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 2018

Double Trouble: Whole-Genome Doubling Distinguishes Early from Late Ovarian Cancer

por Yang, Shih Yu Cindy, Pugh, Trevor J., Oza, Amit M.
Publicado 2022

MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis

por Zeng, Yong, Ye, Wenbin, Stutheit-Zhao, Eric Y, Han, Ming, Bratman, Scott V, Pugh, Trevor J, He, Housheng Hansen
Publicado 2023

Elevation in viral entry genes and innate immunity compromise underlying increased infectivity and severity of COVID-19 in cancer patients

por Kwan, Jennifer Yin Yee, Lin, Liang-Tzung, Bell, Rachel, Bruce, Jeffrey P., Richardson, Christopher, Pugh, Trevor J., Liu, Fei-Fei
Publicado 2021

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 2016

Single-cell profiling of multiple myeloma reveals molecular response to FGFR3 inhibitor despite clinical progression

por Croucher, Danielle C., Devasia, Anup Joseph, Abelman, Dor D., Mahdipour-Shirayeh, Ali, Li, Zhihua, Erdmann, Natalie, Tiedemann, Rodger, Pugh, Trevor J., Trudel, Suzanne
Publicado 2023

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 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 2015

IMMU-14. COMPUTATIONAL DECONVOLUTION OF TUMOR-INFILTRATING IMMUNE COMPONENTS IN PEDIATRIC NERVOUS SYSTEM TUMORS

por Beck, Pengbo, Nabbi, Arash, Sill, Martin, Sudhaman, Sumedha, Kool, Marcel, Resnick, Adam C, Jones, David T W, Pfister, Stefan M, Pugh, Trevor J, Jäger, Natalie
Publicado 2021

HPV Sequencing Facilitates Ultrasensitive Detection of HPV Circulating Tumor DNA

por Leung, Eric, Han, Kathy, Zou, Jinfeng, Zhao, Zhen, Zheng, Yangqiao, Wang, Ting Ting, Rostami, Ariana, Siu, Lillian L., Pugh, Trevor J., Bratman, Scott V.
Publicado 2021

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 2019

Myeloma immunoglobulin rearrangement and translocation detection through targeted capture sequencing

por Chow, Signy, Kis, Olena, Mulder, David T, Danesh, Arnavaz, Bruce, Jeff, Wang, Ting Ting, Reece, Donna, Bhalis, Nizar, Neri, Paola, Sabatini, Peter JB, Keats, Jonathan, Trudel, Suzanne, Pugh, Trevor J
Publicado 2022

Longitudinal single-cell analysis of a myeloma mouse model identifies subclonal molecular programs associated with progression

por Croucher, Danielle C., Richards, Laura M., Tsofack, Serges P., Waller, Daniel, Li, Zhihua, Wei, Ellen Nong, Huang, Xian Fang, Chesi, Marta, Bergsagel, P. Leif, Sebag, Michael, Pugh, Trevor J., Trudel, Suzanne
Publicado 2021

Multimodal immunogenomic biomarker analysis of tumors from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab

por Nabbi, Arash, Danesh, Arnavaz, Espin-Garcia, Osvaldo, Pedersen, Stephanie, Wellum, Johanna, Fu, Lingyan Helen, Paulson, Joseph N., Geoerger, Birgit, Marshall, Lynley V., Trippett, Tanya, Rossato, Gianluca, Pugh, Trevor J., Hutchinson, Katherine E.
Publicado 2023

IMMU-08. SALVAGE IMMUNOTHERAPIES FOR REPLICATION REPAIR DEFICIENT (RRD) HIGH-GRADE GLIOMA FAILING ANTI-PD1 MONOTHERAPY: AN IRRDC REPORT

por Das, Anirban, Fernandez, Nicholas R, Levine, Adrian, Bianchi, Vanessa, Stengs, Lucie, Edwards, Melissa, Nobre, Liana, Pugh, Trevor J, Tsang, Derek S, Ertl-Wagner, Birgit, Morgenstern, Daniel A, Bouffet, Eric, Hawkins, Cynthia, Tabori, Uri
Publicado 2023

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 2020

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 2007

Predicting Toxicity and Response to Pembrolizumab Through Germline Genomic HLA Class 1 Analysis

por Iafolla, Marco A J, Yang, Cindy, Chandran, Vinod, Pintilie, Melania, Li, Quan, Bedard, Philippe L, Hansen, Aaron, Lheureux, Stephanie, Spreafico, Anna, Razak, Albiruni A, Hakgor, Sevan, Giesler, Amanda, Pugh, Trevor J, Siu, Lillian L
Publicado 2020

Defining and targeting tumor-associated macrophages in malignant mesothelioma

por Wu, Licun, Kohno, Mikihiro, Murakami, Junichi, Zia, Amin, Allen, Jonathan, Yun, Hana, Chan, Meilin, Baciu, Cristina, Liu, Mingyao, Serre-Beinier, Veronique, De Palma, Michele, Felley-Bosco, Emanuela, Yeung, Jonathan, Pugh, Trevor J., de Perrot, Marc
Publicado 2023

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 2013