15 results on '"Ariyaratne, Pramila N."'
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2. A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer
- Author
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Ng, King Pan, Hillmer, Axel M., Chuah, Charles T.H., Juan, Wen Chun, Ko, Tun Kiat, Teo, Audrey S.M., Ariyaratne, Pramila N., Takahashi, Naoto, Sawada, Kenichi, Fei, Yao, Soh, Sheila, Lee, Wah Heng, Huang, John W.J., Allen, Jr., John C., Woo, Xing Yi, Nagarajan, Niranjan, Kumar, Vikrant, Thalamuthu, Anbupalam, Poh, Wan Ting, Ang, Ai Leen, Mya, Hae Tha, How, Gee Fung, Yang, Li Yi, Koh, Liang Piu, Chowbay, Balram, Chang, Chia-Tien, Nadarajan, Veera S., Chng, Wee Joo, Than, Hein, Lim, Lay Cheng, Goh, Yeow Tee, Zhang, Shenli, Poh, Dianne, Tan, Patrick, Seet, Ju-Ee, Ang, Mei-Kim, Chau, Noan-Minh, Ng, Quan-Sing, Tan, Daniel S.W., Soda, Manabu, Isobe, Kazutoshi, Nothen, Markus M., Wong, Tien Y., Shahab, Atif, Ruan, Xiaoan, Cacheux-Rataboul, Valere, Sung, Wing-Kin, Tan, Eng Huat, Yatabe, Yasushi, Mano, Hiroyuki, Soo, Ross A., Chin, Tan Min, Lim, Wan-Teck, Ruan, Yijun, and Ong, S. Tiong
- Subjects
Tumor proteins -- Physiological aspects -- Genetic aspects -- Research ,Antineoplastic agents -- Dosage and administration -- Genetic aspects -- Research ,Genetic polymorphisms -- Physiological aspects -- Research -- Genetic aspects ,Protein tyrosine kinase -- Physiological aspects -- Genetic aspects -- Research ,Antimitotic agents -- Dosage and administration -- Genetic aspects -- Research ,Biological sciences ,Health - Abstract
Tyrosine kinase inhibitors (TKIs) elicit high response rates among individuals with kinase-driven malignancies, including chronic myeloid leukemia (CML) and epidermal growth factor receptor-mutated non-small-cell lung cancer (EGFR NSCLC). However, the [...]
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- 2012
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3. An oestrogen-receptor-α-bound human chromatin interactome
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Fullwood, Melissa J., Liu, Mei Hui, Pan, You Fu, Liu, Jun, Xu, Han, Mohamed, Yusoff Bin, Orlov, Yuriy L., Velkov, Stoyan, Ho, Andrea, Mei, Poh Huay, Chew, Elaine G. Y., Huang, Phillips Yao Hui, Welboren, Willem-Jan, Han, Yuyuan, Ooi, Hong Sain, Ariyaratne, Pramila N., Vega, Vinsensius B., Luo, Yanquan, Tan, Peck Yean, Choy, Pei Ye, Wansa, Senali Abayratna K. D., Zhao, Bing, Lim, Kar Sian, Leow, Shi Chi, Yow, Jit Sin, Joseph, Roy, Li, Haixia, Desai, Kartiki V., Thomsen, Jane S., Lee, Yew Kok, Karuturi, Krishna Murthy R., Herve, Thoreau, Bourque, Guillaume, Stunnenberg, Hendrik G., Ruan, Xiaoan, Cacheux-Rataboul, Valere, Sung, Wing-Kin, Liu, Edison T., Wei, Chia-Lin, Cheung, Edwin, and Ruan, Yijun
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- 2009
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4. Detection of Chromosomal Breakpoints in Patients with Developmental Delay and Speech Disorders
