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1. Effects of Different Bridges of A Series of c-Donor-nc-Bridge-cf- Acceptor Type Block Copolymers for Potential Solar Cell Applications

Author

Hasib, Muhammad A., Sun, Sam-Shajing, Hasib, Muhammad A., and Sun, Sam-Shajing

Abstract

A series of c-D-nc-B-cf-A (or DBpfA, p=0,1,2,4,6) type of block copolymers has been designed, synthesized, and systematically studied for photo induced charge separations; where c-D is an electron-donating conjugated block, nc-B is a non-conjugated bridge unit, and cf-A is an electron-accepting conjugated and fluorinated block. A series of photoluminescence quenching measurements with and without different bridge units were evaluated for DBpfA. This study highlights the chemical molecular bridge effects on the optoelectronic property of the DBpfA type block copolymer. Specifically, the DB1fA block copolymer (where only one methylene unit is present in the bridge unit) appears exhibiting the best optoelectronic performance. DfA block copolymer (without any bridge unit) exhibits photoluminescence quenching and optoelectronic property that is between the shortest and longest bridge units, and this can be explained by the calculated four stable state twisting angles (most stable state is at a seventeen degree twist) between conjugated donor and conjugated acceptor blocks. The optoelectronic properties appear following the PL quenching nicely.

Published
2019

2. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Author

Gao, Qingsong, Gao, Qingsong, Liang, Wen-Wei, Foltz, Steven M, Mutharasu, Gnanavel, Jayasinghe, Reyka G, Cao, Song, Liao, Wen-Wei, Reynolds, Sheila M, Wyczalkowski, Matthew A, Yao, Lijun, Yu, Lihua, Sun, Sam Q, Fusion Analysis Working Group, Cancer Genome Atlas Research Network, Chen, Ken, Lazar, Alexander J, Fields, Ryan C, Wendl, Michael C, Van Tine, Brian A, Vij, Ravi, Chen, Feng, Nykter, Matti, Shmulevich, Ilya, Ding, Li, Gao, Qingsong, Gao, Qingsong, Liang, Wen-Wei, Foltz, Steven M, Mutharasu, Gnanavel, Jayasinghe, Reyka G, Cao, Song, Liao, Wen-Wei, Reynolds, Sheila M, Wyczalkowski, Matthew A, Yao, Lijun, Yu, Lihua, Sun, Sam Q, Fusion Analysis Working Group, Cancer Genome Atlas Research Network, Chen, Ken, Lazar, Alexander J, Fields, Ryan C, Wendl, Michael C, Van Tine, Brian A, Vij, Ravi, Chen, Feng, Nykter, Matti, Shmulevich, Ilya, and Ding, Li

Abstract

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy.

Published
2018

3. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Author

Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, The Cancer Genome Atlas Research Network, Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, and The Cancer Genome Atlas Research Network

Published
2018

4. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

Author

Gao, Qingsong, Liang, Wen Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, de Krijger, Ronald, The Fusion Analysis Working Group, The Cancer Genome Atlas Research Network, Gao, Qingsong, Liang, Wen Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, de Krijger, Ronald, The Fusion Analysis Working Group, and The Cancer Genome Atlas Research Network

Published
2018

5. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

Author

Gao, Qingsong, Liang, Wen Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, de Krijger, Ronald, The Fusion Analysis Working Group, The Cancer Genome Atlas Research Network, Gao, Qingsong, Liang, Wen Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, de Krijger, Ronald, The Fusion Analysis Working Group, and The Cancer Genome Atlas Research Network

Published
2018

6. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Author

Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, The Cancer Genome Atlas Research Network, Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, and The Cancer Genome Atlas Research Network

