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34 results on '"Dooling, David J."'

1. Whole-genome analysis informs breast cancer response to aromatase inhibition

Author

Ellis, Matthew J, Ding, Li, Shen, Dong, Luo, Jingqin, Suman, Vera J, Wallis, John W, Van Tine, Brian A, Hoog, Jeremy, Goiffon, Reece J, Goldstein, Theodore C, Ng, Sam, Lin, Li, Crowder, Robert, Snider, Jacqueline, Ballman, Karla, Weber, Jason, Chen, Ken, Koboldt, Daniel C, Kandoth, Cyriac, Schierding, William S, McMichael, Joshua F, Miller, Christopher A, Lu, Charles, Harris, Christopher C, McLellan, Michael D, Wendl, Michael C, DeSchryver, Katherine, Allred, D Craig, Esserman, Laura, Unzeitig, Gary, Margenthaler, Julie, Babiera, GV, Marcom, P Kelly, Guenther, JM, Leitch, Marilyn, Hunt, Kelly, Olson, John, Tao, Yu, Maher, Christopher A, Fulton, Lucinda L, Fulton, Robert S, Harrison, Michelle, Oberkfell, Ben, Du, Feiyu, Demeter, Ryan, Vickery, Tammi L, Elhammali, Adnan, Piwnica-Worms, Helen, McDonald, Sandra, Watson, Mark, Dooling, David J, Ota, David, Chang, Li-Wei, Bose, Ron, Ley, Timothy J, Piwnica-Worms, David, Stuart, Joshua M, Wilson, Richard K, and Mardis, Elaine R

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Clinical Sciences, Oncology and Carcinogenesis, Cancer Genomics, Human Genome, Biotechnology, Clinical Research, Women's Health, Breast Cancer, Cancer, Clinical Trials and Supportive Activities, 2.1 Biological and endogenous factors, 4.2 Evaluation of markers and technologies, 4.1 Discovery and preclinical testing of markers and technologies, 6.1 Pharmaceuticals, Anastrozole, Androstadienes, Antineoplastic Agents, Aromatase, Aromatase Inhibitors, Breast Neoplasms, DNA Repair, Exome, Exons, Female, Genetic Variation, Genome, Human, Humans, Letrozole, MAP Kinase Kinase 4, MAP Kinase Kinase Kinase 1, Mutation, Nitriles, Receptors, Estrogen, Treatment Outcome, Triazoles, General Science & Technology
Abstract

To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, we studied pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant aromatase inhibitor therapy by massively parallel sequencing and analysis. Eighteen significantly mutated genes were identified, including five genes (RUNX1, CBFB, MYH9, MLL3 and SF3B1) previously linked to haematopoietic disorders. Mutant MAP3K1 was associated with luminal A status, low-grade histology and low proliferation rates, whereas mutant TP53 was associated with the opposite pattern. Moreover, mutant GATA3 correlated with suppression of proliferation upon aromatase inhibitor treatment. Pathway analysis demonstrated that mutations in MAP2K4, a MAP3K1 substrate, produced similar perturbations as MAP3K1 loss. Distinct phenotypes in oestrogen-receptor-positive breast cancer are associated with specific patterns of somatic mutations that map into cellular pathways linked to tumour biology, but most recurrent mutations are relatively infrequent. Prospective clinical trials based on these findings will require comprehensive genome sequencing.

Published
2012

2. A novel retinoblastoma therapy from genomic and epigenetic analyses.

Author

Zhang, Jinghui, Benavente, Claudia A, McEvoy, Justina, Flores-Otero, Jacqueline, Ding, Li, Chen, Xiang, Ulyanov, Anatoly, Wu, Gang, Wilson, Matthew, Wang, Jianmin, Brennan, Rachel, Rusch, Michael, Manning, Amity L, Ma, Jing, Easton, John, Shurtleff, Sheila, Mullighan, Charles, Pounds, Stanley, Mukatira, Suraj, Gupta, Pankaj, Neale, Geoff, Zhao, David, Lu, Charles, Fulton, Robert S, Fulton, Lucinda L, Hong, Xin, Dooling, David J, Ochoa, Kerri, Naeve, Clayton, Dyson, Nicholas J, Mardis, Elaine R, Bahrami, Armita, Ellison, David, Wilson, Richard K, Downing, James R, and Dyer, Michael A

Subjects
Cell Line, Animals, Humans, Mice, Retinoblastoma, Aneuploidy, Chromosomal Instability, Intracellular Signaling Peptides and Proteins, Retinoblastoma Protein, Protein Kinase Inhibitors, Xenograft Model Antitumor Assays, Sequence Analysis, DNA, Genomics, Cell Death, Cell Survival, Epigenesis, Genetic, Gene Expression Regulation, Neoplastic, Mutation, Genes, Retinoblastoma, Protein-Tyrosine Kinases, Molecular Targeted Therapy, Syk Kinase, Epigenesis, Genetic, Gene Expression Regulation, Neoplastic, Genes, Sequence Analysis, DNA, General Science & Technology
Abstract

Retinoblastoma is an aggressive childhood cancer of the developing retina that is initiated by the biallelic loss of RB1. Tumours progress very quickly following RB1 inactivation but the underlying mechanism is not known. Here we show that the retinoblastoma genome is stable, but that multiple cancer pathways can be epigenetically deregulated. To identify the mutations that cooperate with RB1 loss, we performed whole-genome sequencing of retinoblastomas. The overall mutational rate was very low; RB1 was the only known cancer gene mutated. We then evaluated the role of RB1 in genome stability and considered non-genetic mechanisms of cancer pathway deregulation. For example, the proto-oncogene SYK is upregulated in retinoblastoma and is required for tumour cell survival. Targeting SYK with a small-molecule inhibitor induced retinoblastoma tumour cell death in vitro and in vivo. Thus, retinoblastomas may develop quickly as a result of the epigenetic deregulation of key cancer pathways as a direct or indirect result of RB1 loss.

Published
2012

3. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

Author

McLendon, Roger, Friedman, Allan, Bigner, Darrell, Van Meir, Erwin G, Brat, Daniel J, M. Mastrogianakis, Gena, Olson, Jeffrey J, Mikkelsen, Tom, Lehman, Norman, Aldape, Ken, Alfred Yung, WK, Bogler, Oliver, VandenBerg, Scott, Berger, Mitchel, Prados, Michael, Muzny, Donna, Morgan, Margaret, Scherer, Steve, Sabo, Aniko, Nazareth, Lynn, Lewis, Lora, Hall, Otis, Zhu, Yiming, Ren, Yanru, Alvi, Omar, Yao, Jiqiang, Hawes, Alicia, Jhangiani, Shalini, Fowler, Gerald, San Lucas, Anthony, Kovar, Christie, Cree, Andrew, Dinh, Huyen, Santibanez, Jireh, Joshi, Vandita, Gonzalez-Garay, Manuel L, Miller, Christopher A, Milosavljevic, Aleksandar, Donehower, Larry, Wheeler, David A, Gibbs, Richard A, Cibulskis, Kristian, Sougnez, Carrie, Fennell, Tim, Mahan, Scott, Wilkinson, Jane, Ziaugra, Liuda, Onofrio, Robert, Bloom, Toby, Nicol, Rob, Ardlie, Kristin, Baldwin, Jennifer, Gabriel, Stacey, Lander, Eric S, Ding, Li, Fulton, Robert S, McLellan, Michael D, Wallis, John, Larson, David E, Shi, Xiaoqi, Abbott, Rachel, Fulton, Lucinda, Chen, Ken, Koboldt, Daniel C, Wendl, Michael C, Meyer, Rick, Tang, Yuzhu, Lin, Ling, Osborne, John R, Dunford-Shore, Brian H, Miner, Tracie L, Delehaunty, Kim, Markovic, Chris, Swift, Gary, Courtney, William, Pohl, Craig, Abbott, Scott, Hawkins, Amy, Leong, Shin, Haipek, Carrie, Schmidt, Heather, Wiechert, Maddy, Vickery, Tammi, Scott, Sacha, Dooling, David J, Chinwalla, Asif, Weinstock, George M, Mardis, Elaine R, Wilson, Richard K, Getz, Gad, Winckler, Wendy, Verhaak, Roel GW, Lawrence, Michael S, O’Kelly, Michael, Robinson, Jim, Alexe, Gabriele, Beroukhim, Rameen, Carter, Scott, Chiang, Derek, and Gould, Josh

Subjects
Cancer, Human Genome, Genetic Testing, Brain Cancer, Genetics, Brain Disorders, Biotechnology, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Aged, Aged, 80 and over, Brain Neoplasms, DNA Methylation, DNA Modification Methylases, DNA Repair, DNA Repair Enzymes, Female, Gene Dosage, Gene Expression Regulation, Neoplastic, Genes, Tumor Suppressor, Genes, erbB-1, Genome, Human, Genomics, Glioblastoma, Humans, Male, Middle Aged, Models, Molecular, Mutation, Neurofibromin 1, Phosphatidylinositol 3-Kinases, Protein Structure, Tertiary, Retrospective Studies, Signal Transduction, Tumor Suppressor Proteins, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas--the most common type of adult brain cancer--and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.

