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153. Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations

Author

Brammeld, Jonathan S., primary, Petljak, Mia, additional, Martincorena, Inigo, additional, Williams, Steven P., additional, Alonso, Luz Garcia, additional, Dalmases, Alba, additional, Bellosillo, Beatriz, additional, Robles-Espinoza, Carla Daniela, additional, Price, Stacey, additional, Barthorpe, Syd, additional, Tarpey, Patrick, additional, Alifrangis, Constantine, additional, Bignell, Graham, additional, Vidal, Joana, additional, Young, Jamie, additional, Stebbings, Lucy, additional, Beal, Kathryn, additional, Stratton, Michael R., additional, Saez-Rodriguez, Julio, additional, Garnett, Mathew, additional, Montagut, Clara, additional, Iorio, Francesco, additional, and McDermott, Ultan, additional

Published
2017
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154. Genomic analysis of exceptional responders to radiotherapy reveals somatic mutations in ATM

Author

Ma, Jennifer, primary, Setton, Jeremy, additional, Morris, Luc, additional, Carrillo Albornoz, Pedro Blecua, additional, Barker, Christopher, additional, Lok, Benjamin H., additional, Sherman, Eric, additional, Katabi, Nora, additional, Beal, Kathryn, additional, Ganly, Ian, additional, Powell, Simon N., additional, Lee, Nancy, additional, Chan, Timothy A., additional, and Riaz, Nadeem, additional

Published
2016
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155. BMET-06. IMPROVED SURVIVAL AND PROGNOSTIC ABILITY IN LUNG CANCER PATIENTS WITH BRAIN METASTASES: AN UPDATE OF THE GRADED PROGNOSTIC ASSESSMENT FOR LUNG CANCER USING MOLECULAR MARKERS (LUNG-molGPA)

Author

Sperduto, Paul, primary, Yang, T. Jonathan, additional, Beal, Kathryn, additional, Pan, Hubert, additional, Brown, Paul, additional, Bangdiwala, Ananta, additional, Shanley, Ryan, additional, Yeh, Norman, additional, Gaspar, Laurie E., additional, Braunstein, Steve, additional, Sneed, Penny, additional, Boyle, John M., additional, Kirkpatrick, John, additional, Mak, Kimberley, additional, Shih, Helen, additional, Engelman, Alex, additional, Roberge, David, additional, Arvold, Nils, additional, Alexander, Brian, additional, Awad, Mark, additional, Contessa, Joseph, additional, Chiang, Veronica, additional, Hardie, John, additional, Ma, Daniel, additional, Lou, Emil, additional, Sperduto, William, additional, and Mehta, Minesh, additional

Published
2016
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157. Clinical Outcomes and Targeted Genomic Analysis of Renal Cell Carcinoma Brain Metastases Treated with Stereotactic Radiosurgery

Author

Ma, Jennifer, del Balzo, Luke, Walch, Henry, Khaleel, Sari, Knezevic, Andrea, Flynn, Jessica, Zhang, Zhigang, Eichholz, Jordan, Doshi, Sahil D., Voss, Martin H., Freeman, Benjamin, Ari Hakimi, A., Lee, Chung-Han, Bale, Tejus A., Kelly, Daniel, Mueller, Boris A., Mann, Justin, Yu, Yao, Zinovoy, Melissa, Chen, Linda, Cuaron, John, Khan, Atif, Yamada, Yoshiya, Shin, Jacob Y., Beal, Kathryn, Moss, Nelson S., Carlo, Maria I., Motzer, Robert J., Imber, Brandon S., Kotecha, Ritesh R., and Pike, Luke R.G.

Abstract

To our knowledge, this is the largest study investigating mutational profiles of renal cell carcinoma brain metastases (BMs) and the only such study with annotated intracranial outcomes. Stereotactic radiosurgery (SRS) provides durable in-field local control of BMs, and recognition of pseudoprogression following SRS is crucial to ensuring appropriate management. The incidence of PI3Kpathway alterations are enriched in BM+ patients compared with BM– patients and warrants further investigation.

