Search Results - "Berger, Alice"

All About That Ras: Novel Fusion Drives Ras Pathway Activation in Lung Cancer by Moorthi, Sitapriya, Berger, Alice H

“…Lung cancers in never- and light-smokers often harbor targetable oncogenic mutations in Ras pathway genes. Here, a novel OCLN-RASGRF1 fusion is identified in…”
Get full text

A continuum model for tumour suppression by Berger, Alice H., Knudson, Alfred G., Pandolfi, Pier Paolo

“…Tumour suppression modelled The 'two-hit' hypothesis of tumorigenesis, originally proposed in 1971 by Alfred Knudson using retinoblastoma as a model, explained…”
Get full text

Haplo-insufficiency: a driving force in cancer by Berger, Alice H, Pandolfi, Pier Paolo

“…It was originally proposed that tumour suppressor genes (TSGs) act in a recessive manner. Instead, numerous TSGs, including p53 and PTEN, exhibit…”
Get full text

Oncogenic KRAS alters splicing factor phosphorylation and alternative splicing in lung cancer by Lo, April, McSharry, Maria, Berger, Alice H

“…Alternative RNA splicing is widely dysregulated in cancers including lung adenocarcinoma, where aberrant splicing events are frequently caused by somatic…”
Get full text

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas by Campbell, Joshua D, Alexandrov, Anton, Kim, Jaegil, Wala, Jeremiah, Berger, Alice H, Pedamallu, Chandra Sekhar, Shukla, Sachet A, Guo, Guangwu, Brooks, Angela N, Murray, Bradley A, Imielinski, Marcin, Hu, Xin, Ling, Shiyun, Akbani, Rehan, Rosenberg, Mara, Cibulskis, Carrie, Ramachandran, Aruna, Collisson, Eric A, Kwiatkowski, David J, Lawrence, Michael S, Weinstein, John N, Verhaak, Roel G W, Wu, Catherine J, Hammerman, Peter S, Cherniack, Andrew D, Getz, Gad, Artyomov, Maxim N, Schreiber, Robert, Govindan, Ramaswamy, Meyerson, Matthew

“…Matthew Meyerson, Ramaswamy Govindan and colleagues examine the exome sequences and copy number profiles of 660 lung adenocarcinoma and 484 lung squamous cell…”
Get full text

Thrombolytic therapy based on fucoidan-functionalized polymer nanoparticles targeting P-selectin by Juenet, Maya, Aid-Launais, Rachida, Li, Bo, Berger, Alice, Aerts, Joël, Ollivier, Véronique, Nicoletti, Antonino, Letourneur, Didier, Chauvierre, Cédric

“…Injection of recombinant tissue plasminogen activator (rt-PA) is the standard drug treatment for thrombolysis. However, rt-PA shows risk of hemorrhages and…”
Get full text

High-throughput Phenotyping of Lung Cancer Somatic Mutations by Berger, Alice H., Brooks, Angela N., Wu, Xiaoyun, Shrestha, Yashaswi, Chouinard, Candace, Piccioni, Federica, Bagul, Mukta, Kamburov, Atanas, Imielinski, Marcin, Hogstrom, Larson, Zhu, Cong, Yang, Xiaoping, Pantel, Sasha, Sakai, Ryo, Watson, Jacqueline, Kaplan, Nathan, Campbell, Joshua D., Singh, Shantanu, Root, David E., Narayan, Rajiv, Natoli, Ted, Lahr, David L., Tirosh, Itay, Tamayo, Pablo, Getz, Gad, Wong, Bang, Doench, John, Subramanian, Aravind, Golub, Todd R., Meyerson, Matthew, Boehm, Jesse S.

“…Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood…”
Get full text

RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons by Thomas, James D., Polaski, Jacob T., Feng, Qing, De Neef, Emma J., Hoppe, Emma R., McSharry, Maria V., Pangallo, Joseph, Gabel, Austin M., Belleville, Andrea E., Watson, Jacqueline, Nkinsi, Naomi T., Berger, Alice H., Bradley, Robert K.

“…While RNA-seq has enabled comprehensive quantification of alternative splicing, no correspondingly high-throughput assay exists for functionally interrogating…”
Get full text

Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome by Parrish, Phoebe C.R., Thomas, James D., Gabel, Austin M., Kamlapurkar, Shriya, Bradley, Robert K., Berger, Alice H.

“…CRISPR screens have accelerated the discovery of important cancer vulnerabilities. However, single-gene knockout phenotypes can be masked by redundancy among…”
Get full text

Diagnostic accuracy of two commercial SARS-CoV-2 antigen-detecting rapid tests at the point of care in community-based testing centers by Berger, Alice, Nsoga, Marie Therese Ngo, Perez-Rodriguez, Francisco Javier, Aad, Yasmine Abi, Sattonnet-Roche, Pascale, Gayet-Ageron, Angèle, Jaksic, Cyril, Torriani, Giulia, Boehm, Erik, Kronig, Ilona, Sacks, Jilian A, de Vos, Margaretha, Bausch, Frédérique Jacquerioz, Chappuis, François, Renzoni, Adriana, Kaiser, Laurent, Schibler, Manuel, Eckerle, Isabella

“…Determine the diagnostic accuracy of two antigen-detecting rapid diagnostic tests (Ag-RDT) for SARS-CoV-2 at the point of care and define individuals'…”
Get full text

