FRI603 Treatment Of Severe Refractory Hypoglycemia Due To Malignant Insulinoma With A Novel Anti-insulin Receptor Antibody

Author

Osataphan, Soravis, primary, Vamvini, Maria, additional, Rosen, Evan D, additional, Pei, Lei, additional, Erlikh, Natanie, additional, Singh, Gurcharan, additional, Dhorajiya, Poojaben, additional, Parker, J Anthony, additional, Dreyfuss, Jonathan M, additional, Rattani, Ahmed, additional, and Patti, Mary-Elizabeth, additional

Published
2023
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10. Dependency of the Spindle Assembly Checkpoint on Cdk1 Renders the Anaphase Transition Irreversible

Author

Rattani, Ahmed, Vinod, P.K., Godwin, Jonathan, Tachibana-Konwalski, Kikuë, Wolna, Magda, Malumbres, Marcos, Novák, Béla, and Nasmyth, Kim

Subjects
Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Report, embryonic structures, biological phenomena, cell phenomena, and immunity
Abstract

Summary Activation of anaphase-promoting complex/cyclosome (APC/CCdc20) by Cdc20 is delayed by the spindle assembly checkpoint (SAC). When all kinetochores come under tension, the SAC is turned off and APC/CCdc20 degrades cyclin B and securin, which activates separase [1]. The latter then cleaves cohesin holding sister chromatids together [2]. Because cohesin cleavage also destroys the tension responsible for turning off the SAC, cells must possess a mechanism to prevent SAC reactivation during anaphase, which could be conferred by a dependence of the SAC on Cdk1 [3–5]. To test this, we analyzed mouse oocytes and embryos expressing nondegradable cyclin B together with a Cdk1-resistant form of separase. After biorientation and SAC inactivation, APC/CCdc20 activates separase but the resulting loss of (some) cohesion is accompanied by SAC reactivation and APC/CCdc20 inhibition, which aborts the process of further securin degradation. Cyclin B is therefore the only APC/CCdc20 substrate whose degradation at the onset of anaphase is necessary to prevent SAC reactivation. The mutual activation of tension sensitive SAC and Cdk1 creates a bistable system that ensures complete activation of separase and total downregulation of Cdk1 when all chromosomes have bioriented., Graphical Abstract, Highlights • Cdk1 activity is necessary for maintaining the spindle assembly checkpoint (SAC) • SAC is reactivated during anaphase if Cdk1 activity is kept high • APC/C blocks SAC reactivation at anaphase solely by promoting cyclin B degradation • The SAC’s dependence on Cdk1 ensures that APC/C activation irreversible, Rattani et al. show that Cdk1 is required for spindle assembly checkpoint (SAC) activation by unattached/tensionless chromosomes. Cdk1 inactivation through degradation of its cyclin B subunit blocks SAC reactivation during anaphase. The SAC’s dependence on Cdk1 makes separase activation irreversible.

Published
2014
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11. Additional file 3: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Abstract

Differentially expressed miRNAs between the two subtypes in the three datasets. The Boston, Utah, and cell line data were analyzed to determine the differential expression of their miRNA population. (PDF 154 kb)

Published
2017
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12. Additional file 7: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Abstract

Association between prognostic 14q32 miRNAs and cell line aggressiveness (binary analysis). An analysis between 14q32 miRNA expression and the following characteristics associated with cell line aggressiveness was performed: proliferation, invasiveness, migration, colony forming, and tumorigenicity. These attributes were analyzed as binary (categorical) variables. (PDF 538 kb)

Published
2017
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13. Additional file 9: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Abstract

Association between DLK1/MEG3 methylation and cell line aggressiveness. The relationship between methylation and cell line aggressiveness was analyzed for methylation site neighboring or on DLK1 and MEG3, both located on 14q32. This analysis was limited by the number of available methylation probes for this region on the Illumina methylation array. Cell line aggressiveness was assessed via colony forming, invasiveness, migration, and tumorigenicity. (PDF 447 kb)

Published
2017
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14. Additional file 1: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Abstract

