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1. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Author

Network, The Cancer Genome Atlas Research, Abeshouse, Adam, Adebamowo, Clement, Adebamowo, Sally N, Akbani, Rehan, Akeredolu, Teniola, Ally, Adrian, Anderson, Matthew L, Anur, Pavana, Appelbaum, Elizabeth L, Armenia, Joshua, Auman, J Todd, Bailey, Matthew H, Baker, Laurence, Balasundaram, Miruna, Balu, Saianand, Barthel, Floris P, Bartlett, John, Baylin, Stephen B, Behera, Madhusmita, Belyaev, Dmitry, Bennett, Joesph, Benz, Christopher, Beroukhim, Rameen, Birrer, Michael, Bocklage, Thèrése, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S, Bowen, Jay, Bowlby, Reanne, Boyd, Jeff, Brohl, Andrew S, Brooks, Denise, Byers, Lauren, Carlsen, Rebecca, Castro, Patricia, Chen, Hsiao-Wei, Cherniack, Andrew D, Chibon, Fréderic, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cooper, Lee AD, Cope, Leslie, Cordes, Matthew G, Crain, Daniel, Curley, Erin, Danilova, Ludmila, Dao, Fanny, Davis, Ian J, Davis, Lara E, Defreitas, Timothy, Delman, Keith, Demchok, John A, Demetri, George D, Demicco, Elizabeth G, Dhalla, Noreen, Diao, Lixia, Ding, Li, DiSaia, Phil, Dottino, Peter, Doyle, Leona A, Drill, Esther, Dubina, Michael, Eschbacher, Jennifer, Fedosenko, Konstantin, Felau, Ina, Ferguson, Martin L, Frazer, Scott, Fronick, Catrina C, Fulidou, Victoria, Fulton, Lucinda A, Fulton, Robert S, Gabriel, Stacey B, Gao, Jianjiong, Gao, Qingsong, Gardner, Johanna, Gastier-Foster, Julie M, Gay, Carl M, Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Godwin, Andrew K, Godwin, Eryn M, Gordienko, Elena, Grilley-Olson, Juneko E, Gutman, David A, Gutmann, David H, Hayes, D Neil, Hegde, Apurva M, Heiman, David I, Heins, Zachary, Helsel, Carmen, Hepperla, Austin J, Higgins, Kelly, Hoadley, Katherine A, and Hobensack, Shital

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Cancer, Human Genome, Digestive Diseases, Rare Diseases, Adult, Aged, Aged, 80 and over, Cluster Analysis, DNA Copy Number Variations, Epigenomics, Genome, Human, Genome-Wide Association Study, Humans, Middle Aged, Mutation, Sarcoma, Young Adult, Cancer Genome Atlas Research Network. Electronic address: elizabeth.demicco@sinaihealthsystem.ca, Cancer Genome Atlas Research Network, DNA methylation, The Cancer Genome Atlas, dedifferentiated liposarcoma, genomics, immune infiltration, leiomyosarcoma, molecular subtype, myxofibrosarcoma, pleomorphism, undifferentiated pleomorphic sarcoma, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (TP53, ATRX, RB1) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types.

Published
2017

2. Multi-disciplinary summit on genetics services for women with gynecologic cancers: A Society of Gynecologic Oncology White Paper.

Author

Randall, Leslie M, Pothuri, Bhavana, Swisher, Elizabeth M, Diaz, John P, Buchanan, Adam, Witkop, Catherine T, Bethan Powell, C, Smith, Ellen Blair, Robson, Mark E, Boyd, Jeff, Coleman, Robert L, and Lu, Karen

Subjects
Humans, Genital Neoplasms, Female, Genetic Services, Genetic Counseling, Gynecology, Patient Selection, Societies, Medical, Female, Congresses as Topic, Consensus Development Conferences as Topic, Practice Guidelines as Topic, Lynch Syndrome II, Genetic Testing, Hereditary Breast and Ovarian Cancer Syndrome, Surgical Oncology, Clinical Research, Prevention, Genetics, Ovarian Cancer, Cancer, Health Services, Rare Diseases, Oncology and Carcinogenesis, Paediatrics and Reproductive Medicine, Oncology & Carcinogenesis
Abstract