Published
2024
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158. Genome-wide nucleotide-level mammalian ancestor reconstruction

Author

Paten, Benedict, Herrero, Javier, Fitzgerald, Stephen, Beal, Kathryn, Flicek, Paul, Holmes, Ian, and Birney, Ewan

Subjects
Nucleotide sequence -- Analysis, Evolution -- Research, Genomics -- Research, Graphic methods -- Usage, Health
Published
2008

160. Molecular and Clinical Effects of Notch Inhibition in Glioma Patients: A Phase 0/I Trial

Author

Xu, Ran, primary, Shimizu, Fumiko, additional, Hovinga, Koos, additional, Beal, Kathryn, additional, Karimi, Sasan, additional, Droms, Leif, additional, Peck, Kyung K., additional, Gutin, Philip, additional, Iorgulescu, J. Bryan, additional, Kaley, Thomas, additional, DeAngelis, Lisa, additional, Pentsova, Elena, additional, Nolan, Craig, additional, Grommes, Christian, additional, Chan, Timothy, additional, Bobrow, Dylan, additional, Hormigo, Adilia, additional, Cross, Justin R., additional, Wu, Nian, additional, Takebe, Naoko, additional, Panageas, Katherine, additional, Ivy, Percy, additional, Supko, Jeffrey G., additional, Tabar, Viviane, additional, and Omuro, Antonio, additional

Published
2016
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161. Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations

Author

Brammeld, Jonathan S., primary, Petljak, Mia, additional, Martincorena, Inigo, additional, Williams, Steven P., additional, Garcia Alonso, Luz, additional, Dalmases, Alba, additional, Bellosillo, Beatriz, additional, Robles-Espinoza, Carla Daniela, additional, Price, Stacey, additional, Barthorpe, Syd, additional, Tarpey, Patrick, additional, Alifrangis, Constantine, additional, Bignell, Graham, additional, Vidal, Joana, additional, Young, Jamie, additional, Stebbings, Lucy, additional, Beal, Kathryn, additional, Stratton, Michael R, additional, Saez-Rodriguez, Julio, additional, Garnett, Mathew, additional, Montagut, Clara, additional, Iorio, Francesco, additional, and McDermott, Ultan, additional

Published
2016
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162. Phase IB trial of carboxyamidotriazole orotate (CTO) and radiotherapy (RT) with concurrent and adjuvant temozolomide (TMZ) in newly diagnosed glioblastoma (GBM).

Author

Omuro, Antonio Marcilio Padula, primary, Beal, Kathryn, additional, McNeill, Katharine Anne, additional, Thomas, Alissa A., additional, Lin, Xuling, additional, Kaley, Thomas Joseph, additional, DeAngelis, Lisa Marie, additional, Mellinghoff, Ingo K., additional, Diamond, Eli L., additional, Chan, Timothy An-thy, additional, Young, Robert J., additional, Yamada, Yoshiya, additional, Gorman, Greg, additional, Lamson, Michael, additional, Bavisotto, Linda M., additional, and Karmali, Rashida A., additional

Published
2016
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166. Extended Survival and Prognostic Factors for Patients With ALK-Rearranged Non–Small-Cell Lung Cancer and Brain Metastasis

Author

Johung, Kimberly L., primary, Yeh, Norman, additional, Desai, Neil B., additional, Williams, Terence M., additional, Lautenschlaeger, Tim, additional, Arvold, Nils D., additional, Ning, Matthew S., additional, Attia, Albert, additional, Lovly, Christine M., additional, Goldberg, Sarah, additional, Beal, Kathryn, additional, Yu, James B., additional, Kavanagh, Brian D., additional, Chiang, Veronica L., additional, Camidge, D. Ross, additional, and Contessa, Joseph N., additional

Published
2016
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167. Ensembl comparative genomics resources

Author

Herrero, Javier, primary, Muffato, Matthieu, additional, Beal, Kathryn, additional, Fitzgerald, Stephen, additional, Gordon, Leo, additional, Pignatelli, Miguel, additional, Vilella, Albert J., additional, Searle, Stephen M. J., additional, Amode, Ridwan, additional, Brent, Simon, additional, Spooner, William, additional, Kulesha, Eugene, additional, Yates, Andrew, additional, and Flicek, Paul, additional

Published
2016
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168. The pig X and Y Chromosomes: structure, sequence, and evolution.

