Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

Por Samadian, Soroush, Bruce, Jeff P., Pugh, Trevor J.
Publicado no PLoS Comput Biol (2018)

Oncotator: cancer variant annotation tool

Por Ramos, Alex H., Lichtenstein, Lee, Gupta, Manaswi, Lawrence, Michael S., Pugh, Trevor J., Saksena, Gordon, Meyerson, Matthew, Getz, Gad
Publicado no Hum Mutat (2015)

VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data

Por Pugh, Trevor J., Amr, Sami S., Bowser, Mark J., Gowrisankar, Sivakumar, Hynes, Elizabeth, Mahanta, Lisa M., Rehm, Heidi L., Funke, Birgit, Lebo, Matthew S.
Publicado no Genet Med (2016)

High efficiency error suppression for accurate detection of low-frequency variants

Por Wang, Ting Ting, Abelson, Sagi, Zou, Jinfeng, Li, Tiantian, Zhao, Zhen, Dick, John E, Shlush, Liran I, Pugh, Trevor J, Bratman, Scott V
Publicado no Nucleic Acids Res (2019)

Next generation sequencing‐based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies

Por Ceyhan‐Birsoy, Ozge, Pugh, Trevor J., Bowser, Mark J., Hynes, Elizabeth, Frisella, Ashley L., Mahanta, Lisa M., Lebo, Matt S., Amr, Sami S., Funke, Birgit H.
Publicado no Mol Genet Genomic Med (2015)

Unsupervised Resolution of Histomorphologic Heterogeneity in Renal Cell Carcinoma Using a Brain Tumor–Educated Neural Network

Por Faust, Kevin, Roohi, Adil, Leon, Alberto J., Leroux, Emeline, Dent, Anglin, Evans, Andrew J., Pugh, Trevor J., Kalimuthu, Sangeetha N., Djuric, Ugljesa, Diamandis, Phedias
Publicado no JCO Clin Cancer Inform (2020)

CapTCR-seq: hybrid capture for T-cell receptor repertoire profiling

Por Mulder, David T., Mahé, Etienne R., Dowar, Mark, Hanna, Youstina, Li, Tiantian, Nguyen, Linh T., Butler, Marcus O., Hirano, Naoto, Delabie, Jan, Ohashi, Pamela S., Pugh, Trevor J.
Publicado no Blood Adv (2018)

Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data

Por Diaz-Mejia, J. Javier, Meng, Elaine C., Pico, Alexander R., MacParland, Sonya A., Ketela, Troy, Pugh, Trevor J., Bader, Gary D., Morris, John H.
Publicado no F1000Res (2019)

A shower of second hit events as the cause of multifocal renal cell carcinoma in tuberous sclerosis complex

Por Tyburczy, Magdalena E., Jozwiak, Sergiusz, Malinowska, Izabela A., Chekaluk, Yvonne, Pugh, Trevor J., Wu, Chin-Lee, Nussbaum, Robert L., Seepo, Sara, Dzik, Tomasz, Kotulska, Katarzyna, Kwiatkowski, David J.
Publicado no Hum Mol Genet (2015)

A Comprehensive Assay for CFTR Mutational Analysis Using Next-Generation Sequencing

Por Tayoun, Ahmad N. Abou, Tunkey, Christopher D., Pugh, Trevor J., Ross, Tristen, Shah, Minita, Lee, Clarence C., Harkins, Timothy T., Wells, Wendy A., Tafe, Laura J., Amos, Christopher I., Tsongalis, Gregory J.
Publicado no Clin Chem (2013)

DNA-demethylating agents target colorectal cancer cells by inducing viral mimicry by endogenous transcripts

Por Roulois, David, Yau, Helen Loo, Singhania, Rajat, Wang, Yadong, Danesh, Arnavaz, Shen, Shu Yi, Han, Han, Liang, Gangning, Pugh, Trevor J., Jones, Peter A., O’Brien, Catherine, De Carvalho, Daniel D.
Publicado no Cell (2015)

The mevalonate pathway is an actionable vulnerability of t(4;14)-positive multiple myeloma

Por Longo, Joseph, Smirnov, Petr, Li, Zhihua, Branchard, Emily, van Leeuwen, Jenna E., Licht, Jonathan D., Haibe-Kains, Benjamin, Andrews, David W., Keats, Jonathan J., Pugh, Trevor J., Trudel, Suzanne, Penn, Linda Z.
Publicado no Leukemia (2020)