ObjectiveTo assess current practice, advise minimum standards, and identify educational gaps relevant to genetic screening, counseling, and testing of women affected by gynecologic cancers.MethodsThe Society of Gynecologic Oncology (SGO) organized a multidisciplinary summit that included representatives from the American College of Obstetricians and Gynecologists (ACOG), the American Society Clinical Oncology (ASCO), the National Society of Genetic Counselors (NSGC), and patient advocacy groups, BrightPink and Facing our Risk of Cancer Empowered (FORCE). Three subject areas were discussed: care delivery models for genetic testing, barriers to genetic testing, and educational opportunities for providers of genetic testing.ResultsThe group endorsed current SGO, National Comprehensive Cancer Network (NCCN), and NSGC genetic testing guidelines for women affected with ovarian, tubal, peritoneal cancers, or DNA mismatch repair deficient endometrial cancer. Three main areas of unmet need were identified: timely and universal genetic testing for women with ovarian, fallopian tube, and peritoneal cancers; education regarding minimum standards for genetic counseling and testing; and barriers to implementation of testing of both affected individuals as well as cascade testing of family members. Consensus building among all stakeholders resulted in an action plan to address gaps in education of gynecologic oncology providers and delivery of cancer genetics care.

Published
2017

4. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Author

Abeshouse, Adam, Adebamowo, Clement, Adebamowo, Sally N., Akbani, Rehan, Akeredolu, Teniola, Ally, Adrian, Anderson, Matthew L., Anur, Pavana, Appelbaum, Elizabeth L., Armenia, Joshua, Auman, J. Todd, Bailey, Matthew H., Baker, Laurence, Balasundaram, Miruna, Balu, Saianand, Barthel, Floris P., Bartlett, John, Baylin, Stephen B., Behera, Madhusmita, Belyaev, Dmitry, Bennett, Joesph, Benz, Christopher, Beroukhim, Rameen, Birrer, Michael, Bocklage, Thèrése, Bodenheimer, Tom, Boice, Lori, Bootwalla, Moiz S., Bowen, Jay, Bowlby, Reanne, Boyd, Jeff, Brohl, Andrew S., Brooks, Denise, Byers, Lauren, Carlsen, Rebecca, Castro, Patricia, Chen, Hsiao-Wei, Cherniack, Andrew D., Chibon, Fréderic, Chin, Lynda, Cho, Juok, Chuah, Eric, Chudamani, Sudha, Cibulskis, Carrie, Cooper, Lee A.D., Cope, Leslie, Cordes, Matthew G., Crain, Daniel, Curley, Erin, Danilova, Ludmila, Dao, Fanny, Davis, Ian J., Davis, Lara E., Defreitas, Timothy, Delman, Keith, Demchok, John A., Demetri, George D., Demicco, Elizabeth G., Dhalla, Noreen, Diao, Lixia, Ding, Li, DiSaia, Phil, Dottino, Peter, Doyle, Leona A., Drill, Esther, Dubina, Michael, Eschbacher, Jennifer, Fedosenko, Konstantin, Felau, Ina, Ferguson, Martin L., Frazer, Scott, Fronick, Catrina C., Fulidou, Victoria, Fulton, Lucinda A., Fulton, Robert S., Gabriel, Stacey B., Gao, Jianjiong, Gao, Qingsong, Gardner, Johanna, Gastier-Foster, Julie M., Gay, Carl M., Gehlenborg, Nils, Gerken, Mark, Getz, Gad, Godwin, Andrew K., Godwin, Eryn M., Gordienko, Elena, Grilley-Olson, Juneko E., Gutman, David A., Gutmann, David