Author

Skinner, Benjamin M, Sargent, Carole A, Churcher, Carol, Hunt, Toby, Herrero, Javier, Loveland, Jane E, Dunn, Matt, Louzada, Sandra, Fu, Beiyuan, Chow, William, Gilbert, James, Austin-Guest, Siobhan, Beal, Kathryn, Carvalho-Silva, Denise, Cheng, William, Gordon, Daria, Grafham, Darren, Hardy, Matt, Harley, Jo, Hauser, Heidi, Howden, Philip, Howe, Kerstin, Lachani, Kim, Ellis, Peter J.I., Kelly, Daniel, Kerry, Giselle, Kerwin, James, Ng, Bee Ling, Threadgold, Glen, Wileman, Thomas, Wood, Jonathan M D, Yang, Fengtang, Harrow, Jen, Affara, Nabeel A, Tyler-Smith, Chris, Skinner, Benjamin M, Sargent, Carole A, Churcher, Carol, Hunt, Toby, Herrero, Javier, Loveland, Jane E, Dunn, Matt, Louzada, Sandra, Fu, Beiyuan, Chow, William, Gilbert, James, Austin-Guest, Siobhan, Beal, Kathryn, Carvalho-Silva, Denise, Cheng, William, Gordon, Daria, Grafham, Darren, Hardy, Matt, Harley, Jo, Hauser, Heidi, Howden, Philip, Howe, Kerstin, Lachani, Kim, Ellis, Peter J.I., Kelly, Daniel, Kerry, Giselle, Kerwin, James, Ng, Bee Ling, Threadgold, Glen, Wileman, Thomas, Wood, Jonathan M D, Yang, Fengtang, Harrow, Jen, Affara, Nabeel A, and Tyler-Smith, Chris

Abstract

We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.

Published
2015

169. A prospective trial of dynamic contrast-enhanced MRI perfusion and fluorine-18 FDG PET-CT in differentiating brain tumor progression from radiation injury after cranial irradiation

Author

Hatzoglou, Vaios, primary, Yang, T. Jonathan, additional, Omuro, Antonio, additional, Gavrilovic, Igor, additional, Ulaner, Gary, additional, Rubel, Jennifer, additional, Schneider, Taylor, additional, Woo, Kaitlin M., additional, Zhang, Zhigang, additional, Peck, Kyung K., additional, Beal, Kathryn, additional, and Young, Robert J., additional

Published
2015
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170. The pig X and Y Chromosomes: structure, sequence, and evolution

Author

Skinner, Benjamin M., primary, Sargent, Carole A., additional, Churcher, Carol, additional, Hunt, Toby, additional, Herrero, Javier, additional, Loveland, Jane E., additional, Dunn, Matt, additional, Louzada, Sandra, additional, Fu, Beiyuan, additional, Chow, William, additional, Gilbert, James, additional, Austin-Guest, Siobhan, additional, Beal, Kathryn, additional, Carvalho-Silva, Denise, additional, Cheng, William, additional, Gordon, Daria, additional, Grafham, Darren, additional, Hardy, Matt, additional, Harley, Jo, additional, Hauser, Heidi, additional, Howden, Philip, additional, Howe, Kerstin, additional, Lachani, Kim, additional, Ellis, Peter J.I., additional, Kelly, Daniel, additional, Kerry, Giselle, additional, Kerwin, James, additional, Ng, Bee Ling, additional, Threadgold, Glen, additional, Wileman, Thomas, additional, Wood, Jonathan M.D., additional, Yang, Fengtang, additional, Harrow, Jen, additional, Affara, Nabeel A., additional, and Tyler-Smith, Chris, additional

Published
2015
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173. Long-term outcomes of adult medulloblastoma patients treated with radiotherapy.

Author

De, Brian, Beal, Kathryn, De Braganca, Kevin C., Souweidane, Mark M., Dunkel, Ira J., Khakoo, Yasmin, Gilheeney, Stephen W., DeAngelis, Lisa M., Menzel, Paul, Patel, Suchit H., and Wolden, Suzanne L.

Abstract

Medulloblastoma (MB) is rare in adults and treatment guidelines are consequently not well-established. Few modern series have reported long-term follow-up and treatment sequelae. We examined long-term outcomes of adult MB patients at one institution. Records of 29 consecutive patients (18 male, 11 female) aged ≥ 18 years who received radiotherapy (RT) for primary MB from 1990 to 2016 were reviewed. Median age at diagnosis was 28 years (range 18-72 years). Seventeen patients were standard risk and 12 were high risk. Nineteen patients had gross total resection, seven had subtotal resection, and three had biopsy only. Median craniospinal irradiation and boost doses were 36 Gy (range 23.4-39.6 Gy) and 55.8 Gy (range 54-59.4 Gy), respectively. Of 24 patients receiving chemotherapy, 20 received concurrent + adjuvant and 4 received adjuvant only. At median follow-up of 9.0 years (range 1.1-20.5 years), five patients recurred: four in the posterior fossa and one in both the posterior fossa and above the tentorium. Five patients died: two of disease progression and three after possible treatment complications (seizure, lobar pneumonia, and multifactorial sepsis). At last follow-up, 23 patients were alive with no evidence of disease. Long-term effects include executive dysfunction (n = 17), weakness/ataxia (n = 16), and depression/anxiety (n = 13). Kaplan-Meier estimates of 10-year overall survival and failure-free survival are 83% (95% confidence interval [CI] 59-93%) and 79% (CI 55-91%), respectively. Despite encouraging disease control in this cohort, long-term sequelae may limit quality of life. Multimodality pediatric regimens using lower RT doses may be considered to reduce treatment-related morbidity. [ABSTRACT FROM AUTHOR]