Correlations of <it>EGFR </it>mutations and increases in <it>EGFR </it>and <it>HER2 </it>copy number to gefitinib response in a retrospective analysis of lung cancer patients

Por English John, Melosky Barbara, Murray Nevin, Ho Cheryl, O'Connor Robert, Salski Chris, Fee John, Sutcliffe Margaret, Barclay Lorena, Bebb Gwyn, Pugh Trevor J, Vielkind Jeurgen, Horsman Doug, Laskin Janessa J, Marra Marco A
Publicado em 2007-07-01

Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients

Por Pugh, Trevor J, Bebb, Gwyn, Barclay, Lorena, Sutcliffe, Margaret, Fee, John, Salski, Chris, O'Connor, Robert, Ho, Cheryl, Murray, Nevin, Melosky, Barbara, English, John, Vielkind, Jeurgen, Horsman, Doug, Laskin, Janessa J, Marra, Marco A
Publicado em 2007

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

Por Costello, Maura, Pugh, Trevor J., Fennell, Timothy J., Stewart, Chip, Lichtenstein, Lee, Meldrim, James C., Fostel, Jennifer L., Friedrich, Dennis C., Perrin, Danielle, Dionne, Danielle, Kim, Sharon, Gabriel, Stacey B., Lander, Eric S., Fisher, Sheila, Getz, Gad
Publicado em 2013

Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates

Por Kis, Olena, Kaedbey, Rayan, Chow, Signy, Danesh, Arnavaz, Dowar, Mark, Li, Tiantian, Li, Zhihua, Liu, Jessica, Mansour, Mark, Masih-Khan, Esther, Zhang, Tong, Bratman, Scott V., Oza, Amit M., Kamel-Reid, Suzanne, Trudel, Suzanne, Pugh, Trevor J.
Publicado no Nat Commun (2017)

Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma

Por Liao, Rachel G., Jung, Joonil, Tchaicha, Jeremy, Wilkerson, Matthew D., Sivachenko, Andrey, Beauchamp, Ellen M., Liu, Qingsong, Pugh, Trevor J., Pedamallu, Chandra Sekhar, Hayes, D. Neil, Gray, Nathanael S., Getz, Gad, Wong, Kwok-Kin, Haddad, Robert I., Meyerson, Matthew, Hammerman, Peter S.
Publicado em 2013

Safety and tolerability of CFI-400945, a first-in-class, selective PLK4 inhibitor in advanced solid tumours: a phase 1 dose-escalation trial

Por Veitch, Zachary W., Cescon, David W., Denny, Trisha, Yonemoto, Lisa-Maria, Fletcher, Graham, Brokx, Richard, Sampson, Peter, Li, Sze-Wan, Pugh, Trevor J., Bruce, Jeffrey, Bray, Mark R., Slamon, Dennis J., Mak, Tak W., Wainberg, Zev A., Bedard, Philippe L.
Publicado no Br J Cancer (2019)

Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor

Por Quevedo, Rene, Spreafico, Anna, Bruce, Jeff, Danesh, Arnavaz, El Ghamrasni, Samah, Giesler, Amanda, Hanna, Youstina, Have, Cherry, Li, Tiantian, Yang, S. Y. Cindy, Zhang, Tong, Asa, Sylvia L., Haibe-Kains, Benjamin, Krzyzanowska, Monika, Smith, Adam C., Singh, Simron, Siu, Lillian L., Pugh, Trevor J.
Publicado no Genome Med (2020)

Therapeutic radiation for childhood cancer drives structural aberrations of NF2 in meningiomas

Por Agnihotri, Sameer, Suppiah, Suganth, Tonge, Peter D., Jalali, Shahrzad, Danesh, Arnavaz, Bruce, Jeffery P., Mamatjan, Yasin, Klironomos, George, Gonen, Lior, Au, Karolyn, Mansouri, Sheila, Karimi, Sharin, Sahm, Felix, von Deimling, Andreas, Taylor, Michael D., Laperriere, Normand J., Pugh, Trevor J., Aldape, Kenneth D., Zadeh, Gelareh
Publicado no Nat Commun (2017)