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Utami, Kagistia H., primary, Hillmer, Axel M., additional, Aksoy, Irene, additional, Chew, Elaine G. Y., additional, Teo, Audrey S. M., additional, Zhang, Zhenshui, additional, Lee, Charlie W. H., additional, Chen, Pauline J., additional, Seng, Chan Chee, additional, Ariyaratne, Pramila N., additional, Rouam, Sigrid L., additional, Soo, Lim Seong, additional, Yousoof, Saira, additional, Prokudin, Ivan, additional, Peters, Gregory, additional, Collins, Felicity, additional, Wilson, Meredith, additional, Kakakios, Alyson, additional, Haddad, Georges, additional, Menuet, Arnaud, additional, Perche, Olivier, additional, Tay, Stacey Kiat Hong, additional, Sung, Ken W. K., additional, Ruan, Xiaoan, additional, Ruan, Yijun, additional, Liu, Edison T., additional, Briault, Sylvain, additional, Jamieson, Robyn V., additional, Davila, Sonia, additional, and Cacheux, Valere, additional
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- 2014
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5. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma
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Sung, Wing-Kin, Zheng, Hancheng, Li, Shuyu, Chen, Ronghua, Liu, Xiao, Li, Yingrui, Lee, Nikki P., Lee, Wah H., Ariyaratne, Pramila N., Tennakoon, Chandana, Mulawadi, Fabianus H., Wong, Kwong F., Liu, Angela M., Poon, Ronnie T., Fan, Sheung Tat, Chan, Kwong L., Gong, Zhuolin, Hu, Yujie, Lin, Zhao, Wang, Guan, Zhang, Qinghui, Barber, Thomas D., Chou, Wen-Chi, Aggarwal, Amit, Hao, Ke, Zhou, Wei, Zhang, Chunsheng, Hardwick, James, Buser, Carolyn, Xu, Jiangchun, Kan, Zhengyan, Dai, Hongyue, Mao, Mao, Reinhard, Christoph, Wang, Jun, Luk, John M., Sung, Wing-Kin, Zheng, Hancheng, Li, Shuyu, Chen, Ronghua, Liu, Xiao, Li, Yingrui, Lee, Nikki P., Lee, Wah H., Ariyaratne, Pramila N., Tennakoon, Chandana, Mulawadi, Fabianus H., Wong, Kwong F., Liu, Angela M., Poon, Ronnie T., Fan, Sheung Tat, Chan, Kwong L., Gong, Zhuolin, Hu, Yujie, Lin, Zhao, Wang, Guan, Zhang, Qinghui, Barber, Thomas D., Chou, Wen-Chi, Aggarwal, Amit, Hao, Ke, Zhou, Wei, Zhang, Chunsheng, Hardwick, James, Buser, Carolyn, Xu, Jiangchun, Kan, Zhengyan, Dai, Hongyue, Mao, Mao, Reinhard, Christoph, Wang, Jun, and Luk, John M.
- Abstract
To survey hepatitis B virus (HBV) integration in liver cancer genomes, we conducted massively parallel sequencing of 81 HBV-positive and 7 HBV-negative hepatocellular carcinomas (HCCs) and adjacent normal tissues. We found that HBV integration is observed more frequently in the tumors (86.4%) than in adjacent liver tissues (30.7%). Copy-number variations (CNVs) were significantly increased at HBV breakpoint locations where chromosomal instability was likely induced. Approximately 40% of HBV breakpoints within the HBV genome were located within a 1,800-bp region where the viral enhancer, X gene and core gene are located. We also identified recurrent HBV integration events (in ≥4 HCCs) that were validated by RNA sequencing (RNA-seq) and Sanger sequencing at the known and putative cancer-related TERT, MLL4 and CCNE1 genes, which showed upregulated gene expression in tumor versus normal tissue. We also report evidence that suggests that the number of HBV integrations is associated with patient survival.