Published
2018
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175. Phase IB trial of carboxyamidotriazole orotate (CTO) and radiotherapy (RT) with concurrent and adjuvant temozolomide (TMZ) in newly diagnosed glioblastoma (GBM).

Author

Thomas, Alissa A., primary, Beal, Kathryn, additional, McNeill, Katharine Anne, additional, Kaley, Thomas Joseph, additional, DeAngelis, Lisa Marie, additional, Mellinghoff, Ingo K., additional, Diamond, Eli L., additional, Chan, Timothy An-thy, additional, Young, Robert J., additional, Arevalo Perez, Julio, additional, Yamada, Yoshiya, additional, Anderson, Barry Douglas, additional, Lamson, Michael, additional, Burch, Brandon, additional, Karmali, Rashida A., additional, and Omuro, Antonio Marcilio Padula, additional

Published
2015
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177. Multicenter Phase I Dose Escalation Study of Hypofractionated Stereotactic Radiotherapy with Bevacizumab in the Treatment of Recurrent Malignant Glioma (S43.005)

Author

Neil, Elizabeth, primary, Clarke, Jennifer, additional, Beal, Kathryn, additional, Gutin, Phillip, additional, Igor, Barani, additional, Kaley, Thomas, additional, Lassman, Andrew, additional, Perezic-Mustafa, Malbora, additional, Young, Robert, additional, and Omuro, Antonio, additional

Published
2015
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179. Alignathon: a competitive assessment of whole-genome alignment methods.

Author

Earl, Dent, Earl, Dent, Nguyen, Ngan, Hickey, Glenn, Harris, Robert S, Fitzgerald, Stephen, Beal, Kathryn, Seledtsov, Igor, Molodtsov, Vladimir, Raney, Brian J, Clawson, Hiram, Kim, Jaebum, Kemena, Carsten, Chang, Jia-Ming, Erb, Ionas, Poliakov, Alexander, Hou, Minmei, Herrero, Javier, Kent, William James, Solovyev, Victor, Darling, Aaron E, Ma, Jian, Notredame, Cedric, Brudno, Michael, Dubchak, Inna, Haussler, David, Paten, Benedict, Earl, Dent, Earl, Dent, Nguyen, Ngan, Hickey, Glenn, Harris, Robert S, Fitzgerald, Stephen, Beal, Kathryn, Seledtsov, Igor, Molodtsov, Vladimir, Raney, Brian J, Clawson, Hiram, Kim, Jaebum, Kemena, Carsten, Chang, Jia-Ming, Erb, Ionas, Poliakov, Alexander, Hou, Minmei, Herrero, Javier, Kent, William James, Solovyev, Victor, Darling, Aaron E, Ma, Jian, Notredame, Cedric, Brudno, Michael, Dubchak, Inna, Haussler, David, and Paten, Benedict

Abstract

Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.

Published
2014

180. The pig X and Y chromosomes: structure, sequence and evolution

Author

Skinner, Benjamin M, primary, Sargent, Carole A, additional, Churcher, Carol, additional, Hunt, Toby, additional, Herrero, Javier, additional, Loveland, Jane, additional, Dunn, Matt, additional, Louzada, Sandra, additional, Fu, Beiyuan, additional, Chow, William, additional, Gilbert, James, additional, Austin-Guest, Siobhan, additional, Beal, Kathryn, additional, Carvalho-Silva, Denise, additional, Cheng, William, additional, Gordon, Daria, additional, Grafham, Darren, additional, Hardy, Matt, additional, Harley, Jo, additional, Hauser, Heidi, additional, Howden, Philip, additional, Howe, Kerstin, additional, Lachani, Kim, additional, Ellis, Peter JI, additional, Kelly, Daniel, additional, Kerry, Giselle, additional, Kerwin, James, additional, Ng, Bee Ling, additional, Threadgold, Glen, additional, Wileman, Thomas, additional, Wood, Jonathan MD, additional, Yang, Fengtang, additional, Harrow, Jen, additional, Affara, Nabeel A, additional, and Tyler-Smith, Chris, additional