Published
2018

7. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Author

Gao, Qingsong, Gao, Qingsong, Liang, Wen-Wei, Foltz, Steven M, Mutharasu, Gnanavel, Jayasinghe, Reyka G, Cao, Song, Liao, Wen-Wei, Reynolds, Sheila M, Wyczalkowski, Matthew A, Yao, Lijun, Yu, Lihua, Sun, Sam Q, Fusion Analysis Working Group, Cancer Genome Atlas Research Network, Chen, Ken, Lazar, Alexander J, Fields, Ryan C, Wendl, Michael C, Van Tine, Brian A, Vij, Ravi, Chen, Feng, Nykter, Matti, Shmulevich, Ilya, Ding, Li, Gao, Qingsong, Gao, Qingsong, Liang, Wen-Wei, Foltz, Steven M, Mutharasu, Gnanavel, Jayasinghe, Reyka G, Cao, Song, Liao, Wen-Wei, Reynolds, Sheila M, Wyczalkowski, Matthew A, Yao, Lijun, Yu, Lihua, Sun, Sam Q, Fusion Analysis Working Group, Cancer Genome Atlas Research Network, Chen, Ken, Lazar, Alexander J, Fields, Ryan C, Wendl, Michael C, Van Tine, Brian A, Vij, Ravi, Chen, Feng, Nykter, Matti, Shmulevich, Ilya, and Ding, Li

Abstract

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy.

Published
2018

8. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

Author

Gao, Qingsong, Liang, Wen Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, de Krijger, Ronald, The Fusion Analysis Working Group, The Cancer Genome Atlas Research Network, Gao, Qingsong, Liang, Wen Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, de Krijger, Ronald, The Fusion Analysis Working Group, and The Cancer Genome Atlas Research Network

Published
2018

9. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Author

Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, The Cancer Genome Atlas Research Network, Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, and The Cancer Genome Atlas Research Network

Published
2018

10. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

Author

Ding, Li, Ding, Li, Bailey, Matthew H, Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L, Weerasinghe, Amila, Huang, Kuan-Lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M, Cherniack, Andrew D, Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M, Mills, Gordon B, Wyczalkowski, Matthew A, Vincent, Benjamin G, Hutter, Carolyn M, Zenklusen, Jean Claude, Hoadley, Katherine A, Wendl, Michael C, Shmulevich, Llya, Lazar, Alexander J, Wheeler, David A, Getz, Gad, Cancer Genome Atlas Research Network, Ding, Li, Ding, Li, Bailey, Matthew H, Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L, Weerasinghe, Amila, Huang, Kuan-Lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M, Cherniack, Andrew D, Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M, Mills, Gordon B, Wyczalkowski, Matthew A, Vincent, Benjamin G, Hutter, Carolyn M, Zenklusen, Jean Claude, Hoadley, Katherine A, Wendl, Michael C, Shmulevich, Llya, Lazar, Alexander J, Wheeler, David A, Getz, Gad, and Cancer Genome Atlas Research Network

Abstract

The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing.

Published
2018

11. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Author

Onderzoeksgroep 6, Pathologie Pathologen staf, Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, The Cancer Genome Atlas Research Network, Onderzoeksgroep 6, Pathologie Pathologen staf, Ding, Li, Bailey, Matthew H., Porta-Pardo, Eduard, Thorsson, Vesteinn, Colaprico, Antonio, Bertrand, Denis, Gibbs, David L., Weerasinghe, Amila, Huang, Kuan lin, Tokheim, Collin, Cortés-Ciriano, Isidro, Jayasinghe, Reyka, Chen, Feng, Yu, Lihua, Sun, Sam, Olsen, Catharina, Kim, Jaegil, Taylor, Alison M., Cherniack, Andrew D., Akbani, Rehan, Suphavilai, Chayaporn, Nagarajan, Niranjan, Stuart, Joshua M., Mills, Gordon B., Wyczalkowski, Matthew A., Vincent, Benjamin G., Hutter, Carolyn M., Zenklusen, Jean Claude, Hoadley, Katherine A., Wendl, Michael C., Shmulevich, llya, Lazar, Alexander J., Wheeler, David A., Getz, Gad, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, de Krijger, Ronald, and The Cancer Genome Atlas Research Network