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing by Imielinski, Marcin, Berger, Alice H., Hammerman, Peter S., Hernandez, Bryan, Pugh, Trevor J., Hodis, Eran, Cho, Jeonghee, Suh, James, Capelletti, Marzia, Sivachenko, Andrey, Sougnez, Carrie, Auclair, Daniel, Lawrence, Michael S., Stojanov, Petar, Cibulskis, Kristian, Choi, Kyusam, de Waal, Luc, Sharifnia, Tanaz, Brooks, Angela, Greulich, Heidi, Banerji, Shantanu, Zander, Thomas, Seidel, Danila, Leenders, Frauke, Ansén, Sascha, Ludwig, Corinna, Engel-Riedel, Walburga, Stoelben, Erich, Wolf, Jürgen, Goparju, Chandra, Thompson, Kristin, Winckler, Wendy, Kwiatkowski, David, Johnson, Bruce E., Jänne, Pasi A., Miller, Vincent A., Pao, William, Travis, William D., Pass, Harvey I., Gabriel, Stacey B., Lander, Eric S., Thomas, Roman K., Garraway, Levi A., Getz, Gad, Meyerson, Matthew

“…Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report…”
Get full text

Massively parallel phenotyping of coding variants in cancer with Perturb-seq by Ursu, Oana, Neal, James T., Shea, Emily, Thakore, Pratiksha I., Jerby-Arnon, Livnat, Nguyen, Lan, Dionne, Danielle, Diaz, Celeste, Bauman, Julia, Mosaad, Mariam Mounir, Fagre, Christian, Lo, April, McSharry, Maria, Giacomelli, Andrew O., Ly, Seav Huong, Rozenblatt-Rosen, Orit, Hahn, William C., Aguirre, Andrew J., Berger, Alice H., Regev, Aviv, Boehm, Jesse S.

“…Genome sequencing studies have identified millions of somatic variants in cancer, but it remains challenging to predict the phenotypic impact of most…”
Get full text

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants by Thornton, Alexis M, Fang, Lishan, Lo, April, McSharry, Maria, Haan, David, O'Brien, Casey, Berger, Alice H, Giannakis, Marios, Brooks, Angela N

“…While advancements in genome sequencing have identified millions of somatic mutations in cancer, their functional impact is poorly understood. We previously…”
Get full text

CRISPR base editor screens identify variant function at scale by Parrish, Phoebe C R, Berger, Alice H

“…Cuella-Martin et al. (2021) and Hanna et al. (2021) showcase CRISPR base editing in large-scale pooled screens in human cells to discover both loss- and…”
Get full text

MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma by Lu, Xinyuan, Peled, Nir, Greer, John, Wu, Wei, Choi, Peter, Berger, Alice H, Wong, Sergio, Jen, Kuang-Yu, Seo, Youngho, Hann, Byron, Brooks, Angela, Meyerson, Matthew, Collisson, Eric A

“…Targeting somatically activated oncogenes has revolutionized the treatment of non-small cell lung cancer (NSCLC). Mutations in the gene mesenchymal-epithelial…”
Get full text

Cell Painting predicts impact of lung cancer variants by Caicedo, Juan C, Arevalo, John, Piccioni, Federica, Bray, Mark-Anthony, Hartland, Cathy L, Wu, Xiaoyun, Brooks, Angela N, Berger, Alice H, Boehm, Jesse S, Carpenter, Anne E, Singh, Shantanu

“…Most variants in most genes across most organisms have an unknown impact on the function of the corresponding gene. This gap in knowledge is especially acute…”
Get full text

Chromosome-level genome editing uncovers aneuploidy addiction in cancer by O’Brien, Siobhan, Berger, Alice H.

“…Publishing in Science, Girish and colleagues achieve chromosome-level genome editing to reveal a requirement for aneuploidy in breast and melanoma cancers…”
Get full text

Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2 by Greulich, Heidi, Kaplan, Bethany, Mertins, Philipp, Chen, Tzu-Hsiu, Tanaka, Kumiko E, Yun, Cai-Hong, Zhang, Xiaohong, Lee, Se-Hoon, Cho, Jeonghee, Ambrogio, Lauren, Liao, Rachel, Imielinski, Marcin, Banerji, Shantanu, Berger, Alice H, Lawrence, Michael S, Zhang, Jinghui, Pho, Nam H, Walker, Sarah R, Winckler, Wendy, Getz, Gad, Frank, David, Hahn, William C, Eck, Michael J, Mani, D. R, Jaffe, Jacob D, Carr, Steven A, Wong, Kwok-Kin, Meyerson, Matthew

“…We assessed somatic alleles of six receptor tyrosine kinase genes mutated in lung adenocarcinoma for oncogenic activity. Five of these genes failed to score in…”
Get full text

Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer by Vichas, Athea, Riley, Amanda K., Nkinsi, Naomi T., Kamlapurkar, Shriya, Parrish, Phoebe C. R., Lo, April, Duke, Fujiko, Chen, Jennifer, Fung, Iris, Watson, Jacqueline, Rees, Matthew, Gabel, Austin M., Thomas, James D., Bradley, Robert K., Lee, John K., Hatch, Emily M., Baine, Marina K., Rekhtman, Natasha, Ladanyi, Marc, Piccioni, Federica, Berger, Alice H.

“…CRISPR-based cancer dependency maps are accelerating advances in cancer precision medicine, but adequate functional maps are limited to the most common…”
Get full text

Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation by Gelman, Hannah, Dines, Jennifer N, Berg, Jonathan, Berger, Alice H, Brnich, Sarah, Hisama, Fuki M, James, Richard G, Rubin, Alan F, Shendure, Jay, Shirts, Brian, Fowler, Douglas M, Starita, Lea M

“…Variants of uncertain significance represent a massive challenge to medical genetics. Multiplexed functional assays, in which the functional effects of…”
Get full text