Published
2008

4. Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

Author

Govindan, Ramaswamy, Ding, Li, Griffith, Malachi, Subramanian, Janakiraman, Dees, Nathan D., Kanchi, Krishna L., Maher, Christopher A., Fulton, Robert, Fulton, Lucinda, Wallis, John, Chen, Ken, Walker, Jason, McDonald, Sandra, Bose, Ron, Ornitz, David, Xiong, Donghai, You, Ming, Dooling, David J., Watson, Mark, Mardis, Elaine R., and Wilson, Richard K.

Published
2012
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5. The Origin and Evolution of Mutations in Acute Myeloid Leukemia

Author

Welch, John S., Ley, Timothy J., Link, Daniel C., Miller, Christopher A., Larson, David E., Koboldt, Daniel C., Wartman, Lukas D., Lamprecht, Tamara L., Liu, Fulu, Xia, Jun, Kandoth, Cyriac, Fulton, Robert S., McLellan, Michael D., Dooling, David J., Wallis, John W., Chen, Ken, Harris, Christopher C., Schmidt, Heather K., Kalicki-Veizer, Joelle M., Lu, Charles, Zhang, Qunyuan, Lin, Ling, O’Laughlin, Michelle D., McMichael, Joshua F., Delehaunty, Kim D., Fulton, Lucinda A., Magrini, Vincent J., McGrath, Sean D., Demeter, Ryan T., Vickery, Tammi L., Hundal, Jasreet, Cook, Lisa L., Swift, Gary W., Reed, Jerry P., Alldredge, Patricia A., Wylie, Todd N., Walker, Jason R., Watson, Mark A., Heath, Sharon E., Shannon, William D., Varghese, Nobish, Nagarajan, Rakesh, Payton, Jacqueline E., Baty, Jack D., Kulkarni, Shashikant, Klco, Jeffery M., Tomasson, Michael H., Westervelt, Peter, Walter, Matthew J., Graubert, Timothy A., DiPersio, John F., Ding, Li, Mardis, Elaine R., and Wilson, Richard K.

Published
2012
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6. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

Author

Ding, Li, Ley, Timothy J., Larson, David E., Miller, Christopher A., Koboldt, Daniel C., Welch, John S., Ritchey, Julie K., Young, Margaret A., Lamprecht, Tamara, McLellan, Michael D., McMichael, Joshua F., Wallis, John W., Lu, Charles, Shen, Dong, Harris, Christopher C., Dooling, David J., Fulton, Robert S., Fulton, Lucinda L., Chen, Ken, Schmidt, Heather, Kalicki-Veizer, Joelle, Magrini, Vincent J., Cook, Lisa, McGrath, Sean D., Vickery, Tammi L., Wendl, Michael C., Heath, Sharon, Watson, Mark A., Link, Daniel C., Tomasson, Michael H., Shannon, William D., Payton, Jacqueline E., Kulkarni, Shashikant, Westervelt, Peter, Walter, Matthew J., Graubert, Timothy A., Mardis, Elaine R., Wilson, Richard K., and DiPersio, John F.

Subjects
Genetic aspects, Abnormalities, Health aspects, DNA sequencing -- Health aspects, Clonal selection (Immunology) -- Abnormalities, Acute myelocytic leukemia -- Genetic aspects, Nucleotide sequencing -- Health aspects, Clonal selection theory -- Abnormalities
Abstract

To investigate the genetic changes associated with AML relapse, and to determine whether clonal evolution contributes to relapse, we performed whole-genome sequencing of primary tumour-relapse pairs and matched skin samples [...], Most patients with acute myeloid leukaemia (AML) die from progressive disease after relapse, which is associated with clonal evolution at the cytogenetic level (1,2). To determine the mutational spectrum associated with relapse, we sequenced the primary tumour and relapse genomes from eight AML patients, and validated hundreds of somatic mutations using deep sequencing; this allowed us to define clonality and clonal evolution patterns precisely at relapse. In addition to discovering novel, recurrently mutated genes (for example, WAC, SMC3, DIS3, DDX41 and DAXX) in AML, we also found two major clonal evolution patterns during AML relapse: (1) the founding clone in the primary tumour gained mutations and evolved into the relapse clone, or (2) a subclone of the founding clone survived initial therapy, gained additional mutations and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone. The comparison of relapse-specific versus primary tumour mutations in all eight cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped, in part, by the chemotherapy that the patients receive to establish and maintain remissions.

Published
2012
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7. Somatic mutations affect key pathways in lung adenocarcinoma

Author

Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, Sougnez, Carrie, Greulich, Heidi, Muzny, Donna M., Morgan, Margaret B., Fulton, Lucinda, Fulton, Robert S., Zhang, Qunyuan, Wendl, Michael C., Lawrence, Michael S., Larson, David E., Chen, Ken, Dooling, David J., Sabo, Aniko, Hawes, Alicia C., Shen, Hua, Jhangiani, Shalini N., Lewis, Lora R., Hall, Otis, Zhu, Yiming, Mathew, Tittu, Ren, Yanru, Yao, Jiqiang, Scherer, Steven E., Clerc, Kerstin, Metcalf, Ginger A., Ng, Brian, Milosavljevic, Aleksandar, Gonzalez-Garay, Manuel L., Osborne, John R., Meyer, Rick, Shi, Xiaoqi, Tang, Yuzhu, Koboldt, Daniel C., Lin, Ling, Abbott, Rachel, Miner, Tracie L., Pohl, Craig, Fewell, Ginger, Haipek, Carrie, Schmidt, Heather, Dunford-Shore, Brian H., Kraja, Aldi, Crosby, Seth D., Sawyer, Christopher S., Vickery, Tammi, Sander, Sacha, Robinson, Jody, Winckler, Wendy, Baldwin, Jennifer, Chirieac, Lucian R., Dutt, Amit, Fennell, Tim, Hanna, Megan, Johnson, Bruce E., Onofrio, Robert C., Thomas, Roman K., Tonon, Giovanni, Weir, Barbara A., Zhao, Xiaojun, Ziaugra, Liuda, Zody, Michael C., Giordano, Thomas, Orringer, Mark B., Roth, Jack A., Spitz, Margaret R., Wistuba, Ignacio I., Ozenberger, Bradley, Good, Peter J., Chang, Andrew C., Beer, David G., Watson, Mark A., Ladanyi, Marc, Broderick, Stephen, Yoshizawa, Akihiko, Travis, William D., Pao, William, Province, Michael A., Weinstock, George M., Varmus, Harold E., Gabriel, Stacey B., Lander, Eric S., Gibbs, Richard A., Meyerson, Matthew, and Wilson, Richard K.

Subjects
Diagnosis, Care and treatment, Physiological aspects, Genetic aspects, Research, Prognosis, Lung cancer -- Genetic aspects -- Research -- Care and treatment -- Diagnosis -- Prognosis, Adenocarcinoma -- Genetic aspects -- Research -- Care and treatment -- Prognosis -- Diagnosis, Gene mutation -- Research -- Physiological aspects -- Genetic aspects, DNA sequencing -- Research -- Physiological aspects -- Genetic aspects, Gene mutations -- Research -- Physiological aspects -- Genetic aspects, Nucleotide sequencing -- Research -- Physiological aspects -- Genetic aspects
Abstract

Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations [...]

