Author: "Dooling, David J." - Searchworks@Jio Institute Digital Library Search Results

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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. DNMT3A mutations in acute myeloid leukemia

Author: Ley, Timothy J., Li Ding, Walter, Matthew J., McLellan, Michael D., Lamprecht, Tamara, Larson, David E., Kandoth, Cyriac, Payton, Jacqueline E., Baty, Jack, Welch, John, Harris, Christopher C., Lichti, Cheryl F., Townsend, R. Reid, Fulton, Robert S., Dooling, David J., Koboldt, Daniel C., Schmidt, Heather, Qunyuan Zhang, Osborne, John R., Ling Lin, O'aughlin, 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, 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.
Subjects: Amino acids -- Chemical properties, Amino acids -- Health aspects, Nucleotide sequencing -- Usage
Abstract: A study was conducted to evaluate whether DNMT3A is recurrently mutated in acute myeloid leukemia samples and whether DNMT3A mutations are associated with poor survival rates. Results indicated that sNMT3A mutations are highly recurrent in such patients and are independently associated with poor outcomes.
Published: 2010

8. Recurring mutations found by sequencing an acute myeloid leukemia genome

Author: Mardis, Elaine R., Ding, Li, Dooling, David J., Larson, David E., McLellan, Michael D., Chen, Ken, Koboldt, Daniel C., Fulton, Robert S., Delehaunty, Kim D., McGrath, Sean D., Fulton, Lucinda A., Locke, Devin P., Magrini, Vincent J., Abbott, Rachel M., Vickery, Tammi L., Reed, Jerry S., Robinson, Jody S., Wylie, Todd, Smith, Scott M., Carmichael, Lynn, Eldred, James M., Harris, Christopher C., Walker, Jason, Peck, Joshua P., Du, Feiyu, Dukes, Adam F., Sanderson, Gabriel E., Brummett, Anthony M., Clark, Eric, McMichael, Joshua F., Meyer, Rick J., Schindler, Jonathan K., Pohl, Craig S., Wallis, John W., Xiaoqi Shi, Ling Lin, Schmidt, Heather, Tang, Tuzhu, Haipek,Carrie, and Wiechert, Madeline E.
Subjects: Gene mutations -- Research, Nucleotide sequencing -- Research
Abstract: The study aims to investigate and understand the DNA mutations that are responsible for sequencing of an acute myeloid leukemia (AML) genome. The results indicate that recurrent mutations that may be relevant for pathogenesis by comparing the sequences of tumor and skin genomes of a patient with AML-M1 have been identified.
Published: 2009

9. 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

10. 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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11. 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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12. 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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13. 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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14. 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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15. SomaticSniper: identification of somatic point mutations in whole genome sequencing data

Author: Larson, David E., Harris, Christopher C., Chen, Ken, Koboldt, Daniel C., Abbott, Travis E., Dooling, David J., Ley, Timothy J., Mardis, Elaine R., Wilson, Richard K., and Ding, Li
Published: 2012
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16. 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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17. 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, 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.
Published: 2011
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18. 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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19. Open-source answer to bibliography problem

Author: Wendl, Michael C. and Dooling, David J.
Published: 2003

20. 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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21. A density-functional study of the interaction of nitrogen with ruthenium clusters

Author: Dooling, David J., Nielsen, Robert J., and Broadbelt, Linda J.
Published: 1999
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22. 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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23. Comprehensive molecular portraits of human breast tumours