Clinical characteristics of the Boston, Utah, and Texas datasets. These published datasets were used to assess the prognostic value of a subset of miRNA subsets located on 14q32 via the tdROC curve method. Available follow-up was different between the two datasets such that we needed to choose a primary endpoint of 120Â months for the Boston dataset and 60Â months for the Utah and Texas datasets. (PDF 141 kb)

Published
2017
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15. Additional file 4: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
fungi
Abstract

Correlations between DICER and differentially expressed miRNAs in the Boston dataset. DICER1 is a gene that encodes for an endoribonuclease essential for the formation of microRNA, and it is also located on 14q32. We analyzed the correlation between miRNA expression on the 14q32 locus and DICER1 expression and found that a small fraction (5%) of miRNAs was significantly correlated with DICER1. (PDF 174 kb)

Published
2017
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16. Additional file 6: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Abstract

Correlations between prognostic miRNAs and other 14q32 transcripts in the Boston dataset. Eighteen prognostic miRNAs that we found on 14q32 were compared with the remaining coding and non-coding transcripts on that same locus to investigate whether a larger pattern of co-regulation may exist. (PDF 424 kb)

Published
2017
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17. An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine E., primary, Kelly, Andrew D., additional, Kuijjer, Marieke L., additional, Barry, William, additional, Rattani, Ahmed, additional, Garbutt, Cassandra C., additional, Kissick, Haydn, additional, Janeway, Katherine, additional, Perez-Atayde, Antonio, additional, Goldsmith, Jeffrey, additional, Gebhardt, Mark C., additional, Arredouani, Mohamed S., additional, Cote, Greg, additional, Hornicek, Francis, additional, Choy, Edwin, additional, Duan, Zhenfeng, additional, Quackenbush, John, additional, Haibe-Kains, Benjamin, additional, and Spentzos, Dimitrios, additional

Published
2017
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19. APC/CCdh1 enables removal of shugoshin-2 from the arms of bivalent chromosomes by moderating cyclin-dependent kinase activity

Author

European Commission, Engineering and Physical Sciences Research Council (UK), Biotechnology and Biological Sciences Research Council (UK), Medical Research Council (UK), Wellcome Trust, Ministerio de Economía y Competitividad (España), Boehringer Ingelheim Fonds, Rattani, Ahmed, Ballesteros Mejia, Randy, Roberts, Katherine, Roig, Maurici B., Godwin, Jonathan, Hopkins, Michael, Eguren, Manuel, Sanchez-Pulido, Luis, Okaz, Elwy, Ogushi, Sugako, Wolna, Magda, Metson, Jean, Pendás, Alberto M., Malumbres, Marcos, Novák, Béla, Herbert, Mary, Nasmyth, Kim, European Commission, Engineering and Physical Sciences Research Council (UK), Biotechnology and Biological Sciences Research Council (UK), Medical Research Council (UK), Wellcome Trust, Ministerio de Economía y Competitividad (España), Boehringer Ingelheim Fonds, Rattani, Ahmed, Ballesteros Mejia, Randy, Roberts, Katherine, Roig, Maurici B., Godwin, Jonathan, Hopkins, Michael, Eguren, Manuel, Sanchez-Pulido, Luis, Okaz, Elwy, Ogushi, Sugako, Wolna, Magda, Metson, Jean, Pendás, Alberto M., Malumbres, Marcos, Novák, Béla, Herbert, Mary, and Nasmyth, Kim

Abstract

In mammalian females, germ cells remain arrested as primordial follicles. Resumption of meiosis is heralded by germinal vesicle breakdown, condensation of chromosomes, and their eventual alignment on metaphase plates. At the first meiotic division, anaphase-promoting complex/cyclosome associated with Cdc20 (APC/C) activates separase and thereby destroys cohesion along chromosome arms. Because cohesion around centromeres is protected by shugoshin-2, sister chromatids remain attached through centromeric/pericentromeric cohesin. We show here that, by promoting proteolysis of cyclins and Cdc25B at the germinal vesicle (GV) stage, APC/C associated with the Cdh1 protein (APC/C) delays the increase in Cdk1 activity, leading to germinal vesicle breakdown (GVBD). More surprisingly, by moderating the rate at which Cdk1 is activated following GVBD, APC/C creates conditions necessary for the removal of shugoshin-2 from chromosome arms by the Aurora B/C kinase, an event crucial for the efficient resolution of chiasmata.