Published
2008

8. Comprehensive molecular portraits of human breast tumours

Author

Koboldt, Daniel C., Fulton, Robert S., McLellan, Michael D., Schmidt, Heather, Kalicki-Veizer, Joelle, McMichael, Joshua F., Fulton, Lucinda L., Dooling, David J., Ding, Li, Mardis, Elaine R., Wilson, Richard K., Ally, Adrian, Balasundaram, Miruna, Butterfield, Yaron S. N., Carlsen, Rebecca, Carter, Candace, Chu, Andy, Chuah, Eric, Chun, Hye-Jung E., Coope, Robin J. N., Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Hirst, Martin, Holt, Robert A., Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Pleasance, Erin, Gordon Robertson, A., Schein, Jacqueline E., Shafiei, Arash, Sipahimalani, Payal, Slobodan, Jared R., Stoll, Dominik, Tam, Angela, Thiessen, Nina, Varhol, Richard J., Wye, Natasja, Zeng, Thomas, Zhao, Yongjun, Birol, Inanc, Jones, Steven J. M., Marra, Marco A., Cherniack, Andrew D., Saksena, Gordon, Onofrio, Robert C., Pho, Nam H., Carter, Scott L., Schumacher, Steven E., Tabak, Barbara, Hernandez, Bryan, Gentry, Jeff, Nguyen, Huy, Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Getz, Gad, Gabriel, Stacey B., Meyerson, Matthew, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Hoadley, Katherine A., Todd Auman, J., Fan, Cheng, Turman, Yidi J., Shi, Yan, Li, Ling, Topal, Michael D., He, Xiaping, Chao, Hann-Hsiang, Prat, Aleix, Silva, Grace O., Iglesia, Michael D., Zhao, Wei, Usary, Jerry, Berg, Jonathan S., Adams, Michael, Booker, Jessica, Wu, Junyuan, Gulabani, Anisha, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Matthew G., Mose, Lisle E., Jefferys, Stuart R., Balu, Saianand, Parker, Joel S., Neil Hayes, D., Perou, Charles M., Malik, Simeen, Mahurkar, Swapna, Shen, Hui, Weisenberger, Daniel J., Triche, Timothy, Jr, Lai, Phillip H., Bootwalla, Moiz S., Maglinte, Dennis T., Berman, Benjamin P., Van Den Berg, David J., Baylin, Stephen B., Laird, Peter W., Creighton, Chad J., Donehower, Lawrence A., Noble, Michael, Voet, Doug, Gehlenborg, Nils, DiCara, Daniel, Zhang, Juinhua, Zhang, Hailei, Wu, Chang-Jiun, Liu, Spring Yingchun, Lawrence, Michael S., Zou, Lihua, Sivachenko, Andrey, Lin, Pei, Stojanov, Petar, Jing, Rui, Cho, Juok, Sinha, Raktim, Park, Richard W., Nazaire, Marc-Danie, Robinson, Jim, Thorvaldsdottir, Helga, Mesirov, Jill, Reynolds, Sheila, Kreisberg, Richard B., Bernard, Brady, Bressler, Ryan, Erkkila, Timo, Lin, Jake, Thorsson, Vesteinn, Zhang, Wei, Shmulevich, Ilya, Ciriello, Giovanni, Weinhold, Nils, Schultz, Nikolaus, Gao, Jianjiong, Cerami, Ethan, Gross, Benjamin, Jacobsen, Anders, Sinha, Rileen, Arman Aksoy, B., Antipin, Yevgeniy, Reva, Boris, Shen, Ronglai, Taylor, Barry S., Ladanyi, Marc, Sander, Chris, Anur, Pavana, Spellman, Paul T., Lu, Yiling, Liu, Wenbin, Verhaak, Roel R. G., Mills, Gordon B., Akbani, Rehan, Zhang, Nianxiang, Broom, Bradley M., Casasent, Tod D., Wakefield, Chris, Unruh, Anna K., Baggerly, Keith, Coombes, Kevin, Weinstein, John N., Haussler, David, Benz, Christopher C., Stuart, Joshua M., Benz, Stephen C., Zhu, Jingchun, Szeto, Christopher C., Scott, Gary K., Yau, Christina, Paull, Evan O., Carlin, Daniel, Wong, Christopher, Sokolov, Artem, Thusberg, Janita, Mooney, Sean, Ng, Sam, Goldstein, Theodore C., Ellrott, Kyle, Grifford, Mia, Wilks, Christopher, Ma, Singer, Craft, Brian, Yan, Chunhua, Hu, Ying, Meerzaman, Daoud, Gastier-Foster, Julie M., Bowen, Jay, Ramirez, Nilsa C., Black, Aaron D., Pyatt, Robert E., White, Peter, Zmuda, Erik J., Frick, Jessica, Lichtenberg, Tara M., Brookens, Robin, George, Myra M., Gerken, Mark A., Harper, Hollie A., Leraas, Kristen M., Wise, Lisa J., Tabler, Teresa R., McAllister, Cynthia, Barr, Thomas, Hart-Kothari, Melissa, Tarvin, Katie, Saller, Charles, Sandusky, George, Mitchell, Colleen, Iacocca, Mary V., Brown, Jennifer, Rabeno, Brenda, Czerwinski, Christine, Petrelli, Nicholas, Dolzhansky, Oleg, Abramov, Mikhail, Voronina, Olga, Potapova, Olga, Marks, Jeffrey R., Suchorska, Wiktoria M., Murawa, Dawid, Kycler, Witold, Ibbs, Matthew, Korski, Konstanty, Spychała, Arkadiusz, Murawa, Paweł, Brzeziński, Jacek J., Perz, Hanna, Łaźniak, Radosław, Teresiak, Marek, Tatka, Honorata, Leporowska, Ewa, Bogusz-Czerniewicz, Marta, Malicki, Julian, Mackiewicz, Andrzej, Wiznerowicz, Maciej, Van Le, Xuan, Kohl, Bernard, Viet Tien, Nguyen, Thorp, Richard, Van Bang, Nguyen, Sussman, Howard, Duc Phu, Bui, Hajek, Richard, Phi Hung, Nguyen, Viet The Phuong, Tran, Quyet Thang, Huynh, Zaki Khan, Khurram, Penny, Robert, Mallery, David, Curley, Erin, Shelton, Candace, Yena, Peggy, Ingle, James N., Couch, Fergus J., Lingle, Wilma L., King, Tari A., Maria Gonzalez-Angulo, Ana, Dyer, Mary D., Liu, Shuying, Meng, Xiaolong, Patangan, Modesto, Waldman, Frederic, Stöppler, Hubert, Kimryn Rathmell, W., Thorne, Leigh, Huang, Mei, Boice, Lori, Hill, Ashley, Morrison, Carl, Gaudioso, Carmelo, Bshara, Wiam, Daily, Kelly, Egea, Sophie C., Pegram, Mark D., Gomez-Fernandez, Carmen, Dhir, Rajiv, Bhargava, Rohit, Brufsky, Adam, Shriver, Craig D., Hooke, Jeffrey A., Leigh Campbell, Jamie, Mural, Richard J., Hu, Hai, Somiari, Stella, Larson, Caroline, Deyarmin, Brenda, Kvecher, Leonid, Kovatich, Albert J., Ellis, Matthew J., Stricker, Thomas, White, Kevin, Olopade, Olufunmilayo, Luo, Chunqing, Chen, Yaqin, Bose, Ron, Chang, Li-Wei, Beck, Andrew H., Pihl, Todd, Jensen, Mark, Sfeir, Robert, Kahn, Ari, Chu, Anna, Kothiyal, Prachi, Wang, Zhining, Snyder, Eric, Pontius, Joan, Ayala, Brenda, Backus, Mark, Walton, Jessica, Baboud, Julien, Berton, Dominique, Nicholls, Matthew, Srinivasan, Deepak, Raman, Rohini, Girshik, Stanley, Kigonya, Peter, Alonso, Shelley, Sanbhadti, Rashmi, Barletta, Sean, Pot, David, Sheth, Margi, Demchok, John A., Mills Shaw, Kenna R., Yang, Liming, Eley, Greg, Ferguson, Martin L., Tarnuzzer, Roy W., Zhang, Jiashan, Dillon, Laura A. L., Buetow, Kenneth, Fielding, Peter, Ozenberger, Bradley A., Guyer, Mark S., Sofia, Heidi J., and Palchik, Jacqueline D.

Published
2012
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9. Novel mutations target distinct subgroups of medulloblastoma

Author

Robinson, Giles, Parker, Matthew, Kranenburg, Tanya A., Lu, Charles, Chen, Xiang, Ding, Li, Phoenix, Timothy N., Hedlund, Erin, Wei, Lei, Zhu, Xiaoyan, Chalhoub, Nader, Baker, Suzanne J., Huether, Robert, Kriwacki, Richard, Curley, Natasha, Thiruvenkatam, Radhika, Wang, Jianmin, Wu, Gang, Rusch, Michael, Hong, Xin, Becksfort, Jared, Gupta, Pankaj, Ma, Jing, Easton, John, Vadodaria, Bhavin, Onar-Thomas, Arzu, Lin, Tong, Li, Shaoyi, Pounds, Stanley, Paugh, Steven, Zhao, David, Kawauchi, Daisuke, Roussel, Martine F., Finkelstein, David, Ellison, David W., Lau, Ching C., Bouffet, Eric, Hassall, Tim, Gururangan, Sridharan, Cohn, Richard, Fulton, Robert S., Fulton, Lucinda L., Dooling, David J., Ochoa, Kerri, Gajjar, Amar, Mardis, Elaine R., Wilson, Richard K., Downing, James R., Zhang, Jinghui, and Gilbertson, Richard J.