Author: Moore, Richard A., Fulton, Lucinda L., Hirst, Martin, Chun, Hye-Jung E., Fulton, Robert S., Mardis, Elaine R., Dhalla, Noreen, Ally, Adrian, Koboldt, Daniel C., Dooling, David J., Chuah, Eric, Holt, Robert A., Ding, Li, Kalicki-Veizer, Joelle, Chu, Andy, Mungall, Andrew J., Butterfield, Yaron S. N., Li, Haiyan I., Pleasance, Erin, Schmidt, Heather, Carlsen, Rebecca, Carter, Candace, McLellan, Michael D., Balasundaram, Miruna, Hirst, Carrie, Guin, Ranabir, Lee, Darlene, Coope, Robin J. N., Wilson, Richard K., McMichael, Joshua F., Mayo, Michael, and Gordon Robertson, A.
Subjects: skin and connective tissue diseases
Abstract: This Article from the Cancer Genome Atlas consortium describes a multifaceted analysis of primary breast cancers in 825 people. Exome sequencing, copy number variation, DNA methylation, messenger RNA arrays, microRNA sequencing and proteomic analyses were performed and integrated to shed light on breast-cancer heterogeneity. Just three genes — TP53, PIK3CA and GATA3 — are mutated at greater than 10% frequency across all breast cancers. Many subtype-associated and novel mutations were identified, as well as two breast-cancer subgroups with specific signalling-pathway signatures. The analyses also suggest that much of the clinically observable plasticity and heterogeneity occurs within, and not across, the major subtypes of breast cancer.
Published: 2012
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24. 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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25. Genome remodelling in a basal-like breast cancer metastasis and xenograft

Author: McLellan, Michael D., Ellis, Matthew J., Tao, Yu, Lin, Li, Vickery, Tammi L., Fulton, Lucinda L., Lin, Ling, Koboldt, Daniel C., Appelbaum, Elizabeth, DeSchryver, Katherine, Zhang, Qunyuan, Schmidt, Heather, Ding, Li, Wallis, John W., Crowder, Robert, Kalicki, Joelle, Larson, David E., McMichael, Joshua F., Fulton, Robert S., Hoog, Jeremy, Li, Shunqiang, Chen, Ken, Cook, Lisa, Magrini, Vincent J., Chen, Lei, Davies, Sherri, Wendl, Michael C., Abbott, Rachel M., Guintoli, Therese, McGrath, Sean D., Harris, Christopher C., and Dooling, David J.
Abstract: Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumor 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 tumor, a brain metastasis, and a xenograft derived from the primary tumor. The metastasis contained two de novo mutations and a large deletion not present in the primary tumor, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumor mutations, and displayed a mutation enrichment pattern that paralleled the metastasis (16 of 20 genes). Two overlapping large deletions, encompassing CTNNA1, were present in all three tumor samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared to the primary tumor suggest that secondary tumors may arise from a minority of cells within the primary.
Published: 2010
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26. DGIdb: mining the druggable genome

Author: Griffith, Malachi, primary, Griffith, Obi L, additional, Coffman, Adam C, additional, Weible, James V, additional, McMichael, Josh F, additional, Spies, Nicholas C, additional, Koval, James, additional, Das, Indraniel, additional, Callaway, Matthew B, additional, Eldred, James M, additional, Miller, Christopher A, additional, Subramanian, Janakiraman, additional, Govindan, Ramaswamy, additional, Kumar, Runjun D, additional, Bose, Ron, additional, Ding, Li, additional, Walker, Jason R, additional, Larson, David E, additional, Dooling, David J, additional, Smith, Scott M, additional, Ley, Timothy J, additional, Mardis, Elaine R, additional, and Wilson, Richard K, additional
Published: 2013
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27. The genomic landscape of hypodiploid acute lymphoblastic leukemia