H., Hayes, D. Neil, Hegde, Apurva M., Heiman, David I., Heins, Zachary, Helsel, Carmen, Hepperla, Austin J., Higgins, Kelly, Hoadley, Katherine A., Hobensack, Shital, Holt, Robert A., Hoon, Dave B., Hornick, Jason L., Hoyle, Alan P., Hu, Xin, Huang, Mei, Hutter, Carolyn M., Iacocca, Mary, Ingram, Davis R., Ittmann, Michael, Iype, Lisa, Jefferys, Stuart R., Jones, Kevin B., Jones, Corbin D., Jones, Steven J.M., Kalir, Tamara, Karlan, Beth Y., Karseladze, Apollon, Kasaian, Katayoon, Kim, Jaegil, Kundra, Ritika, Kuo, Hanluen, Ladanyi, Marc, Lai, Phillip H., Laird, Peter W., Larsson, Erik, Lawrence, Michael S., Lazar, Alexander J., Lee, Sanghoon, Lee, Darlene, Lehmann, Kjong-Van, Leraas, Kristen M., Lester, Jenny, Levine, Douglas A., Li, Irene, Lichtenberg, Tara M., Lin, Pei, Liu, Jia, Liu, Wenbin, Liu, Eric Minwei, Lolla, Laxmi, Lu, Yiling, Ma, Yussanne, Madan, Rashna, Maglinte, Dennis T., Magliocco, Anthony, Maki, Robert G., Mallery, David, Manikhas, Georgy, Mardis, Elaine R., Mariamidze, Armaz, Marra, Marco A., Martignetti, John A., Martinez, Cathleen, Mayo, Michael, McLellan, Michael D., Meier, Sam, Meng, Shaowu, Meyerson, Matthew, Mieczkowski, Piotr A., Miller, Christopher A., Mills, Gordon B., Moore, Richard A., Morris, Scott, Mose, Lisle E., Mozgovoy, Evgeny, Mungall, Andrew J., Mungall, Karen, Nalisnik, Michael, Naresh, Rashi, Newton, Yulia, Noble, Michael S., Novak, Janet E., Ochoa, Angelica, Olvera, Narciso, Owonikoko, Taofeek K., Paklina, Oxana, Parfitt, Jeremy, Parker, Joel S., Pastore, Alessandro, Paulauskis, Joseph, Penny, Robert, Pereira, Elena, Perou, Charles M., Perou, Amy H., Pihl, Todd, Pollock, Raphael E., Potapova, Olga, Radenbaugh, Amie J., Ramalingam, Suresh S., Ramirez, Nilsa C., Rathmell, W. Kimryn, Raut, Chandrajit P., Riedel, Richard F., Reilly, Colleen, Reynolds, Sheila M., Roach, Jeffrey, Robertson, A. Gordon, Roszik, Jason, Rubin, Brian P., Sadeghi, Sara, Saksena, Gordon, Salner, Andrew, Sanchez-Vega, Francisco, Sander, Chris, Schein, Jacqueline E., Schmidt, Heather K., Schultz, Nikolaus, Schumacher, Steven E., Sekhon, Harman, Senbabaoglu, Yasin, Setdikova, Galiya, Shelton, Candace, Shelton, Troy, Shen, Ronglai, Shi, Yan, Shih, Juliann, Shmulevich, Ilya, Sica, Gabriel L., Simons, Janae V., Singer, Samuel, Sipahimalani, Payal, Skelly, Tara, Socci, Nicholas, Sofia, Heidi J., Soloway, Matthew G., Spellman, Paul, Sun, Qiang, Swanson, Patricia, Tam, Angela, Tan, Donghui, Tarnuzzer, Roy, Thiessen, Nina, Thompson, Eric, Thorne, Leigh B., Tong, Pan, Torres, Keila E., van de Rijn, Matt, Van Den Berg, David J., Van Tine, Brian A., Veluvolu, Umadevi, Verhaak, Roel, Voet, Doug, Voronina, Olga, Wan, Yunhu, Wang, Zhining, Wang, Jing, Weinstein, John N., Weisenberger, Daniel J., Wilkerson, Matthew D., Wilson, Richard K., Wise, Lisa, Wong, Tina, Wong, Winghing, Wrangle, John, Wu, Ye, Wyczalkowski, Matthew, Yang, Liming, Yau, Christina, Yellapantula, Venkata, Zenklusen, Jean C., Zhang, Jiashan (Julia), Zhang, Hailei, Zhang, Hongxin, and Zmuda, Erik

Published
2017
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5. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.