Published
2018

12. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

Author

Onderzoeksgroep 6, Pathologie Pathologen staf, Gao, Qingsong, Liang, Wen Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, de Krijger, Ronald, The Fusion Analysis Working Group, The Cancer Genome Atlas Research Network, Onderzoeksgroep 6, Pathologie Pathologen staf, Gao, Qingsong, Liang, Wen Wei, Foltz, Steven M., Mutharasu, Gnanavel, Jayasinghe, Reyka G., Cao, Song, Liao, Wen Wei, Reynolds, Sheila M., Wyczalkowski, Matthew A., Yao, Lijun, Yu, Lihua, Sun, Sam Q., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, de Krijger, Ronald, The Fusion Analysis Working Group, and The Cancer Genome Atlas Research Network

Published
2018

13. Design, Synthesis, Characterizations, and Processing of a Novel c-Donor-nc-Bridge-cf-Acceptor Type Block Copolymer for Optoelecronic Applications

Author

H. Nguyen, Thuong, Hasib, Muhammad, Wang, Dan, Sun, Sam-Shajing, H. Nguyen, Thuong, Hasib, Muhammad, Wang, Dan, and Sun, Sam-Shajing

Abstract

A novel c-D-nc-B-cf-A (or DBfA) type of block copolymer has been designed, synthesized, characterized, and preliminarily studied for optoectronic applications, where c-D is a conjugated donor type polyphenylenevinylene (PPV) block, nc-B is a non-conjugated bridge unit, and cf-A is a conjugated and fluorinated acceptor type PPV block. The frontier HOMO/LUMO orbital levels of D and fA conjugated blocks are -5.22/-3.06 and -6.10/-3.43 as determined from electrochemical and optical measurements. Photoluminescence emissions of D and fA are quenched in DBfA indicating a potential photo induced charge separation pathway between the donor and the acceptor blocks. Solid state thin film studies revealed more uniform and nano-scale phase separated morphologies in DBfA as compared to D/fA blend. A two orders of magnitude enhancement of photoelectric energy conversion efficiency was observed in a best solar cell fabricated from the DBfA block copolymer as compared to a best cell fabricated from the corresponding D/fA blend. Such significant photoelectric conversion enhancement could be attributed to the improvements of phase separated and bicontinously ordered nanostructure (BONS) morphology in DBfA as compared to D/fA.

Published
2016

14. Highly Efficient Flexible Hybrid Photovoltaic Cells Based on Low-Band-Gap Conjugated Polymers Sensitized by Nanoparticle-Grafted Carbon

Author

AIR FORCE RESEARCH LAB WRIGHT-PATTERSON AFB OH MATERIALS AND MANUFACTURING DIRECTORATE, Sun, Sam-Shajing, Dai, Liming, AIR FORCE RESEARCH LAB WRIGHT-PATTERSON AFB OH MATERIALS AND MANUFACTURING DIRECTORATE, Sun, Sam-Shajing, and Dai, Liming

Abstract

During the entire project period, significant progress was made on the design, modeling, synthesis, and characterization of several series functional and processable electro-active conjugated polymers with evolving frontier orbital energy levels and energy gaps that are very attractive for optoelectronic applications at VIS-NIR radiation energy ranges. Details of these new functional polymer developments are described. In addition, quantum dot grafted carbon nanotubes for potential optoelectronic applications were studied. All materials developed were fabricated into devices and their performance characteristics were evaluated. These include low-band-gap conjugated polymers such as 55-C12-PTV, SFPTV and P(C6OTV-SFTV), as well as the (-DBAB-)n block copolymer systems, and quantum dot-grafted carbon nanotubes., Prepared in cooperation with University of Dayton, Dayton, OH.