Author: Holmfeldt, Linda, primary, Wei, Lei, additional, Diaz-Flores, Ernesto, additional, Walsh, Michael, additional, Zhang, Jinghui, additional, Ding, Li, additional, Payne-Turner, Debbie, additional, Churchman, Michelle, additional, Andersson, Anna, additional, Chen, Shann-Ching, additional, McCastlain, Kelly, additional, Becksfort, Jared, additional, Ma, Jing, additional, Wu, Gang, additional, Patel, Samir N, additional, Heatley, Susan L, additional, Phillips, Letha A, additional, Song, Guangchun, additional, Easton, John, additional, Parker, Matthew, additional, Chen, Xiang, additional, Rusch, Michael, additional, Boggs, Kristy, additional, Vadodaria, Bhavin, additional, Hedlund, Erin, additional, Drenberg, Christina, additional, Baker, Sharyn, additional, Pei, Deqing, additional, Cheng, Cheng, additional, Huether, Robert, additional, Lu, Charles, additional, Fulton, Robert S, additional, Fulton, Lucinda L, additional, Tabib, Yashodhan, additional, Dooling, David J, additional, Ochoa, Kerri, additional, Minden, Mark, additional, Lewis, Ian D, additional, To, L Bik, additional, Marlton, Paula, additional, Roberts, Andrew W, additional, Raca, Gordana, additional, Stock, Wendy, additional, Neale, Geoffrey, additional, Drexler, Hans G, additional, Dickins, Ross A, additional, Ellison, David W, additional, Shurtleff, Sheila A, additional, Pui, Ching-Hon, additional, Ribeiro, Raul C, additional, Devidas, Meenakshi, additional, Carroll, Andrew J, additional, Heerema, Nyla A, additional, Wood, Brent, additional, Borowitz, Michael J, additional, Gastier-Foster, Julie M, additional, Raimondi, Susana C, additional, Mardis, Elaine R, additional, Wilson, Richard K, additional, Downing, James R, additional, Hunger, Stephen P, additional, Loh, Mignon L, additional, and Mullighan, Charles G, additional
Published: 2013
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28. 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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29. Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes

Author: Graubert, Timothy A, primary, Shen, Dong, additional, Ding, Li, additional, Okeyo-Owuor, Theresa, additional, Lunn, Cara L, additional, Shao, Jin, additional, Krysiak, Kilannin, additional, Harris, Christopher C, additional, Koboldt, Daniel C, additional, Larson, David E, additional, McLellan, Michael D, additional, Dooling, David J, additional, Abbott, Rachel M, additional, Fulton, Robert S, additional, Schmidt, Heather, additional, Kalicki-Veizer, Joelle, additional, O'Laughlin, Michelle, additional, Grillot, Marcus, additional, Baty, Jack, additional, Heath, Sharon, additional, Frater, John L, additional, Nasim, Talat, additional, Link, Daniel C, additional, Tomasson, Michael H, additional, Westervelt, Peter, additional, DiPersio, John F, additional, Mardis, Elaine R, additional, Ley, Timothy J, additional, Wilson, Richard K, additional, and Walter, Matthew J, additional
Published: 2011
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30. SomaticSniper: identification of somatic point mutations in whole genome sequencing data

Author: Larson, David E., primary, Harris, Christopher C., additional, Chen, Ken, additional, Koboldt, Daniel C., additional, Abbott, Travis E., additional, Dooling, David J., additional, Ley, Timothy J., additional, Mardis, Elaine R., additional, Wilson, Richard K., additional, and Ding, Li, additional
Published: 2011
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31. 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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32. 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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33. A vertebrate case study of the quality of assemblies derived from next-generation sequences

Author: Ye, Liang, primary, Hillier, LaDeana W, additional, Minx, Patrick, additional, Thane, Nay, additional, Locke, Devin P, additional, Martin, John C, additional, Chen, Lei, additional, Mitreva, Makedonka, additional, Miller, Jason R, additional, Haub, Kevin V, additional, Dooling, David J, additional, Mardis, Elaine R, additional, Wilson, Richard K, additional, Weinstock, George M, additional, and Warren, Wesley C, additional
Published: 2011
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34. DNMT3AMutations in Acute Myeloid Leukemia

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, 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, 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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35. 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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36. 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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37. 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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38. 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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39. Microkinetic models and dynamic Monte Carlo simulations of nonuniform catalytic systems

Author: Dooling, David J., primary and Broadbelt, Linda J., additional
Published: 2001
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40. Generic Monte Carlo Tool for Kinetic Modeling

Author: Dooling, David J., primary and Broadbelt, Linda J., additional
Published: 2000
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41. Computer Generation of Reaction Mechanisms Using Quantitative Rate Information: Application to Long-Chain Hydrocarbon Pyrolysis

Author: De Witt, Matthew J., primary, Dooling, David J., additional, and Broadbelt, Linda J., additional
Published: 2000
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42. Microkinetic Models of Catalytic Reactions on Nonuniform Surfaces: Application to Model and Real Systems

Author: Dooling, David J., primary, Rekoske, James E., additional, and Broadbelt, Linda J., additional
Published: 1999
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43. Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes.