Published
2014
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182. Outcomes and Prognostic Factors in Women With 1 to 3 Breast Cancer Brain Metastases Treated With Definitive Stereotactic Radiosurgery

Author

Yang, T. Jonathan, primary, Oh, Jung Hun, additional, Folkert, Michael R., additional, Gupta, Gaorav, additional, Shi, Weiji, additional, Zhang, Zhigang, additional, Morikawa, Aki, additional, Seidman, Andrew, additional, Brennan, Cameron, additional, Yamada, Yoshiya, additional, Chan, Timothy A., additional, and Beal, Kathryn, additional

Published
2014
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185. Ensembl 2015

Author

Cunningham, Fiona, primary, Amode, M. Ridwan, additional, Barrell, Daniel, additional, Beal, Kathryn, additional, Billis, Konstantinos, additional, Brent, Simon, additional, Carvalho-Silva, Denise, additional, Clapham, Peter, additional, Coates, Guy, additional, Fitzgerald, Stephen, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Johnson, Nathan, additional, Juettemann, Thomas, additional, Kähäri, Andreas K., additional, Keenan, Stephen, additional, Martin, Fergal J., additional, Maurel, Thomas, additional, McLaren, William, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Overduin, Bert, additional, Parker, Anne, additional, Patricio, Mateus, additional, Perry, Emily, additional, Pignatelli, Miguel, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Aken, Bronwen L., additional, Birney, Ewan, additional, Harrow, Jennifer, additional, Kinsella, Rhoda, additional, Muffato, Matthieu, additional, Ruffier, Magali, additional, Searle, Stephen M.J., additional, Spudich, Giulietta, additional, Trevanion, Stephen J., additional, Yates, Andy, additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2014
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187. Alignathon: a competitive assessment of whole-genome alignment methods

Author

Earl, Dent, primary, Nguyen, Ngan, additional, Hickey, Glenn, additional, Harris, Robert S., additional, Fitzgerald, Stephen, additional, Beal, Kathryn, additional, Seledtsov, Igor, additional, Molodtsov, Vladimir, additional, Raney, Brian J., additional, Clawson, Hiram, additional, Kim, Jaebum, additional, Kemena, Carsten, additional, Chang, Jia-Ming, additional, Erb, Ionas, additional, Poliakov, Alexander, additional, Hou, Minmei, additional, Herrero, Javier, additional, Kent, William James, additional, Solovyev, Victor, additional, Darling, Aaron E., additional, Ma, Jian, additional, Notredame, Cedric, additional, Brudno, Michael, additional, Dubchak, Inna, additional, Haussler, David, additional, and Paten, Benedict, additional

Published
2014
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188. Phase II Study of Bevacizumab, Temozolomide, and Hypofractionated Stereotactic Radiotherapy for Newly Diagnosed Glioblastoma

Author

Omuro, Antonio, primary, Beal, Kathryn, additional, Gutin, Philip, additional, Karimi, Sasan, additional, Correa, Denise D., additional, Kaley, Thomas J., additional, DeAngelis, Lisa M., additional, Chan, Timothy A., additional, Gavrilovic, Igor T., additional, Nolan, Craig, additional, Hormigo, Adilia, additional, Lassman, Andrew B., additional, Mellinghoff, Ingo, additional, Grommes, Christian, additional, Reiner, Anne S., additional, Panageas, Katherine S., additional, Baser, Raymond E., additional, Tabar, Viviane, additional, Pentsova, Elena, additional, Sanchez, Juan, additional, Barradas-Panchal, Renata, additional, Zhang, Jianan, additional, Faivre, Geraldine, additional, Brennan, Cameron W., additional, Abrey, Lauren E., additional, and Huse, Jason T., additional

Published
2014
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189. The Ensembl REST API: Ensembl Data for Any Language

Author

Yates, Andrew, primary, Beal, Kathryn, additional, Keenan, Stephen, additional, McLaren, William, additional, Pignatelli, Miguel, additional, Ritchie, Graham R. S., additional, Ruffier, Magali, additional, Taylor, Kieron, additional, Vullo, Alessandro, additional, and Flicek, Paul, additional

Published
2014
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192. Erratum: Corrigendum: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Author