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- 2012
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6. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons
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Yao, Fei, primary, Ariyaratne, Pramila N., additional, Hillmer, Axel M., additional, Lee, Wah Heng, additional, Li, Guoliang, additional, Teo, Audrey S. M., additional, Woo, Xing Yi, additional, Zhang, Zhenshui, additional, Chen, Jieqi P., additional, Poh, Wan Ting, additional, Zawack, Kelson F. B., additional, Chan, Chee Seng, additional, Leong, See Ting, additional, Neo, Say Chuan, additional, Choi, Poh Sum D., additional, Gao, Song, additional, Nagarajan, Niranjan, additional, Thoreau, Hervé, additional, Shahab, Atif, additional, Ruan, Xiaoan, additional, Cacheux-Rataboul, Valère, additional, Wei, Chia-Lin, additional, Bourque, Guillaume, additional, Sung, Wing-Kin, additional, Liu, Edison T., additional, and Ruan, Yijun, additional
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- 2012
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7. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma
- Author
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Sung, Wing-Kin, primary, Zheng, Hancheng, additional, Li, Shuyu, additional, Chen, Ronghua, additional, Liu, Xiao, additional, Li, Yingrui, additional, Lee, Nikki P, additional, Lee, Wah H, additional, Ariyaratne, Pramila N, additional, Tennakoon, Chandana, additional, Mulawadi, Fabianus H, additional, Wong, Kwong F, additional, Liu, Angela M, additional, Poon, Ronnie T, additional, Fan, Sheung Tat, additional, Chan, Kwong L, additional, Gong, Zhuolin, additional, Hu, Yujie, additional, Lin, Zhao, additional, Wang, Guan, additional, Zhang, Qinghui, additional, Barber, Thomas D, additional, Chou, Wen-Chi, additional, Aggarwal, Amit, additional, Hao, Ke, additional, Zhou, Wei, additional, Zhang, Chunsheng, additional, Hardwick, James, additional, Buser, Carolyn, additional, Xu, Jiangchun, additional, Kan, Zhengyan, additional, Dai, Hongyue, additional, Mao, Mao, additional, Reinhard, Christoph, additional, Wang, Jun, additional, and Luk, John M, additional
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- 2012
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8. Abstract 1911: A common BIM polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer
- Author
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Ong, S. Tiong, primary, Ng, King Pan, additional, Hillmer, Axel M., additional, Chuah, Charles T.H., additional, Juan, Wen Chun, additional, Ko, Tun-Kiat, additional, Teo, Audrey S.M., additional, Ariyaratne, Pramila N., additional, Takahashi, Naoto, additional, Sawada, Kenichi, additional, Fei, Yao, additional, Lee, Wah Heng, additional, Huang, John W.J., additional, Allen, John C., additional, Woo, Xing Yi, additional, Nagarajan, Niranjan, additional, Kumar, Vikrant, additional, Thalamuthu, Anbupalam, additional, Poh, Wan Ting, additional, Yang, Li Yi, additional, Koh, Liang Piu, additional, Nadarajan, Veera S., additional, Chng, Wee Joo, additional, Than, Hein, additional, Lim, Lay Cheng, additional, Goh, Yeow Tee, additional, Soh, Sheila, additional, Zhang, Shenli, additional, Poh, Dianne, additional, Tan, Patrick, additional, Seet, Ju-Ee, additional, Ang, Mei-Kim, additional, Chau, Noan-Minh, additional, Ng, Quan-Sing, additional, Tan, Daniel S.W., additional, Nöthen, Markus M., additional, Wong, Tien Y., additional, Shahab, Atif, additional, Ruan, Xiaoan, additional, Cacheux-Rataboul, Valère, additional, Sung, Wing-Kin, additional, Soda, Manabu, additional, Isobe, Kazutoshi, additional, Tan, Eng Huat, additional, Yatabe, Yasushi, additional, Mano, Hiroyuki, additional, Soo, Ross A., additional, Chin, Tan Min, additional, Lim, Wan-Teck, additional, and Ruan, Yijun, additional
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- 2012
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9. Whole-genome reconstruction and mutational signatures in gastric cancer