Published
2012
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10. Comprehensive molecular characterization of human colon and rectal cancer

Author

Muzny, Donna M., Bainbridge, Matthew N., Chang, Kyle, Dinh, Huyen H., Drummond, Jennifer A., Fowler, Gerald, Kovar, Christie L., Lewis, Lora R., Morgan, Margaret B., Newsham, Irene F., Reid, Jeffrey G., Santibanez, Jireh, Shinbrot, Eve, Trevino, Lisa R., Wu, Yuan-Qing, Wang, Min, Gunaratne, Preethi, Donehower, Lawrence A., Creighton, Chad J., Wheeler, David A., Gibbs, Richard A., Lawrence, Michael S., Voet, Douglas, Jing, Rui, Cibulskis, Kristian, Sivachenko, Andrey, Stojanov, Petar, McKenna, Aaron, Lander, Eric S., Gabriel, Stacey, Getz, Gad, Ding, Li, Fulton, Robert S., Koboldt, Daniel C., Wylie, Todd, Walker, Jason, Dooling, David J., Fulton, Lucinda, Delehaunty, Kim D., Fronick, Catrina C., Demeter, Ryan, Mardis, Elaine R., Wilson, Richard K., Chu, Andy, Chun, Hye-Jung E., Mungall, Andrew J., Pleasance, Erin, Robertson, Gordon A., Stoll, Dominik, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron S. N., Chuah, Eric, Coope, Robin J. N., Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Hirst, Martin, Holt, Robert A., Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Schein, Jacqueline E., Slobodan, Jared R., Tam, Angela, Thiessen, Nina, Varhol, Richard, Zeng, Thomas, Zhao, Yongjun, Jones, Steven J. M., Marra, Marco A., Bass, Adam J., Ramos, Alex H., Saksena, Gordon, Cherniack, Andrew D., Schumacher, Stephen E., Tabak, Barbara, Carter, Scott L., Pho, Nam H., Nguyen, Huy, Onofrio, Robert C., Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Meyerson, Matthew, Protopopov, Alexei, Zhang, Juinhua, Hadjipanayis, Angela, Lee, Eunjung, Xi, Ruibin, Yang, Lixing, Ren, Xiaojia, Zhang, Hailei, Sathiamoorthy, Narayanan, Shukla, Sachet, Chen, Peng-Chieh, Haseley, Psalm, Xiao, Yonghong, Lee, Semin, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Auman, Todd J., Hoadley, Katherine A., Du, Ying, Wilkerson, Matthew D., Shi, Yan, Liquori, Christina, Meng, Shaowu, Li, Ling, Turman, Yidi J., Topal, Michael D., Tan, Donghui, Waring, Scot, Buda, Elizabeth, Walsh, Jesse, Jones, Corbin D., Mieczkowski, Piotr A., Singh, Darshan, Wu, Junyuan, Gulabani, Anisha, Dolina, Peter, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Matthew, Mose, Lisle E., Jefferys, Stuart R., Balu, Saianand, O’Connor, Brian D., Prins, Jan F., Chiang, Derek Y., Hayes, Neil D., Perou, Charles M., Hinoue, Toshinori, Weisenberger, Daniel J., Maglinte, Dennis T., Pan, Fei, Berman, Benjamin P., Van Den Berg, David J., Shen, Hui, Triche, Timothy, Jr, Baylin, Stephen B., Laird, Peter W., Noble, Michael, Voet, Doug, Gehlenborg, Nils, DiCara, Daniel, Wu, Chang-Jiun, Yingchun Liu, Spring, Zhou, Lihua, Lin, Pei, Park, Richard W., Nazaire, Marc-Danie, Robinson, Jim, Thorvaldsdottir, Helga, Mesirov, Jill, Thorsson, Vesteinn, Reynolds, Sheila M., Bernard, Brady, Kreisberg, Richard, Lin, Jake, Iype, Lisa, Bressler, Ryan, Erkkilä, Timo, Gundapuneni, Madhumati, Liu, Yuexin, Norberg, Adam, Robinson, Tom, Yang, Da, Zhang, Wei, Shmulevich, Ilya, de Ronde, Jorma J., Schultz, Nikolaus, Cerami, Ethan, Ciriello, Giovanni, Goldberg, Arthur P., Gross, Benjamin, Jacobsen, Anders, Gao, Jianjiong, Kaczkowski, Bogumil, Sinha, Rileen, Aksoy, Arman B., Antipin, Yevgeniy, Reva, Boris, Shen, Ronglai, Taylor, Barry S., Chan, Timothy A., Ladanyi, Marc, Sander, Chris, Akbani, Rehan, Zhang, Nianxiang, Broom, Bradley M., Casasent, Tod, Unruh, Anna, Wakefield, Chris, Hamilton, Stanley R., Cason, Craig R., Baggerly, Keith A., Weinstein, John N., Haussler, David, Benz, Christopher C., Stuart, Joshua M., Benz, Stephen C., Sanborn, Zachary J., Vaske, Charles J., Zhu, Jingchun, Szeto, Christopher, Scott, Gary K., Yau, Christina, Ng, Sam, Goldstein, Ted, Ellrott, Kyle, Collisson, Eric, Cozen, Aaron E., Zerbino, Daniel, Wilks, Christopher, Craft, Brian, Spellman, Paul, Penny, Robert, Shelton, Troy, Hatfield, Martha, Morris, Scott, Yena, Peggy, Shelton, Candace, Sherman, Mark, Paulauskis, Joseph, Gastier-Foster, Julie M., Bowen, Jay, Ramirez, Nilsa C., Black, Aaron, Pyatt, Robert, Wise, Lisa, White, Peter, Bertagnolli, Monica, Brown, Jen, Chu, Gerald C., Czerwinski, Christine, Denstman, Fred, Dhir, Rajiv, Dörner, Arnulf, Fuchs, Charles S., Guillem, Jose G., Iacocca, Mary, Juhl, Hartmut, Kaufman, Andrew, Kohl, Bernard, III, Van Le, Xuan, Mariano, Maria C., Medina, Elizabeth N., Meyers, Michael, Nash, Garrett M., Paty, Phillip B., Petrelli, Nicholas, Rabeno, Brenda, Richards, William G., Solit, David, Swanson, Pat, Temple, Larissa, Tepper, Joel E., Thorp, Richard, Vakiani, Efsevia, Weiser, Martin R., Willis, Joseph E., Witkin, Gary, Zeng, Zhaoshi, Zinner, Michael J., Zornig, Carsten, Jensen, Mark A., Sfeir, Robert, Kahn, Ari B., Chu, Anna L., Kothiyal, Prachi, Wang, Zhining, Snyder, Eric E., Pontius, Joan, Pihl, Todd D., Ayala, Brenda, Backus, Mark, Walton, Jessica, Whitmore, Jon, Baboud, Julien, Berton, Dominique L., Nicholls, Matthew C., Srinivasan, Deepak, Raman, Rohini, Girshik, Stanley, Kigonya, Peter A., Alonso, Shelley, Sanbhadti, Rashmi N., Barletta, Sean P., Greene, John M., Pot, David A., Mills Shaw, Kenna R., Dillon, Laura A. L., Buetow, Ken, Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin, Fielding, Peter, Schaefer, Carl, Sheth, Margi, Yang, Liming, Guyer, Mark S., Ozenberger, Bradley A., Palchik, Jacqueline D., Peterson, Jane, Sofia, Heidi J., and Thomson, Elizabeth

Published
2012
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11. A framework for human microbiome research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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12. Structure, function and diversity of the healthy human microbiome

Author

Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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14. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