Wang, Zhuo, primary, Pascual-Anaya, Juan, additional, Zadissa, Amonida, additional, Li, Wenqi, additional, Niimura, Yoshihito, additional, Huang, Zhiyong, additional, Li, Chunyi, additional, White, Simon, additional, Xiong, Zhiqiang, additional, Fang, Dongming, additional, Wang, Bo, additional, Ming, Yao, additional, Chen, Yan, additional, Zheng, Yuan, additional, Kuraku, Shigehiro, additional, Pignatelli, Miguel, additional, Herrero, Javier, additional, Beal, Kathryn, additional, Nozawa, Masafumi, additional, Li, Qiye, additional, Wang, Juan, additional, Zhang, Hongyan, additional, Yu, Lili, additional, Shigenobu, Shuji, additional, Wang, Junyi, additional, Liu, Jiannan, additional, Flicek, Paul, additional, Searle, Steve, additional, Wang, Jun, additional, Kuratani, Shigeru, additional, Yin, Ye, additional, Aken, Bronwen, additional, Zhang, Guojie, additional, and Irie, Naoki, additional

Published
2014
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193. A phase I trial of sorafenib with whole brain radiotherapy (WBRT) in breast cancer patients with brain metastases and a correlative study of FLT-PET brain imaging to evaluate treatment response after WBRT sorafenib.

Author

Morikawa, Aki, primary, Jhaveri, Komal L., additional, Patil, Sujata, additional, Chen, Melanie, additional, McDonnell, Edward, additional, Neville, Deirdre A., additional, Mak, Fung Ming, additional, Gansukh, Bolorsukh, additional, John, Humm L., additional, Holodny, Andrei, additional, Schöder, Heiko, additional, Beal, Kathryn, additional, and Seidman, Andrew David, additional

Published
2014
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194. A Phase 2 Trial of Stereotactic Radiosurgery Boost After Surgical Resection for Brain Metastases

Author

Brennan, Cameron, primary, Yang, T. Jonathan, additional, Hilden, Patrick, additional, Zhang, Zhigang, additional, Chan, Kelvin, additional, Yamada, Yoshiya, additional, Chan, Timothy A., additional, Lymberis, Stella C., additional, Narayana, Ashwatha, additional, Tabar, Viviane, additional, Gutin, Philip H., additional, Ballangrud, Åse, additional, Lis, Eric, additional, and Beal, Kathryn, additional

Published
2014
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195. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Author

Wang, Zhuo, Pascual-Anaya, Juan, Zadissa, Amonida, Li, Wenqi, Niimura, Yoshihito, Huang, Zhiyong, Li, Chunyi, White, Simon, Xiong, Zhiqiang, Fang, Dongming, Wang, Bo, Ming, Yao, Chen, Yan, Zheng, Yuan, Kuraku, Shigehiro, Pignatelli, Miguel, Herrero, Javier, Beal, Kathryn, Nozawa, Masafumi, Li, Qiye, Wang, Juan, Zhang, Hongyan, Yu, Lili, Shigenobu, Shuji, Wang, Junyi, Liu, Jiannan, Flicek, Paul, Searle, Steve, Wang, Jun, Kuratani, Shigeru, Yin, Ye, Aken, Bronwen, Zhang, Guojie, Irie, Naoki, Wang, Zhuo, Pascual-Anaya, Juan, Zadissa, Amonida, Li, Wenqi, Niimura, Yoshihito, Huang, Zhiyong, Li, Chunyi, White, Simon, Xiong, Zhiqiang, Fang, Dongming, Wang, Bo, Ming, Yao, Chen, Yan, Zheng, Yuan, Kuraku, Shigehiro, Pignatelli, Miguel, Herrero, Javier, Beal, Kathryn, Nozawa, Masafumi, Li, Qiye, Wang, Juan, Zhang, Hongyan, Yu, Lili, Shigenobu, Shuji, Wang, Junyi, Liu, Jiannan, Flicek, Paul, Searle, Steve, Wang, Jun, Kuratani, Shigeru, Yin, Ye, Aken, Bronwen, Zhang, Guojie, and Irie, Naoki