Published
2017

21. Abstract PR11: APC/CCdh1 maintains primordial follicles, germinal vesicle arrest and ensures balanced segregation of chromosomes by enabling removal of Shugoshin-2 from chromosomes arms

Author

Rattani, Ahmed, primary, Mejia, Randy Ballestros, additional, Roberts, Katherine, additional, Roig, Maurici B, additional, Godwin, Jonathan, additional, Eguren, Manuel, additional, Ogushi, Sugako, additional, Okaz, Elwy, additional, Pendas, Alberto, additional, Marcos, Malumbres, additional, Herbert, Mary, additional, and Nasmyth, Kim, additional

Published
2016
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25. Sgol2 provides a regulatory platform that coordinates essential cell cycle processes during meiosis I in oocytes

Author

Ministerio de Ciencia e Innovación (España), German Research Foundation, Boehringer Ingelheim Fonds, Medical Research Council (UK), European Commission, Wellcome Trust, Rattani, Ahmed, Pendás, Alberto M., Nasmyth, Kim, Ministerio de Ciencia e Innovación (España), German Research Foundation, Boehringer Ingelheim Fonds, Medical Research Council (UK), European Commission, Wellcome Trust, Rattani, Ahmed, Pendás, Alberto M., and Nasmyth, Kim

Abstract

Accurate chromosome segregation depends on coordination between cohesion resolution and kinetochore-microtubule interactions (K-fibers), a process regulated by the spindle assembly checkpoint (SAC). How these diverse processes are coordinated remains unclear. We show that in mammalian oocytes Shugoshin-like protein 2 (Sgol2) in addition to protecting cohesin, plays an important role in turning off the SAC, in promoting the congression and bi-orientation of bivalents on meiosis I spindles, in facilitating formation of K-fibers and in limiting bivalent stretching. Sgol2's ability to protect cohesin depends on its interaction with PP2A, as is its ability to silence the SAC, with the latter being mediated by direct binding to Mad2. In contrast, its effect on bivalent stretching and K-fiber formation is independent of PP2A and mediated by recruitment of MCAK and inhibition of Aurora C kinase activity respectively. By virtue of its multiple interactions, Sgol2 links many of the processes essential for faithful chromosome segregation.

Published
2013

29. An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine E., Kelly, Andrew D., Kuijjer, Marieke L., Barry, William, Rattani, Ahmed, Garbutt, Cassandra C., Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark C., Arredouani, Mohamed S., Cote, Greg, Hornicek, Francis, Choy, Edwin, Duan, Zhenfeng, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
Osteosarcoma prognosis, Molecular subtypes, MicroRNA expression, Methylation, Loss of imprinting
Abstract

Background: A microRNA (miRNA) collection on the imprinted 14q32 MEG3 region has been associated with outcome in osteosarcoma. We assessed the clinical utility of this miRNA set and their association with methylation status. Methods: We integrated coding and non-coding RNA data from three independent annotated clinical osteosarcoma cohorts (n = 65, n = 27, and n = 25) and miRNA and methylation data from one in vitro (19 cell lines) and one clinical (NCI Therapeutically Applicable Research to Generate Effective Treatments (TARGET) osteosarcoma dataset, n = 80) dataset. We used time-dependent receiver operating characteristic (tdROC) analysis to evaluate the clinical value of candidate miRNA profiles and machine learning approaches to compare the coding and non-coding transcriptional programs of high- and low-risk osteosarcoma tumors and high- versus low-aggressiveness cell lines. In the cell line and TARGET datasets, we also studied the methylation patterns of the MEG3 imprinting control region on 14q32 and their association with miRNA expression and tumor aggressiveness. Results: In the tdROC analysis, miRNA sets on 14q32 showed strong discriminatory power for recurrence and survival in the three clinical datasets. High- or low-risk tumor classification was robust to using different microRNA sets or classification methods. Machine learning approaches showed that genome-wide miRNA profiles and miRNA regulatory networks were quite different between the two outcome groups and mRNA profiles categorized the samples in a manner concordant with the miRNAs, suggesting potential molecular subtypes. Further, miRNA expression patterns were reproducible in comparing high-aggressiveness versus low-aggressiveness cell lines. Methylation patterns in the MEG3 differentially methylated region (DMR) also distinguished high-aggressiveness from low-aggressiveness cell lines and were associated with expression of several 14q32 miRNAs in both the cell lines and the large TARGET clinical dataset. Within the limits of available CpG array coverage, we observed a potential methylation-sensitive regulation of the non-coding RNA cluster by CTCF, a known enhancer-blocking factor. Conclusions: Loss of imprinting/methylation changes in the 14q32 non-coding region defines reproducible previously unrecognized osteosarcoma subtypes with distinct transcriptional programs and biologic and clinical behavior. Future studies will define the precise relationship between 14q32 imprinting, non-coding RNA expression, genomic enhancer binding, and tumor aggressiveness, with possible therapeutic implications for both early- and advanced-stage patients. Electronic supplementary material The online version of this article (doi:10.1186/s13045-017-0465-4) contains supplementary material, which is available to authorized users.