Author

Zhang, Jinghui, Ding, Li, Holmfeldt, Linda, Wu, Gang, Heatley, Sue L., Payne-Turner, Debbie, Easton, John, Chen, Xiang, Wang, Jianmin, Rusch, Michael, Lu, Charles, Chen, Shann-Ching, Wei, Lei, Collins-Underwood, Racquel J., Ma, Jing, Roberts, Kathryn G., Pounds, Stanley B., Ulyanov, Anatoly, Becksfort, Jared, Gupta, Pankaj, Huether, Robert, Kriwacki, Richard W., Parker, Matthew, McGoldrick, Daniel J., Zhao, David, Alford, Daniel, Espy, Stephen, Bobba, Kiran Chand, Song, Guangchun, Pei, Deqing, Cheng, Cheng, Roberts, Stefan, Barbato, Michael I., Campana, Dario, Coustan-Smith, Elaine, Shurtleff, Sheila A., Raimondi, Susana C., Kleppe, Maria, Cools, Jan, Shimano, Kristin A., Hermiston, Michelle L., Doulatov, Sergei, Eppert, Kolja, Laurenti, Elisa, Notta, Faiyaz, Dick, John E., Basso, Giuseppe, Hunger, Stephen P., Loh, Mignon L., Devidas, Meenakshi, Wood, Brent, Winter, Stuart, Dunsmore, Kimberley P., Fulton, Robert S., Fulton, Lucinda L., Hong, Xin, Harris, Christopher C., Dooling, David J., Ochoa, Kerri, Johnson, Kimberly J., Obenauer, John C., Evans, William E., Pui, Ching-Hon, Naeve, Clayton W., Ley, Timothy J., Mardis, Elaine R., Wilson, Richard K., Downing, James R., and Mullighan, Charles G.

Published
2012
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15. Genome remodelling in a basal-like breast cancer metastasis and xenograft

Author

Ding, Li, Ellis, Matthew J., Li, Shunqiang, Larson, David E., Chen, Ken, Wallis, John W., Harris, Christopher C., McLellan, Michael D., Fulton, Robert S., Fulton, Lucinda L., Abbott, Rachel M., Hoog, Jeremy, Dooling, David J., Koboldt, Daniel C., Schmidt, Heather, Kalicki, Joelle, Zhang, Qunyuan, Chen, Lei, Lin, Ling, Wendl, Michael C., McMichael, Joshua F., Magrini, Vincent J., Cook, Lisa, McGrath, Sean D., Vickery, Tammi L., Appelbaum, Elizabeth, DeSchryver, Katherine, Davies, Sherri, Guintoli, Therese, Lin, Li, Crowder, Robert, Tao, Yu, Snider, Jacqueline E., Smith, Scott M., Dukes, Adam F., Sanderson, Gabriel E., Pohl, Craig S., Delehaunty, Kim D., Fronick, Catrina C., Pape, Kimberley A., Reed, Jerry S., Robinson, Jody S., Hodges, Jennifer S., Schierding, William, Dees, Nathan D., Shen, Dong, Locke, Devin P., Wiechert, Madeline E., Eldred, James M., Peck, Josh B., Oberkfell, Benjamin J., Lolofie, Justin T., Du, Feiyu, Hawkins, Amy E., OʼLaughlin, Michelle D., Bernard, Kelly E., Cunningham, Mark, Elliott, Glendoria, Mason, Mark D., Thompson, Dominic M., Jr, Ivanovich, Jennifer L., Goodfellow, Paul J., Perou, Charles M., Weinstock, George M., Aft, Rebecca, Watson, Mark, Ley, Timothy J., Wilson, Richard K., and Mardis, Elaine R.

Published
2010
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17. Design and implementation of a generalized laboratory data model

Author

Nhan Mike, Carmichael Lynn, Leong Shin, Hepler Todd, Crouse Kevin, Chinwalla Asif T, Dooling David J, Pohl Craig S, Smith Scott, Wendl Michael C, Oberkfell Benjamin J, Mardis Elaine R, Hillier LaDeana W, and Wilson Richard K

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselves also evolve in a rapid and fluid manner. These observations point to the importance of robust information management systems in the modern laboratory. Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable. Results We describe a general modeling framework for laboratory data and its implementation as an information management system. The model utilizes several abstraction techniques, focusing especially on the concepts of inheritance and meta-data. Traditional approaches commingle event-oriented data with regular entity data in ad hoc ways. Instead, we define distinct regular entity and event schemas, but fully integrate these via a standardized interface. The design allows straightforward definition of a "processing pipeline" as a sequence of events, obviating the need for separate workflow management systems. A layer above the event-oriented schema integrates events into a workflow by defining "processing directives", which act as automated project managers of items in the system. Directives can be added or modified in an almost trivial fashion, i.e., without the need for schema modification or re-certification of applications. Association between regular entities and events is managed via simple "many-to-many" relationships. We describe the programming interface, as well as techniques for handling input/output, process control, and state transitions. Conclusion The implementation described here has served as the Washington University Genome Sequencing Center's primary information system for several years. It handles all transactions underlying a throughput rate of about 9 million sequencing reactions of various kinds per month and has handily weathered a number of major pipeline reconfigurations. The basic data model can be readily adapted to other high-volume processing environments.

Published
2007
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19. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