Published
2013

197. A high-resolution map of human evolutionary constraint using 29 mammals

Author

Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F., Parker, Brian J., Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D., Lowe, Craig B., Holloway, Alisha K., Clamp, Michele, Gnerre, Sante, Alfoeldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J., Jaffe, David B., Jungreis, Irwin, Kent, W. James, Kostka, Dennis, Lara, Marcia, Martins, Andre L., Massingham, Tim, Moltke, Ida, Raney, Brian J., Rasmussen, Matthew D., Robinson, Jim, Stark, Alexander, Vilella, Albert J., Wen, Jiayu, Xie, Xiaohui, Zody, Michael C., Worley, Kim C., Kovar, Christie L., Muzny, Donna M., Gibbs, Richard A., Warren, Wesley C., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Birney, Ewan, Margulies, Elliott H., Herrero, Javier, Green, Eric D., Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S., Pedersen, Jakob S., Lander, Eric S., Kellis, Manolis, Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F., Parker, Brian J., Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D., Lowe, Craig B., Holloway, Alisha K., Clamp, Michele, Gnerre, Sante, Alfoeldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J., Jaffe, David B., Jungreis, Irwin, Kent, W. James, Kostka, Dennis, Lara, Marcia, Martins, Andre L., Massingham, Tim, Moltke, Ida, Raney, Brian J., Rasmussen, Matthew D., Robinson, Jim, Stark, Alexander, Vilella, Albert J., Wen, Jiayu, Xie, Xiaohui, Zody, Michael C., Worley, Kim C., Kovar, Christie L., Muzny, Donna M., Gibbs, Richard A., Warren, Wesley C., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Birney, Ewan, Margulies, Elliott H., Herrero, Javier, Green, Eric D., Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S., Pedersen, Jakob S., Lander, Eric S., and Kellis, Manolis

Abstract

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering similar to 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for similar to 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate-and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

Published
2011
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198. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, Levchenko, Tanya, Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, and Levchenko, Tanya

Abstract

BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Published
2011

199. Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

Author

Dalloul, Rami A., Long, Julie A., Zimin, Aleksey V., Aslam, Luqman, Beal, Kathryn, Blomberg, Le Ann, Bouffard, Pascal, Burt, David W., Crasta, Oswald, Crooijmans, Richard P. M. A., Cooper, Kristal, Coulombe, Roger A., De, Supriyo, Delany, Mary E., Dodgson, Jerry B., Dong, Jennifer J., Evans, Clive, Frederickson, Karin M., Flicek, Paul, Florea, Liliana, Folkerts, Otto, Groenen, Martien A. M., Harkins, Tim T., Herrero, Javier, Hoffmann, Steve, Megens, Hendrik-Jan, Jiang, Andrew, de Jong, Pieter, Kaiser, Pete, Kim, Heebal, Kim, Kyu-Won, Kim, Sungwon, Langenberger, David, Lee, Mi-Kyung, Lee, Taeheon, Mane, Shrinivasrao P., Marcais, Guillaume, Marz, Manja, McElroy, Audrey P., Modise, Thero, Nefedov, Mikhail, Notredame, Cédric, Paton, Ian R., Payne, William S., Pertea, Geo, Prickett, Dennis, Puiu, Daniela, Qioa, Dan, Raineri, Emanuele, Ruffier, Magali, Salzberg, Steven L., Schatz, Michael C., Scheuring, Chantel, Schmidt, Carl J., Schroeder, Steven, Searle, Stephen M. J., Smith, Edward J., Smith, Jacqueline, Sonstegard, Tad S., Stadler, Peter F., Tafer, Hakim, Tu, Zhijian Jake, Van Tassell, Curtis P., Vilella, Albert J., Williams, Kelly P., Yorke, James A., Zhang, Liqing, Zhang, Hong-Bin, Zhang, Xiaojun, Zhang, Yang, Reed, Kent M., Dalloul, Rami A., Long, Julie A., Zimin, Aleksey V., Aslam, Luqman, Beal, Kathryn, Blomberg, Le Ann, Bouffard, Pascal, Burt, David W., Crasta, Oswald, Crooijmans, Richard P. M. A., Cooper, Kristal, Coulombe, Roger A., De, Supriyo, Delany, Mary E., Dodgson, Jerry B., Dong, Jennifer J., Evans, Clive, Frederickson, Karin M., Flicek, Paul, Florea, Liliana, Folkerts, Otto, Groenen, Martien A. M., Harkins, Tim T., Herrero, Javier, Hoffmann, Steve, Megens, Hendrik-Jan, Jiang, Andrew, de Jong, Pieter, Kaiser, Pete, Kim, Heebal, Kim, Kyu-Won, Kim, Sungwon, Langenberger, David, Lee, Mi-Kyung, Lee, Taeheon, Mane, Shrinivasrao P., Marcais, Guillaume, Marz, Manja, McElroy, Audrey P., Modise, Thero, Nefedov, Mikhail, Notredame, Cédric, Paton, Ian R., Payne, William S., Pertea, Geo, Prickett, Dennis, Puiu, Daniela, Qioa, Dan, Raineri, Emanuele, Ruffier, Magali, Salzberg, Steven L., Schatz, Michael C., Scheuring, Chantel, Schmidt, Carl J., Schroeder, Steven, Searle, Stephen M. J., Smith, Edward J., Smith, Jacqueline, Sonstegard, Tad S., Stadler, Peter F., Tafer, Hakim, Tu, Zhijian Jake, Van Tassell, Curtis P., Vilella, Albert J., Williams, Kelly P., Yorke, James A., Zhang, Liqing, Zhang, Hong-Bin, Zhang, Xiaojun, Zhang, Yang, and Reed, Kent M.