Published
2010

15. Nonlinear Optical Properties of Nanostructured Supramolecular Organic Semiconductor

Author

HAMPTON UNIV VA DEPT OF PHYSICS, Seo, JaeTae, Yang, Qiguang, Ma, SeongMin, Creekmore, Liawood, Battle, Russell, Jackson, Ashley, Skyles, Tifney, Brown, Herbert, Tabibi, Bagher, Sun, Sam-Shajing, Zhang, Chen, HAMPTON UNIV VA DEPT OF PHYSICS, Seo, JaeTae, Yang, Qiguang, Ma, SeongMin, Creekmore, Liawood, Battle, Russell, Jackson, Ashley, Skyles, Tifney, Brown, Herbert, Tabibi, Bagher, Sun, Sam-Shajing, and Zhang, Chen

Abstract

Resonant third-order optical susceptibility and hyperpolarizability of donor polymer in chloroform were revealed to be ~2.5 - 9.1x10(exp -20) sq m/V2 and ~8.6 10(exp -42) m5/V2 by degenerate four-wave mixing in nanosecond scale at 532 nm, which was attributed to the resonant enhancement., THE SEVENTH INTERNATIONAL CONFERENCE ON NEW PHENOMENA IN MESOSCOPIC STRUCTURES & THE FIFTH INTERNATIONAL CONFERENCE ON SURFACES AND INTERFACES OF MESOSCOPIC DEVICES 27 November-2 December 2005, Maui, Hawaii, USA. Pub. in Journal of Physics, v38, p53-56, 2006. Sponsored part by Army Research Office contract W911NF-04-1-0393, NSF grant EEC-0532472, HRD-0400041, PHY0139048, DOE grant DE-EF02-97ER41035.

Published
2006

16. Novel Nano-Phase Ordered Polymer Systems for Efficient Photovoltaic Applications

Author

NORFOLK STATE UNIV VA, Sun, Sam, NORFOLK STATE UNIV VA, and Sun, Sam

Abstract

A novel polythiophene -DBAB- type block copolymer system has been developed, where D is a new sulfide derivatized polythiophene donor block, A is a fluorine derivatized polythiophene acceptor block, and B is a non conjugated and flexible bridge chain. In donor block, a dithiathiophene ring derivatized polythiophene was used due to it is chemically more stable than the no-ring analogs. This structure also drastically limits the large steric hindrance in non-cyclized ones and is expected to result in high electrical conductivity. Additionally, the monomers have no possibility for alpha,beta' or beta, beta' coupling during the polymerization. Sulfur is also known to be more electron donating and electro polarizable then oxygen. Most importantly, a fluorine derivatized polythiophene acceptor block has also been successfully developed. The fluorine substituted groups are known to be more easily phase separated from hydrocarbon groups due to their hydrophilicity differences, therefore, nano phase separation between the donor and acceptor blocks would be greatly enhanced. The newly developed polythiophenes have been characterized using spectroscopic, electrochemical, and electron microscopic methods.

Published
2005

23. A Center for Organic Photonic Materials Research

Author

NORFOLK STATE UNIV VA, Sun, Sam, NORFOLK STATE UNIV VA, and Sun, Sam

Abstract

A Center for Organic Photonic Materials Research (COPMR) was established at Norfolk State University (NSU). Novel and high efficiency optoelectronic and nano structured polymeric materials are the main research focus. Specifically, during the performance period, a series of -DBAB- type of block copolymers, where D is a conjugated electron donating block, A is a conjugated electron withdrawing acceptor block, and B is a non conjugated and flexible bridge unit, have been designed, synthesized and characterized. It was found that the photoconductivity of the synthesized -DBAB- type block copolymers was much better then the simple donor/acceptor blends under identical conditions. This was attributed mainly to the improvement in spatial domain for photo induced charge separation and transportation. Energy level domain optimizations have also been analyzed using classic electron transfer theory. These materials can be potentially developed to fabricate inexpensive, lightweight and flexible plastic' solar cells. Additionally, a new photo crosslinkable nonlinear optical polymer system has also been developed that may provide a photolithographic alternative for polymeric electro-optical modulator device fabrication.

Published
2004

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