Author

Hoadley, Katherine A., Yau, Christina, Wolf, Denise M., Cherniack, Andrew D., Tamborero, David, Sam, Ng, Leiserson, Max D. M., Niu, Beifang, Mclellan, Michael D., Uzunangelov, Vladislav, Zhang, Jiashan, Kandoth, Cyriac, Akbani, Rehan, Shen, Hui, Omberg, Larsson, Chu, Andy, Margolin, Adam A., Van'T Veer, Laura J., Lopez Bigas, Nuria, Laird, Peter W., Raphael, Benjamin J., Ding, Li, Robertson, A. Gordon, Byers, Lauren A., Mills, Gordon B., Weinstein, John N., Van Waes, Carter, Chen, Zhong, Collisson, Eric A., Benz, Christopher C, Perou, Charles M., Stuart, Joshua M., Rachel, Abbott, Scott, Abbott, Arman Aksoy, B., Kenneth, Aldape, Adrian, Ally, Samirku mar Amin, Dimitris, Anastassiou, Todd Auman, J., Baggerly, Keith A., Miruna, Balasundaram, Saianand, Balu, Baylin, Stephen B., Benz, Stephen C., Berman, Benjamin P., Brady, Bernard, Bhatt, Ami S., Inanc, Birol, Black, Aaron D., Tom, Bodenheimer, Bootwalla, Moiz S., Jay, Bowen, Ryan, Bressler, Bristow, Christopher A., Brooks, Angela N., Bradley, Broom, Elizabeth, Buda, Robert, Burton, Butterfield, Yaron S. N., Daniel, Carlin, Carter, Scott L., Casasent, Tod D., Kyle, Chang, Stephen, Chanock, Lynda, Chin, Dong Yeon Cho, Juok, Cho, Eric, Chuah, Chun, Hye Jung E., Kristian, Cibulskis, Giovanni, Ciriello, James Cle land, Melisssa, Cline, Brian, Craft, Creighton, Chad J., Ludmila, Danilova, Tanja, Davidsen, Caleb, Davis, Dees, Nathan D., Kim, Delehaunty, Demchok, John A., Noreen, Dhalla, Daniel, Dicara, Huyen, Dinh, Dobson, Jason R., Deepti, Dodda, Harshavardhan, Doddapaneni, Lawrence, Donehower, Dooling, David J., Gideon, Dresdner, Jennifer, Drummond, Andrea, Eakin, Mary, Edgerton, Eldred, Jim M., Greg, Eley, Kyle, Ellrott, Cheng, Fan, Suzanne, Fei, Ina, Felau, Scott, Frazer, Freeman, Samuel S., Jessica, Frick, Fronick, Catrina C., Ful ton, Lucinda L., Robert, Fulton, Gabriel, Stacey B., Jianjiong, Gao, Gastier Foster, Julie M., Nils, Gehlenborg, Myra, George, Gad, Getz, Richard, Gibbs, Mary, Goldman, Abel Gonzalez Perez, Benjamin, Gross, Ranabir, Guin, Preethi, Gunaratne, Angela, Hadjipanayis, Hamilton, Mark P., Hamilton, Stanley R., Leng, Han, Han, Yi, Harper, Hollie A., Psalm, Haseley, David, Haussler, Neil Hayes, D., Heiman, David I., Elena, Helman, Carmen, Helsel, Herbrich, Shelley M., Her man, James G., Toshinori, Hinoue, Carrie, Hirst, Martin, Hirst, Holt, Robert A., Hoyle, Alan P., Lisa, Iype, Anders, Jacobsen, Jeffreys, Stuart R., Jensen, Mark A., Jones, Corbin D., Jones, Steven J. M., Zhenlin, Ju, Joonil, Jung, Andre, Kahles, Ari, Kahn, Joelle Kalicki Veizer, Divya, Kalra, Krishna Latha Kanchi, Kane, David W., Hoon, Kim, Jaegil, Kim, Theo, Knijnenburg, Koboldt, Daniel C., Christie, Kovar, Roger, Kramer, Richard, Kreisberg, Raju, Kucherlapati, Marc, Ladanyi, Lander, Eric S., Larson, David E., Lawrence, Michael S., Darlene, Lee, Eunjung, Lee, Semin, Lee, William, Lee, Kjong Van Lehmann, Kalle, Leinonen, Ler aas, Kristen M., Seth, Lerner, Levine, Douglas A., Lora, Lewis, Ley, Timothy J., Haiyan I., Li, Jun, Li, Wei, Li, Han, Liang, Lichtenberg, Tara M., Jake, Lin, Ling, Lin, Pei, Lin, Wen bin Liu, Yingchun, Liu, Yuexin, Liu, Lorenzi, Philip L., Charles, Lu, Yiling, Lu, Luquette, Love lace J., Singer, Ma, Magrini, Vincent J., Mahadeshwar, Harshad S., Mardis, Elaine R., Adam, Margolin, Marra, Marco A., Michael, Mayo, Cynthia, Mcallister, Mcguire, Sean E., Mcmichael, Joshua F., James, Melott, Shaowu, Meng, Matthew, Meyerson, Mieczkowski, Piotr A., Miller, Christopher A., Miller, Martin L., Michael, Miller, Moore, Richard A., Margaret, Morgan, Donna, Morton, Mose, Lisle E., Mungall, Andrew J., Donna, Muzny, Lam, Nguyen, Noble, Michael S., Houtan, Noushmehr, Michelle, O’Laughlin, Ojesina, Akinyemi I., Tai Hsien Ou Yang, Brad, Ozenberger, Angeliki, Pantazi, Michael, Parfenov, Park, Peter J., Parker, Joel S., Evan, Paull, Chandra Sekhar Pedamallu, Todd, Pihl, Craig, Pohl, David, Pot, Alexei, Protopopov, Teresa, Przytycka, Amie Raden baugh, Ramirez, Nilsa C., Ricardo, Ramirez, Gunnar Ra, ̈ tsch, Jeffrey, Reid, Xiao jia Ren, Boris, Reva, Reynolds, Sheila M., Rhie, Suhn K., Jeffrey, Roach, Hector, Rovira, Michael, Ryan, Gordon, Saksena, Sofie, Salama, Chris, Sander, Netty, Santoso, Schein, Jacqueline E., Heather, Schmidt, Nikolaus, Schultz, Schumacher, Steven E., Jonathan, Seidman, Yasin, Senbabaoglu, Sahil, Seth, Saman tha Sharpe, Ronglai, Shen, Margi, Sheth, Yan, Shi, Ilya, Shmulevich, Silva, Grace O., Simons, Janae V., Rileen, Sinha, Payal, Sipahimalani, Smith, Scott M., Sofia, Heidi J., Artem, Sokolov, Soloway, Mathew G., Xingzhi, Song, Carrie Soug nez, Paul, Spellman, Louis, Staudt, Chip, Stewart, Petar, Stojanov, Xiaoping, Su, Onur Sumer, S., Yichao, Sun, Teresa, Swatloski, Barbara, Tabak, Angela, Tam, Donghui, Tan, Jiabin, Tang, Roy, Tarnuzzer, Taylor, Barry S., Nina, Thiessen, Ves teinn Thorsson, Timothy Triche, J. r., Van Den Berg, David J., Vandin, Fabio, Varhol, Richard J., Vaske, Charles J., Umadevi, Veluvolu, Roeland, Verhaak, Doug, Voet, Jason, Walker, Wallis, John W., Peter, Waltman, Yunhu, Wan, Min, Wang, Wenyi, Wang, Zhining, Wang, Scot, Waring, Nils, Weinhold, Weisenberger, Daniel J., Wendl, Michael C., David, Wheeler, Wilkerson, Matthew D., Wilson, Richard K., Lisa, Wise, Andrew, Wong, Chang Jiun Wu, Chia Chin Wu, Hsin Ta Wu, Junyuan, Wu, Todd, Wylie, Liu, Xi, Ruibin, Xi, Zheng, Xia, Andrew W., Xu, Yang, Da, Liming, Yang, Lixing, Yang, Yang, Yang, Jun, Yao, Rong, Yao, Kai, Ye, Ko suke Yoshihara, Yuan, Yuan, Yung, Alfred K., Travis, Zack, Dong, Zeng, Jean Claude Zenklusen, Hailei, Zhang, Jianhua, Zhang, Nianxiang, Zhang, Qunyuan, Zhang, Wei, Zhang, Wei, Zhao, Siyuan, Zheng, Jing, Zhu, Erik, Zmuda, and Lihua, Zou

Subjects
Genetics and Molecular Biology (all), Cluster Analysis, Humans, Neoplasms, Transcriptome, Biochemistry, Genetics and Molecular Biology (all), Extramural, Biochemistry, Genetics and Molecular Biology(all), Cancer, Computational biology, Disease, Biology, medicine.disease, Bioinformatics, Biochemistry, General Biochemistry, Genetics and Molecular Biology, Article, 3. Good health, Molecular classification, TP63, CLUSTERS (ANÁLISE), medicine, Head and neck, Gene
Abstract

Summary Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All data sets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies.

Published
2014
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20. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML

Author

Link, Daniel C., Schuettpelz, Laura G., Shen, Dong, Wang, Jinling, Walter, Matthew J., Kulkarni, Shashikant, Payton, Jacqueline E., Ivanovich, Jennifer, Goodfellow, Paul J., Le Beau, Michelle, Koboldt, Daniel C., Dooling, David J., Fulton, Robert S., Bender, R. Hugh F., Fulton, Lucinda L., Delehaunty, Kimberly D., Fronick, Catrina C., Appelbaum, Elizabeth L., Schmidt, Heather, Abbott, Rachel, O'Laughlin, Michelle, Chen, Ken, McLellan, Michael D., Varghese, Nobish, Nagarajan, Rakesh, Heath, Sharon, Graubert, Timothy A., Ding, Li, Ley, Timothy J., Zambetti, Gerard P., Wilson, Richard K., and Mardis, Elaine R.

Subjects
Adult, Ovarian Neoplasms, Genome, Human, Breast Neoplasms, DNA, Neoplasm, Sequence Analysis, DNA, Genes, p53, Polymorphism, Single Nucleotide, Article, Cystadenocarcinoma, Serous, Leukemia, Myeloid, Acute, Humans, Female, Genetic Predisposition to Disease, Age of Onset, Tumor Suppressor Protein p53, Sequence Deletion
Abstract

The identification of patients with inherited cancer susceptibility syndromes facilitates early diagnosis, prevention, and treatment. However, in many cases of suspected cancer susceptibility, the family history is unclear and genetic testing of common cancer susceptibility genes is unrevealing.To apply whole-genome sequencing to a patient without any significant family history of cancer but with suspected increased cancer susceptibility because of multiple primary tumors to identify rare or novel germline variants in cancer susceptibility genes. DESIGN, SETTING, AND PARTICIPANT: Skin (normal) and bone marrow (leukemia) DNA were obtained from a patient with early-onset breast and ovarian cancer (negative for BRCA1 and BRCA2 mutations) and therapy-related acute myeloid leukemia (t-AML) and analyzed with the following: whole-genome sequencing using paired-end reads, single-nucleotide polymorphism (SNP) genotyping, RNA expression profiling, and spectral karyotyping.Structural variants, copy number alterations, single-nucleotide variants, and small insertions and deletions (indels) were detected and validated using the described platforms. RESULTS; Whole-genome sequencing revealed a novel, heterozygous 3-kilobase deletion removing exons 7-9 of TP53 in the patient's normal skin DNA, which was homozygous in the leukemia DNA as a result of uniparental disomy. In addition, a total of 28 validated somatic single-nucleotide variations or indels in coding genes, 8 somatic structural variants, and 12 somatic copy number alterations were detected in the patient's leukemia genome.Whole-genome sequencing can identify novel, cryptic variants in cancer susceptibility genes in addition to providing unbiased information on the spectrum of mutations in a cancer genome.