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Nagarajan, Niranjan, primary, Bertrand, Denis, additional, Hillmer, Axel M, additional, Zang, Zhi, additional, Yao, Fei, additional, Jacques, Pierre-Étienne, additional, Teo, Audrey SM, additional, Cutcutache, Ioana, additional, Zhang, Zhenshui, additional, Lee, Wah, additional, Sia, Yee, additional, Gao, Song, additional, Ariyaratne, Pramila N, additional, Ho, Andrea, additional, Woo, Xing, additional, Veeravali, Lavanya, additional, Ong, Choon, additional, Deng, Niantao, additional, Desai, Kartiki V, additional, Khor, Chiea, additional, Hibberd, Martin L, additional, Shahab, Atif, additional, Rao, Jaideepraj, additional, Wu, Mengchu, additional, Teh, Ming, additional, Zhu, Feng, additional, Chin, Sze, additional, Pang, Brendan, additional, So, Jimmy BY, additional, Bourque, Guillaume, additional, Soong, Richie, additional, Sung, Wing-Kin, additional, Tean Teh, Bin, additional, Rozen, Steven, additional, Ruan, Xiaoan, additional, Yeoh, Khay, additional, Tan, Patrick BO, additional, and Ruan, Yijun, additional
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- 2012
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10. A Common Deletion Polymorphism in the BIM Gene Contributes to Intrinsic Imatinib Resistance in Chronic Myelogenous Leukemia
- Author
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Hillmer, Axel M, primary, Ng, King-Pan, additional, Chuah, Charles, additional, Juan, Wen Chun, additional, Ko, Tun-Kiat, additional, Teo, Audrey S.M., additional, Ariyaratne, Pramila N, additional, Takahashi, Naoto, additional, Sawada, Kenichi, additional, Fei, Yao, additional, Lee, Wah Heng, additional, Huang, Weijie, additional, Allen, John C, additional, Woo, Xing Yi, additional, Nagarajan, Niranjan, additional, Kumar, Vikrant, additional, Thalamuthu, Anbupalam, additional, Poh, Wan Ting, additional, Ang, Ai Leen, additional, Mya, Hae Tha, additional, How, Gee Fung, additional, Yang, Li Yi, additional, Koh, Liang Piu, additional, Nadarajan, Veera S, additional, Chng, Wee-Joo, additional, Than, Hein, additional, Lim, Lay Cheng, additional, Goh, Yeow-Tee, additional, Nöthen, Markus M, additional, Wong, Tien Y, additional, Shahab, Atif, additional, Ruan, Xiaoan, additional, Cacheux-Rataboul, Valère, additional, Sung, Wing-Kin, additional, Ruan, Yijun, additional, and Ong, S. Tiong, additional
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- 2011
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11. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
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Hillmer, Axel M., primary, Yao, Fei, additional, Inaki, Koichiro, additional, Lee, Wah Heng, additional, Ariyaratne, Pramila N., additional, Teo, Audrey S.M., additional, Woo, Xing Yi, additional, Zhang, Zhenshui, additional, Zhao, Hao, additional, Ukil, Leena, additional, Chen, Jieqi P., additional, Zhu, Feng, additional, So, Jimmy B.Y., additional, Salto-Tellez, Manuel, additional, Poh, Wan Ting, additional, Zawack, Kelson F.B., additional, Nagarajan, Niranjan, additional, Gao, Song, additional, Li, Guoliang, additional, Kumar, Vikrant, additional, Lim, Hui Ping J., additional, Sia, Yee Yen, additional, Chan, Chee Seng, additional, Leong, See Ting, additional, Neo, Say Chuan, additional, Choi, Poh Sum D., additional, Thoreau, Hervé, additional, Tan, Patrick B.O., additional, Shahab, Atif, additional, Ruan, Xiaoan, additional, Bergh, Jonas, additional, Hall, Per, additional, Cacheux-Rataboul, Valère, additional, Wei, Chia-Lin, additional, Yeoh, Khay Guan, additional, Sung, Wing-Kin, additional, Bourque, Guillaume, additional, Liu, Edison T., additional, and Ruan, Yijun, additional
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- 2011
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12. Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26Induces Loss of Epithelial Integrity
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Yao, Fei, Kausalya, Jaya P., Sia, Yee Yen, Teo, Audrey S.M., Lee, Wah Heng, Ong, Alicia G.M., Zhang, Zhenshui, Tan, Joanna H.J., Li, Guoliang, Bertrand, Denis, Liu, Xingliang, Poh, Huay Mei, Guan, Peiyong, Zhu, Feng, Pathiraja, Thushangi Nadeera, Ariyaratne, Pramila N., Rao, Jaideepraj, Woo, Xing Yi, Cai, Shaojiang, Mulawadi, Fabianus H., Poh, Wan Ting, Veeravalli, Lavanya, Chan, Chee Seng, Lim, Seong Soo, Leong, See Ting, Neo, Say Chuan, Choi, Poh Sum D., Chew, Elaine G.Y., Nagarajan, Niranjan, Jacques, Pierre-Étienne, So, Jimmy B.Y., Ruan, Xiaoan, Yeoh, Khay Guan, Tan, Patrick, Sung, Wing-Kin, Hunziker, Walter, Ruan, Yijun, and Hillmer, Axel M.