Author: Graubert, Timothy A, Shen, Dong, Ding, Li, Okeyo-Owuor, Theresa, Lunn, Cara L, Shao, Jin, Krysiak, Kilannin, Harris, Christopher C, Koboldt, Daniel C, Larson, David E, McLellan, Michael D, Dooling, David J, Abbott, Rachel M, Fulton, Robert S, Schmidt, Heather, Kalicki-Veizer, Joelle, O'Laughlin, Michelle, Grillot, Marcus, Baty, Jack, and Heath, Sharon
Subjects: MYELODYSPLASTIC syndromes, GENETIC mutation, RNA splicing, HEMATOPOIETIC stem cell transplantation, DRUG therapy, ACUTE myeloid leukemia, NUCLEOTIDE sequence
Abstract: Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders that often progress to chemotherapy-resistant secondary acute myeloid leukemia (sAML). We used whole-genome sequencing to perform an unbiased comprehensive screen to discover the somatic mutations in a sample from an individual with sAML and genotyped the loci containing these mutations in the matched MDS sample. Here we show that a missense mutation affecting the serine at codon 34 (Ser34) in U2AF1 was recurrently present in 13 out of 150 (8.7%) subjects with de novo MDS, and we found suggestive evidence of an increased risk of progression to sAML associated with this mutation. U2AF1 is a U2 auxiliary factor protein that recognizes the AG splice acceptor dinucleotide at the 3? end of introns, and the alterations in U2AF1 are located in highly conserved zinc fingers of this protein. Mutant U2AF1 promotes enhanced splicing and exon skipping in reporter assays in vitro. This previously unidentified, recurrent mutation in U2AF1 implicates altered pre-mRNA splicing as a potential mechanism for MDS pathogenesis. [ABSTRACT FROM AUTHOR]
Published: 2012
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44. 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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45. 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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46. 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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47. 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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48. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas.

Author: Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, and Ellison DW
Subjects: Adolescent, Animals, Base Sequence, Brain Neoplasms pathology, Child, Child, Preschool, Female, Gene Duplication, Gene Rearrangement, Genes, myb, Genome-Wide Association Study, Glioma pathology, Humans, Infant, Male, Mice, Mice, Nude, Molecular Sequence Data, Mutation, Neoplasm Grading, Neoplasm Transplantation, Proto-Oncogene Proteins genetics, Proto-Oncogene Proteins B-raf, Receptor, Fibroblast Growth Factor, Type 1 genetics, Sequence Analysis, DNA, Signal Transduction, Trans-Activators genetics, Transcriptome, Brain Neoplasms genetics, Glioma genetics
Abstract: The most common pediatric brain tumors are low-grade gliomas (LGGs). We used whole-genome sequencing to identify multiple new genetic alterations involving BRAF, RAF1, FGFR1, MYB, MYBL1 and genes with histone-related functions, including H3F3A and ATRX, in 39 LGGs and low-grade glioneuronal tumors (LGGNTs). Only a single non-silent somatic alteration was detected in 24 of 39 (62%) tumors. Intragenic duplications of the portion of FGFR1 encoding the tyrosine kinase domain (TKD) and rearrangements of MYB were recurrent and mutually exclusive in 53% of grade II diffuse LGGs. Transplantation of Trp53-null neonatal astrocytes expressing FGFR1 with the duplication involving the TKD into the brains of nude mice generated high-grade astrocytomas with short latency and 100% penetrance. FGFR1 with the duplication induced FGFR1 autophosphorylation and upregulation of the MAPK/ERK and PI3K pathways, which could be blocked by specific inhibitors. Focusing on the therapeutically challenging diffuse LGGs, our study of 151 tumors has discovered genetic alterations and potential therapeutic targets across the entire range of pediatric LGGs and LGGNTs.
Published: 2013
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