Published
2011

21. Genome Modeling System: A Knowledge Management Platform for Genomics

Author

Griffith, Malachi, primary, Griffith, Obi L., additional, Smith, Scott M., additional, Ramu, Avinash, additional, Callaway, Matthew B., additional, Brummett, Anthony M., additional, Kiwala, Michael J., additional, Coffman, Adam C., additional, Regier, Allison A., additional, Oberkfell, Ben J., additional, Sanderson, Gabriel E., additional, Mooney, Thomas P., additional, Nutter, Nathaniel G., additional, Belter, Edward A., additional, Du, Feiyu, additional, Long, Robert L., additional, Abbott, Travis E., additional, Ferguson, Ian T., additional, Morton, David L., additional, Burnett, Mark M., additional, Weible, James V., additional, Peck, Joshua B., additional, Dukes, Adam, additional, McMichael, Joshua F., additional, Lolofie, Justin T., additional, Derickson, Brian R., additional, Hundal, Jasreet, additional, Skidmore, Zachary L., additional, Ainscough, Benjamin J., additional, Dees, Nathan D., additional, Schierding, William S., additional, Kandoth, Cyriac, additional, Kim, Kyung H., additional, Lu, Charles, additional, Harris, Christopher C., additional, Maher, Nicole, additional, Maher, Christopher A., additional, Magrini, Vincent J., additional, Abbott, Benjamin S., additional, Chen, Ken, additional, Clark, Eric, additional, Das, Indraniel, additional, Fan, Xian, additional, Hawkins, Amy E., additional, Hepler, Todd G., additional, Wylie, Todd N., additional, Leonard, Shawn M., additional, Schroeder, William E., additional, Shi, Xiaoqi, additional, Carmichael, Lynn K., additional, Weil, Matthew R., additional, Wohlstadter, Richard W., additional, Stiehr, Gary, additional, McLellan, Michael D., additional, Pohl, Craig S., additional, Miller, Christopher A., additional, Koboldt, Daniel C., additional, Walker, Jason R., additional, Eldred, James M., additional, Larson, David E., additional, Dooling, David J., additional, Ding, Li, additional, Mardis, Elaine R., additional, and Wilson, Richard K., additional

Published
2015
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22. Abstract LB-423: Whole genome comparisons of pre- and post- aromatase inhibitor treatment in estrogen receptor positive breast cancer

Author

Ellis, Matthew J., primary, Li, Ding, additional, Shen, Dong, additional, Luo, Jingqin, additional, Suman, Vera J., additional, Wallis, John W., additional, Van Tine, Brian A., additional, Hoog, Jeremy, additional, Crowder, Robert J., additional, Snider, Jacqueline E., additional, Ballman, Karla, additional, Chen, Ken, additional, Koboldt, Daniel C., additional, Schierding, William S., additional, McMichael, Joshua F., additional, Miller, Christopher A., additional, Kandoth, Cyriac, additional, Lu, Charles, additional, Harris, Christopher C., additional, McLellan, Michael D., additional, Wendl, Michael C., additional, DeSchryver, Katherine, additional, Allred, D. Craig, additional, Esserman, Laura, additional, Unzeitig, Gary, additional, Margenthaler, Julie, additional, Babiera, G.V., additional, Marcom, P. Kelly, additional, Guenther, J.M., additional, Leitch, Marilyn, additional, Hunt, Kelly, additional, Olson, John, additional, Tao, Yu, additional, Fulton, Lucinda L., additional, Fulton, Robert S., additional, Harrison, Michelle, additional, Oberkfell, Ben, additional, Du, Feiyu, additional, Demeter, Ryan, additional, Griffith, Malachi, additional, Vickery, Tammi L., additional, McDonald, Sandra A., additional, Watson, Mark, additional, Dooling, David J., additional, Ota, David, additional, Chang, Li-Wei, additional, Bose, Ron, additional, Ley, Timothy J., additional, Wilson, Richard K., additional, and Mardis, Elaine R., additional

Published
2012
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24. Complete Sequencing and Comparison of 12 Normal Karyotype M1 AML Genomes with 12 t(15;17) Positive M3-APL Genomes

Author

Welch, John S., primary, Larson, David, additional, Ding, Li, additional, McLellan, Michael D., additional, Lamprecht, Tamara, additional, Kandoth, Cyriac, additional, Payton, Jacqueline E., additional, Baty, Jack, additional, Harris, Christopher C., additional, Lichti, Cheryl F., additional, Fulton, Robert S., additional, Dooling, David J., additional, Koboldt, Daniel C, additional, Schmidt, Heather, additional, Zhang, Qunyuan, additional, Osborne, John R., additional, Lin, Ling, additional, O'Laughlin, Michelle, additional, McMichael, Joshua F., additional, Delehaunty, Kim D., additional, McGrath, Sean D., additional, Fulton, Lucinda A., additional, Magrini, Vincent J, additional, Vickery, Tammi L., additional, Wylie, Todd, additional, Walker, Jason, additional, Westervelt, Peter, additional, Tomasson, Michael H., additional, Watson, Mark A., additional, Heath, Sharon, additional, Shannon, William D., additional, Nagarajan, Rakesh, additional, Link, Daniel C., additional, Graubert, Timothy, additional, DiPersio, John F., additional, Mardis, Elaine R., additional, Wilson, Richard K., additional, and Ley, Timothy J, additional

Published
2011
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25. Discovery of Novel Recurrent Mutations in Childhood Early T-Cell Precursor Acute Lymphoblastic Leukemia by Whole Genome Sequencing - a Report From the St Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project

Author

Zhang, Jinghui, primary, Ding, Li, additional, Holmfeldt, Linda, additional, Wu, Gang, additional, Heatley, Susan L., additional, Payne-Turner, Debbie, additional, Easton, John, additional, Chen, Xiang, additional, Wang, Jianmin, additional, Rusch, Michael, additional, Lu, Charles, additional, Chen, Shann-Ching, additional, Collins-Underwood, Racquel, additional, Ma, Jing, additional, Roberts, Kathryn G., additional, Pounds, Stanley, additional, Wei, Lei, additional, Ulyanov, Anatoly, additional, Becksfort, Jared, additional, Gupta, Pankaj, additional, Huether, Robert, additional, Kriwacki, Richard, additional, McGoldrick, Daniel, additional, Zhao, David, additional, Alford, Daniel, additional, Espy, Stephen, additional, Bobba, Kiran Chand, additional, Song, Guangchun, additional, Pei, Deqing, additional, Cheng, Cheng, additional, Roberts, Stefan, additional, Barbato, Michael, additional, Campana, Dario, additional, Coustan-Smith, Elaine, additional, Evans, William E., additional, Shurtleff, Sheila A, additional, Kleppe, Maria, additional, Cools, Jan, additional, Shimano, Kristin, additional, Hermiston, Michelle L., additional, Doulatov, Sergei, additional, Eppert, Kolja, additional, Laurenti, Elisa, additional, Notta, Faiyaz, additional, Dick, John E, additional, Basso, Giuseppe, additional, Hunger, Stephen P., additional, Loh, Mignon L, additional, Devidas, Meenakshi, additional, Wood, Brent L., additional, Winter, Stuart S., additional, Dunsmore, Kimberly, additional, Fulton, Robert S., additional, Fulton, Lucinda A., additional, Hong, Xin, additional, Harris, Christopher C., additional, Dooling, David J., additional, Ochoa, Kerri, additional, Johnson, Kimberly J, additional, Obenauer, John C, additional, Pui, Ching-Hon, additional, Raimondi, Susana C., additional, Naeve, Clayton W, additional, Ley, Timothy J, additional, Mardis, Elaine R, additional, Wilson, Richard K, additional, Downing, James R, additional, and Mullighan, Charles G, additional

Published
2011
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26. Detection of Novel Mutations In MDS/AML by Whole Genome Sequencing

Author

Walter, Matthew J., primary, Shen, Dong, additional, Ding, Li, additional, Shao, Jin, additional, Witowski, Sarah, additional, Chen, Ken, additional, Koboldt, Daniel C., additional, Dooling, David J., additional, Maupin, Rachel, additional, Fulton, Robert S., additional, Schmidt, Heather, additional, O'Laughlin, Michelle, additional, McLellan, Michael D., additional, Frater, John, additional, Westervelt, Peter, additional, DiPersio, John F, additional, Mardis, Elaine R, additional, Wilson, Richard, additional, Ley, Timothy J, additional, and Graubert, Timothy, additional

Published
2010
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27. DNA Sequence of the Cancer Genome of a Patient with Therapy-Related Acute Myeloid Leukemia