Published
2017
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31. Additional file 10: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Network edge differences between the two subtypes. (PDF 557 kb)

32. Additional file 5: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Boston dataset hierarchical clustering using the messenger RNA (whole-genome) profiles. (Based on data available for a subset of 37 patients only). (PDF 20 kb)

33. Additional file 11: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Significant network GO categories. (PDF 412 kb)

34. Additional file 2: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
fungi, 3. Good health
Abstract

Multivariate prognostic models including 14q32 miRNA profiles and clinicopathologic covariates, analyzed at the follow-up time of 120Â months. (PDF 447 kb)

35. Additional file 2: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
fungi, 3. Good health
Abstract

Multivariate prognostic models including 14q32 miRNA profiles and clinicopathologic covariates, analyzed at the follow-up time of 120Â months. (PDF 447 kb)

36. Additional file 11: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Significant network GO categories. (PDF 412 kb)

37. Additional file 13: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Supplementary methods. Additional details are provided on certain aspects of our analytical procedures. (PDF 461 kb)

38. Additional file 14: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Supplementary PUMA methods. This file is the detailed protocol followed for the implementation of PUMA in order to reconstruct networks for high- and low-risk osteosarcoma subtypes. (PDF 998 kb)

39. Additional file 12: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Network gene-drug screen interactions. This includes a detailed list of possible gene-drug interactions as a result from the screen applied between the significant edges from the 5-miRNA network and the Drug Gene Interaction Database. (PDF 488 kb)

40. Additional file 10: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Network edge differences between the two subtypes. (PDF 557 kb)

41. Additional file 12: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Network gene-drug screen interactions. This includes a detailed list of possible gene-drug interactions as a result from the screen applied between the significant edges from the 5-miRNA network and the Drug Gene Interaction Database. (PDF 488 kb)

42. Additional file 5: of An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

Author

Hill, Katherine, Kelly, Andrew, Kuijjer, Marieke, Barry, William, Rattani, Ahmed, Garbutt, Cassandra, Kissick, Haydn, Janeway, Katherine, Perez-Atayde, Antonio, Goldsmith, Jeffrey, Gebhardt, Mark, Arredouani, Mohamed, Cote, Greg, Hornicek, Francis, Choy, Edwin, Zhenfeng Duan, Quackenbush, John, Haibe-Kains, Benjamin, and Spentzos, Dimitrios

Subjects
3. Good health
Abstract

Boston dataset hierarchical clustering using the messenger RNA (whole-genome) profiles. (Based on data available for a subset of 37 patients only). (PDF 20 kb)

43. Author's reply.

Author

Noor, Nudrat and Rattani, Ahmed

Subjects
*LETTERS to the editor, *MALARIA
Abstract

Presents a letter to the editor in response to the article "Comparison of proguanil-dapsone with sulfadoxine-pyrimethamine for the treatment of uncomplicated falciparum malaria in young African children: double-blind randomised controlled trial," by A. Alloueche, W. Bailey, S. Barton, et al. in issue 363, 2004, of "Lancet."

Published
2004

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