Author

Olshen, Adam B, Gold, Bert, Lohmueller, Kirk E, Struewing, Jeffery P, Satagopan, Jaya, Stefanov, Stefan A, Eskin, Eleazar, Kirchhoff, Tomas, Lautenberger, James A, Klein, Robert J, Friedman, Eitan, Norton, Larry, Ellis, Nathan A, Viale, Agnes, Lee, Catherine S, Borgen, Patrick I, Clark, Andrew G, Offit, Kenneth, and Boyd, Jeff

Subjects
Humans, Chromosome Mapping, Gene Frequency, Genotype, Haplotypes, Homozygote, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Principal Component Analysis, Jews, Female, Genetic Variation, Polymorphism, Single Nucleotide, Genetics & Heredity, Genetics
Abstract

BackgroundGenetic isolates such as the Ashkenazi Jews (AJ) potentially offer advantages in mapping novel loci in whole genome disease association studies. To analyze patterns of genetic variation in AJ, genotypes of 101 healthy individuals were determined using the Affymetrix EAv3 500 K SNP array and compared to 60 CEPH-derived HapMap (CEU) individuals. 435,632 SNPs overlapped and met annotation criteria in the two groups.ResultsA small but significant global difference in allele frequencies between AJ and CEU was demonstrated by a mean FST of 0.009 (P < 0.001); large regions that differed were found on chromosomes 2 and 6. Haplotype blocks inferred from pairwise linkage disequilibrium (LD) statistics (Haploview) as well as by expectation-maximization haplotype phase inference (HAP) showed a greater number of haplotype blocks in AJ compared to CEU by Haploview (50,397 vs. 44,169) or by HAP (59,269 vs. 54,457). Average haplotype blocks were smaller in AJ compared to CEU (e.g., 36.8 kb vs. 40.5 kb HAP). Analysis of global patterns of local LD decay for closely-spaced SNPs in CEU demonstrated more LD, while for SNPs further apart, LD was slightly greater in the AJ. A likelihood ratio approach showed that runs of homozygous SNPs were approximately 20% longer in AJ. A principal components analysis was sufficient to completely resolve the CEU from the AJ.ConclusionLD in the AJ versus was lower than expected by some measures and higher by others. Any putative advantage in whole genome association mapping using the AJ population will be highly dependent on regional LD structure.

Published
2008

19. Data from Microarray Analysis of Early Stage Serous Ovarian Cancers Shows Profiles Predictive of Favorable Outcome

Author

Berchuck, Andrew, primary, Iversen, Edwin S., primary, Luo, Jingqin, primary, Clarke, Jennifer P., primary, Horne, Hisani, primary, Levine, Douglas A., primary, Boyd, Jeff, primary, Alonso, Miguel A., primary, Secord, Angeles Alvarez, primary, Bernardini, Marcus Q., primary, Barnett, Jason C., primary, Boren, Todd, primary, Murphy, Susan K., primary, Dressman, Holly K., primary, Marks, Jeffrey R., primary, and Lancaster, Johnathan M., primary

Published
2023
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22. Supplementary Figure S1 from Gene Expression Profiles Associated with Response to Chemotherapy in Epithelial Ovarian Cancers

Author

Jazaeri, Amir A., primary, Awtrey, Christopher S., primary, Chandramouli, Gadisetti V.R., primary, Chuang, Yao Eric, primary, Khan, Javed, primary, Sotiriou, Christos, primary, Aprelikova, Olga, primary, Yee, Cindy J., primary, Zorn, Kristin K., primary, Birrer, Michael J., primary, Barrett, J. Carl, primary, and Boyd, Jeff, primary

Published
2023
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23. Supplementary Tables S1-S3 from Microarray Analysis of Early Stage Serous Ovarian Cancers Shows Profiles Predictive of Favorable Outcome

Author

Berchuck, Andrew, primary, Iversen, Edwin S., primary, Luo, Jingqin, primary, Clarke, Jennifer P., primary, Horne, Hisani, primary, Levine, Douglas A., primary, Boyd, Jeff, primary, Alonso, Miguel A., primary, Secord, Angeles Alvarez, primary, Bernardini, Marcus Q., primary, Barnett, Jason C., primary, Boren, Todd, primary, Murphy, Susan K., primary, Dressman, Holly K., primary, Marks, Jeffrey R., primary, and Lancaster, Johnathan M., primary