- Abstract
Genome rearrangements, a hallmark of cancer, can result in gene fusions with oncogenic properties. Using DNA paired-end-tag (DNA-PET) whole-genome sequencing, we analyzed 15 gastric cancers (GCs) from Southeast Asians. Rearrangements were enriched in open chromatin and shaped by chromatin structure. We identified seven rearrangement hot spots and 136 gene fusions. In three out of 100 GC cases, we found recurrent fusions between CLDN18, a tight junction gene, and ARHGAP26, a gene encoding a RHOA inhibitor. Epithelial cell lines expressing CLDN18-ARHGAP26displayed a dramatic loss of epithelial phenotype and long protrusions indicative of epithelial-mesenchymal transition (EMT). Fusion-positive cell lines showed impaired barrier properties, reduced cell-cell and cell-extracellular matrix adhesion, retarded wound healing, and inhibition of RHOA. Gain of invasion was seen in cancer cell lines expressing the fusion. Thus, CLDN18-ARHGAP26mediates epithelial disintegration, possibly leading to stomach H+leakage, and the fusion might contribute to invasiveness once a cell is transformed.
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- 2015
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13. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons.
- Author
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Fei Yao, Ariyaratne, Pramila N., Hillmer, Axel M., Wah Heng Lee, Guoliang Li, Teo, Audrey S. M., Xing Yi Woo, Zhenshui Zhang, Jieqi P. Chen, Wan Ting Poh, Zawack, Kelson F. B., Chee Seng Chan, See Ting Leong, Say Chuan Neo, Poh Sum D. Cho, Song Gao, Nagarajan, Niranjan, Thoreau, Hervé, Shahab, Atif, and Ruan, Xiaoan
- Subjects
- *
HUMAN genome , *CANCER genetics , *GENE mapping research , *GENETIC techniques , *GENOMICS - Abstract
Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10-20 kb and compared their characteristics with short insert (1 kb) libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer. [ABSTRACT FROM AUTHOR]
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- 2012
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14. A Common Deletion Polymorphism in the BIMGene Contributes to Intrinsic Imatinib Resistance in Chronic Myelogenous Leukemia
- Author
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Hillmer, Axel M, Ng, King-Pan, Chuah, Charles, Juan, Wen Chun, Ko, Tun-Kiat, Teo, Audrey S.M., Ariyaratne, Pramila N, Takahashi, Naoto, Sawada, Kenichi, Fei, Yao, Lee, Wah Heng, Huang, Weijie, Allen, John C, Woo, Xing Yi, Nagarajan, Niranjan, Kumar, Vikrant, Thalamuthu, Anbupalam, Poh, Wan Ting, Ang, Ai Leen, Mya, Hae Tha, How, Gee Fung, Yang, Li Yi, Koh, Liang Piu, Nadarajan, Veera S, Chng, Wee-Joo, Than, Hein, Lim, Lay Cheng, Goh, Yeow-Tee, Nöthen, Markus M, Wong, Tien Y, Shahab, Atif, Ruan, Xiaoan, Cacheux-Rataboul, Valère, Sung, Wing-Kin, Ruan, Yijun, and Ong, S. Tiong
- Abstract
Abstract 1666
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- 2011
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15. An oestrogen-receptor-alpha-bound human chromatin interactome.
- Author
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Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, and Ruan Y
- Subjects
- Binding Sites, Cell Line, Chromatin Immunoprecipitation, Cross-Linking Reagents, Formaldehyde, Humans, Promoter Regions, Genetic genetics, Protein Binding, Reproducibility of Results, Sequence Analysis, DNA, Transcription, Genetic, Transcriptional Activation, Chromatin genetics, Chromatin metabolism, Estrogen Receptor alpha metabolism, Genome, Human genetics
- Abstract
Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor alpha (ER-alpha) in the human genome. We found that most high-confidence remote ER-alpha-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-alpha functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.
- Published
- 2009
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