Author

Schuettpelz, Laura, primary, Link, Daniel C., additional, Shen, Dong, additional, Walter, Matthew J., additional, Koboldt, Daniel C, additional, Dooling, David J., additional, Fulton, Robert S., additional, Schmidt, Heather, additional, Maupin, Rachel, additional, O'Laughlin, Michelle, additional, Chen, Ken, additional, McLellan, Michael D., additional, Kulkarni, Shashikant, additional, Ivanovich, Jennifer, additional, Lebeau, Michelle, additional, Varghese, Nobish, additional, Nagarajan, Rakesh, additional, Ding, Li, additional, Graubert, Timothy A., additional, Ley, Timothy J, additional, Wilson, Richard K., additional, and Mardis, Elaine R., additional

Published
2010
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28. Mutations In the DNA Methyltransferase Gene DNMT3A Are Highly Recurrent In Patients with Intermediate Risk Acute Myeloid Leukemia, and Predict Poor Outcomes

Author

Ley, Timothy J, primary, Ding, Li, additional, Walter, Matthew J., additional, McLellan, Michael D., additional, Lamprecht, Tamara, additional, Larson, David E., additional, Kandoth, Cyriac, additional, Payton, Jacqueline E., additional, Baty, Jack, additional, Welch, John S., additional, Harris, Christopher C., additional, Lichti, Cheryl F., additional, Townsend, R. Reid, additional, Fulton, Robert S., additional, Dooling, David J., additional, Koboldt, Daniel C., additional, Schmidt, Heather, additional, Zhang, Qunyuan, additional, Osborne, John R., additional, Lin, Ling, additional, O'Laughlin, Michelle, additional, McMichael, Joshua F., additional, Delehaunty, Kim D., additional, McGrath, Sean D., additional, Fulton, Lucinda A., additional, Magrini, Vincent J., additional, Vickery, Tammi L., additional, Hundal, Jasreet, additional, Cook, Lisa L., additional, Conyers, Joshua J., additional, Swift, Gary W., additional, Reed, Jerry P., additional, Alldredge, Patricia A., additional, Wylie, Todd, additional, Walker, Jason, additional, Kalicki-Veizer, Joelle, additional, Watson, Mark A., additional, Heath, Sharon, additional, Shannon, William D., additional, Varghese, Nobish, additional, Nagarajan, Rakesh, additional, Westervelt, Peter, additional, Tomasson, Michael H., additional, Link, Daniel C., additional, Graubert, Timothy A., additional, DiPersio, John F., additional, Mardis, Elaine R., additional, and Wilson, Richard K., additional

Published
2010
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29. Design and implementation of a generalized laboratory data model

Author

Wendl, Michael C, primary, Smith, Scott, additional, Pohl, Craig S, additional, Dooling, David J, additional, Chinwalla, Asif T, additional, Crouse, Kevin, additional, Hepler, Todd, additional, Leong, Shin, additional, Carmichael, Lynn, additional, Nhan, Mike, additional, Oberkfell, Benjamin J, additional, Mardis, Elaine R, additional, Hillier, LaDeana W, additional, and Wilson, Richard K, additional

Published
2007
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31. Genome remodelling in a basal-like breast cancer metastasis and xenograft.

Author

Li Ding, Ellis, Matthew J., Shunqiang Li, Larson, David E., Ken Chen, Wallis, John W., Harris, Christopher C., McLellan, Michael D., Fulton, Robert S., Fulton, Lucinda L., Abbott, Rachel M., Hoog, Jeremy, Dooling, David J., Koboldt, Daniel C., Schmidt, Heather, Kalicki, Joelle, Qunyuan Zhang, Lei Chen, Ling Lin, and Wendl, Michael C.

Subjects
BREAST cancer, GENOMES, BASAL cell carcinoma, XENOGRAFTS, METASTASIS, CANCER invasiveness
Abstract

Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The metastasis contained two de novo mutations and a large deletion not present in the primary tumour, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumour mutations and displayed a mutation enrichment pattern that resembled the metastasis. Two overlapping large deletions, encompassing CTNNA1, were present in all three tumour samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour. [ABSTRACT FROM AUTHOR]

Published
2010
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32. Somatic mutations affect key pathways in lung adenocarcinoma.

Author

Li Ding, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, Sougnez, Carrie, Greulich, Heidi, Muzny, Donna M., Morgan, Margaret B., Fulton, Lucinda, Fulton, Robert S., Qunyuan Zhang, Wendl, Michael C., Lawrence, Michael S., Larson, David E., Chen, Ken, Dooling, David J., Sabo, Aniko, and Hawes, Alicia C.

Subjects
ADENOCARCINOMA, CANCER, HISTOPATHOLOGY, TUMORS, GENETIC mutation, DNA
Abstract

Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers—including NF1, APC, RB1 and ATM—and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment. [ABSTRACT FROM AUTHOR]

Published
2008
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33. Mutations In the DNA Methyltransferase Gene DNMT3AAre Highly Recurrent In Patients with Intermediate Risk Acute Myeloid Leukemia, and Predict Poor Outcomes

Author

Ley, Timothy J, Ding, Li, Walter, Matthew J., McLellan, Michael D., Lamprecht, Tamara, Larson, David E., Kandoth, Cyriac, Payton, Jacqueline E., Baty, Jack, Welch, John S., Harris, Christopher C., Lichti, Cheryl F., Townsend, R. Reid, Fulton, Robert S., Dooling, David J., Koboldt, Daniel C., Schmidt, Heather, Zhang, Qunyuan, Osborne, John R., Lin, Ling, O'Laughlin, Michelle, McMichael, Joshua F., Delehaunty, Kim D., McGrath, Sean D., Fulton, Lucinda A., Magrini, Vincent J., Vickery, Tammi L., Hundal, Jasreet, Cook, Lisa L., Conyers, Joshua J., Swift, Gary W., Reed, Jerry P., Alldredge, Patricia A., Wylie, Todd, Walker, Jason, Kalicki-Veizer, Joelle, Watson, Mark A., Heath, Sharon, Shannon, William D., Varghese, Nobish, Nagarajan, Rakesh, Westervelt, Peter, Tomasson, Michael H., Link, Daniel C., Graubert, Timothy A., DiPersio, John F., Mardis, Elaine R., and Wilson, Richard K.

Abstract

Abstract 99

Published
2010
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34. RB1 gene inactivation by chromothripsis in human retinoblastoma.

Author

McEvoy J, Nagahawatte P, Finkelstein D, Richards-Yutz J, Valentine M, Ma J, Mullighan C, Song G, Chen X, Wilson M, Brennan R, Pounds S, Becksfort J, Huether R, Lu C, Fulton RS, Fulton LL, Hong X, Dooling DJ, Ochoa K, Mardis ER, Wilson RK, Easton J, Zhang J, Downing JR, Ganguly A, and Dyer MA

Subjects
Gene Expression, Gene Expression Regulation, Neoplastic, Gene Silencing, Humans, Oncogene Proteins metabolism, Retinoblastoma metabolism, Retinoblastoma pathology, Retinoblastoma Protein metabolism, Chromosome Aberrations, Genes, Retinoblastoma, Oncogene Proteins genetics, Retinal Neoplasms genetics, Retinoblastoma genetics, Retinoblastoma Protein genetics
Abstract

Retinoblastoma is a rare childhood cancer of the developing retina. Most retinoblastomas initiate with biallelic inactivation of the RB1 gene through diverse mechanisms including point mutations, nucleotide insertions, deletions, loss of heterozygosity and promoter hypermethylation. Recently, a novel mechanism of retinoblastoma initiation was proposed. Gallie and colleagues discovered that a small proportion of retinoblastomas lack RB1 mutations and had MYCN amplification [1]. In this study, we identified recurrent chromosomal, regional and focal genomic lesions in 94 primary retinoblastomas with their matched normal DNA using SNP 6.0 chips. We also analyzed the RB1 gene mutations and compared the mechanism of RB1 inactivation to the recurrent copy number variations in the retinoblastoma genome. In addition to the previously described focal amplification of MYCN and deletions in RB1 and BCOR, we also identified recurrent focal amplification of OTX2, a transcription factor required for retinal photoreceptor development. We identified 10 retinoblastomas in our cohort that lacked RB1 point mutations or indels. We performed whole genome sequencing on those 10 tumors and their corresponding germline DNA. In one of the tumors, the RB1 gene was unaltered, the MYCN gene was amplified and RB1 protein was expressed in the nuclei of the tumor cells. In addition, several tumors had complex patterns of structural variations and we identified 3 tumors with chromothripsis at the RB1 locus. This is the first report of chromothripsis as a mechanism for RB1 gene inactivation in cancer.

Published
2014
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