Abstract

A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (,1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Published
2010
Full Text
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200. Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

Author

Animal and Poultry Sciences, Biochemistry, Computer Science, Fralin Life Sciences Institute, Dalloul, Rami A., Long, Julie A., Zimin, Aleksey V., Aslam, Luqman, Beal, Kathryn, Blomberg, Le Ann, Bouffard, Pascal, Burt, David W., Crasta, Oswald, Crooijmans, Richard P. M. A., Cooper, Kristal, Coulombe, Roger A., De, Supriyo, Delany, Mary E., Dodgson, Jerry B., Dong, Jennifer J., Evans, Clive, Frederickson, Karin M., Flicek, Paul, Florea, Liliana, Folkerts, Otto, Groenen, Martien A. M., Harkins, Tim T., Herrero, Javier, Hoffmann, Steve, Megens, Hendrik-Jan, Jiang, Andrew, de Jong, Pieter, Kaiser, Pete, Kim, Heebal, Kim, Kyu-Won, Kim, Sungwon, Langenberger, David, Lee, Mi-Kyung, Lee, Taeheon, Mane, Shrinivasrao P., Marcais, Guillaume, Marz, Manja, McElroy, Audrey P., Modise, Thero, Nefedov, Mikhail, Notredame, Cédric, Paton, Ian R., Payne, William S., Pertea, Geo, Prickett, Dennis, Puiu, Daniela, Qioa, Dan, Raineri, Emanuele, Ruffier, Magali, Salzberg, Steven L., Schatz, Michael C., Scheuring, Chantel, Schmidt, Carl J., Schroeder, Steven, Searle, Stephen M. J., Smith, Edward J., Smith, Jacqueline, Sonstegard, Tad S., Stadler, Peter F., Tafer, Hakim, Tu, Zhijian Jake, Van Tassell, Curtis P., Vilella, Albert J., Williams, Kelly P., Yorke, James A., Zhang, Liqing, Zhang, Hong-Bin, Zhang, Xiaojun, Zhang, Yang, Reed, Kent M., Animal and Poultry Sciences, Biochemistry, Computer Science, Fralin Life Sciences Institute, Dalloul, Rami A., Long, Julie A., Zimin, Aleksey V., Aslam, Luqman, Beal, Kathryn, Blomberg, Le Ann, Bouffard, Pascal, Burt, David W., Crasta, Oswald, Crooijmans, Richard P. M. A., Cooper, Kristal, Coulombe, Roger A., De, Supriyo, Delany, Mary E., Dodgson, Jerry B., Dong, Jennifer J., Evans, Clive, Frederickson, Karin M., Flicek, Paul, Florea, Liliana, Folkerts, Otto, Groenen, Martien A. M., Harkins, Tim T., Herrero, Javier, Hoffmann, Steve, Megens, Hendrik-Jan, Jiang, Andrew, de Jong, Pieter, Kaiser, Pete, Kim, Heebal, Kim, Kyu-Won, Kim, Sungwon, Langenberger, David, Lee, Mi-Kyung, Lee, Taeheon, Mane, Shrinivasrao P., Marcais, Guillaume, Marz, Manja, McElroy, Audrey P., Modise, Thero, Nefedov, Mikhail, Notredame, Cédric, Paton, Ian R., Payne, William S., Pertea, Geo, Prickett, Dennis, Puiu, Daniela, Qioa, Dan, Raineri, Emanuele, Ruffier, Magali, Salzberg, Steven L., Schatz, Michael C., Scheuring, Chantel, Schmidt, Carl J., Schroeder, Steven, Searle, Stephen M. J., Smith, Edward J., Smith, Jacqueline, Sonstegard, Tad S., Stadler, Peter F., Tafer, Hakim, Tu, Zhijian Jake, Van Tassell, Curtis P., Vilella, Albert J., Williams, Kelly P., Yorke, James A., Zhang, Liqing, Zhang, Hong-Bin, Zhang, Xiaojun, Zhang, Yang, and Reed, Kent M.

Abstract

A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (,1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Published
2010

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