Published
2023
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24. Article Figures 1-4 from Gene Expression Profiles Associated with Response to Chemotherapy in Epithelial Ovarian Cancers

Author

Jazaeri, Amir A., primary, Awtrey, Christopher S., primary, Chandramouli, Gadisetti V.R., primary, Chuang, Yao Eric, primary, Khan, Javed, primary, Sotiriou, Christos, primary, Aprelikova, Olga, primary, Yee, Cindy J., primary, Zorn, Kristin K., primary, Birrer, Michael J., primary, Barrett, J. Carl, primary, and Boyd, Jeff, primary

Published
2023
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26. Supplementary Figure 3A Gene List from Gene Expression Profiles Associated with Response to Chemotherapy in Epithelial Ovarian Cancers

Author

Jazaeri, Amir A., primary, Awtrey, Christopher S., primary, Chandramouli, Gadisetti V.R., primary, Chuang, Yao Eric, primary, Khan, Javed, primary, Sotiriou, Christos, primary, Aprelikova, Olga, primary, Yee, Cindy J., primary, Zorn, Kristin K., primary, Birrer, Michael J., primary, Barrett, J. Carl, primary, and Boyd, Jeff, primary

Published
2023
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40. Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

Author

Yan, Xiaohui, Hu, Zhongyi, Feng, Yi, Hu, Xiaowen, Yuan, Jiao, Zhao, Sihai D., Zhang, Youyou, Yang, Lu, Shan, Weiwei, He, Qun, Fan, Lingling, Kandalaft, Lana E., Tanyi, Janos L., Li, Chunsheng, Yuan, Chao-Xing, Zhang, Dongmei, Yuan, Huiqing, Hua, Keqin, Lu, Yiling, Katsaros, Dionyssios, Huang, Qihong, Montone, Kathleen, Fan, Yi, Coukos, George, Boyd, Jeff, Sood, Anil K., Rebbeck, Timothy, Mills, Gordon B., Dang, Chi V., and Zhang, Lin

Published
2015
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42. A Functional Genomic Approach Identifies FAL1 as an Oncogenic Long Noncoding RNA that Associates with BMI1 and Represses p21 Expression in Cancer

Author

Hu, Xiaowen, Feng, Yi, Zhang, Dongmei, Zhao, Sihai D., Hu, Zhongyi, Greshock, Joel, Zhang, Youyou, Yang, Lu, Zhong, Xiaomin, Wang, Li-Ping, Jean, Stephanie, Li, Chunsheng, Huang, Qihong, Katsaros, Dionyssios, Montone, Kathleen T., Tanyi, Janos L., Lu, Yiling, Boyd, Jeff, Nathanson, Katherine L., Li, Hongzhe, Mills, Gordon B., and Zhang, Lin

Published
2014
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43. Classification of Ovarian Cancer: A Genomic Analysis

Author

Stany, Michael P., Bonome, Tomas, Wamunyokoli, Fred, Zorn, Kristen, Ozbun, Laurent, Park, Dong-Choon, Hao, Ke, Boyd, Jeff, Sood, Anil K., Gershenson, David M., Berkowitz, Ross S., Mok, Samuel C., Birrer, Michael J., Coukos, George, editor, Berchuck, Andrew, editor, and Ozols, Robert, editor

Published
2008
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45. Pancreatic Cancer Patient-derived Organoids Can Predict Response to Neoadjuvant Chemotherapy

Author

Demyan, Lyudmyla, primary, Habowski, Amber N., additional, Plenker, Dennis, additional, King, Daniel A., additional, Standring, Oliver J., additional, Tsang, Caitlin, additional, St. Surin, Luce, additional, Rishi, Arvind, additional, Crawford, James M., additional, Boyd, Jeff, additional, Pasha, Shamsher A., additional, Patel, Hardik, additional, Galluzzo, Zachary, additional, Metz, Christine, additional, Gregersen, Peter K., additional, Fox, Sharon, additional, Valente, Cristina, additional, Abadali, Sonya, additional, Matadial-Ragoo, Steffi, additional, DePeralta, Danielle K., additional, Deutsch, Gary B., additional, Herman, Joseph M., additional, Talamini, Mark A., additional, Tuveson, David A., additional, and Weiss, Matthew J., additional

Published
2022
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