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Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden.
Published in:
Journal of Pathology, 2015, v. 236, n. 2, p. 201, doi. 10.1002/path.4516
By:
- Anglesio, Michael S;
- Bashashati, Ali;
- Wang, Yi Kan;
- Senz, Janine;
- Ha, Gavin;
- Yang, Winnie;
- Aniba, Mohamed R;
- Prentice, Leah M;
- Farahani, Hossein;
- Li Chang, Hector;
- Karnezis, Anthony N;
- Marra, Marco A;
- Yong, Paul J;
- Hirst, Martin;
- Gilks, Blake;
- Shah, Sohrab P;
- Huntsman, David G
Publication type:
Article
Multiplexed functional genomic analysis of 5' untranslated region mutations across the spectrum of prostate cancer.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24445-6
By:
- Lim, Yiting;
- Arora, Sonali;
- Schuster, Samantha L.;
- Corey, Lukas;
- Fitzgibbon, Matthew;
- Wladyka, Cynthia L.;
- Wu, Xiaoying;
- Coleman, Ilsa M.;
- Delrow, Jeffrey J.;
- Corey, Eva;
- True, Lawrence D.;
- Nelson, Peter S.;
- Ha, Gavin;
- Hsieh, Andrew C.
Publication type:
Article
Haplotype-resolved germline and somatic alterations in renal medullary carcinomas.
Published in:
Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00929-4
By:
- Tan, Kar-Tong;
- Kim, Hyunji;
- Carrot-Zhang, Jian;
- Zhang, Yuxiang;
- Kim, Won Jun;
- Kugener, Guillaume;
- Wala, Jeremiah A.;
- Howard, Thomas P.;
- Chi, Yueh-Yun;
- Beroukhim, Rameen;
- Li, Heng;
- Ha, Gavin;
- Alper, Seth L.;
- Perlman, Elizabeth J.;
- Mullen, Elizabeth A.;
- Hahn, William C.;
- Meyerson, Matthew;
- Hong, Andrew L.
Publication type:
Article
Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer.
Published in:
Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00895-x
By:
- Weber, Zachary T.;
- Collier, Katharine A.;
- Tallman, David;
- Forman, Juliet;
- Shukla, Sachet;
- Asad, Sarah;
- Rhoades, Justin;
- Freeman, Samuel;
- Parsons, Heather A.;
- Williams, Nicole O.;
- Barroso-Sousa, Romualdo;
- Stover, Elizabeth H.;
- Mahdi, Haider;
- Cibulskis, Carrie;
- Lennon, Niall J.;
- Ha, Gavin;
- Adalsteinsson, Viktor A.;
- Tolaney, Sara M.;
- Stover, Daniel G.
Publication type:
Article
Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.
Published in:
Journal of Pathology, 2013, v. 231, n. 1, p. 21, doi. 10.1002/path.4230
By:
- Bashashati, Ali;
- Ha, Gavin;
- Tone, Alicia;
- Ding, Jiarui;
- Prentice, Leah M;
- Roth, Andrew;
- Rosner, Jamie;
- Shumansky, Karey;
- Kalloger, Steve;
- Senz, Janine;
- Yang, Winnie;
- McConechy, Melissa;
- Melnyk, Nataliya;
- Anglesio, Michael;
- Luk, Margaret TY;
- Tse, Kane;
- Zeng, Thomas;
- Moore, Richard;
- Zhao, Yongjun;
- Marra, Marco A
Publication type:
Article
Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.
Published in:
Journal of Pathology, 2011, v. 225, n. 1, p. 12, doi. 10.1002/path.2941
By:
- Schrader, Kasmintan A;
- Heravi-Moussavi, Alireza;
- Waters, Paula J;
- Senz, Janine;
- Whelan, James;
- Ha, Gavin;
- Eydoux, Patrice;
- Nielsen, Torsten;
- Gallagher, Barry;
- Oloumi, Arusha;
- Boyd, Niki;
- Fernandez, Bridget A;
- Young, Terry-Lynn;
- Jones, Steven JM;
- Hirst, Martin;
- Shah, Sohrab P;
- Marra, Marco A;
- Green, Jane;
- Huntsman, David G
Publication type:
Article
PyClone: statistical inference of clonal population structure in cancer.
Published in:
Nature Methods, 2014, v. 11, n. 4, p. 396, doi. 10.1038/nmeth.2883
By:
- Roth, Andrew;
- Khattra, Jaswinder;
- Yap, Damian;
- Wan, Adrian;
- Laks, Emma;
- Biele, Justina;
- Ha, Gavin;
- Aparicio, Samuel;
- Bouchard-Côté, Alexandre;
- Shah, Sohrab P
Publication type:
Article
Mutation Discovery in Regions of Segmental Cancer Genome Amplifications with CoNAn-SNV: A Mixture Model for Next Generation Sequencing of Tumors.
Published in:
PLoS ONE, 2012, v. 7, n. 8, p. 1, doi. 10.1371/journal.pone.0041551
By:
- Crisan, Anamaria;
- Goya, Rodrigo;
- Ha, Gavin;
- Jiarui Ding;
- Prentice, Leah M.;
- Oloumi, Arusha;
- Senz, Janine;
- Zeng, Thomas;
- Tse, Kane;
- Delaney, Allen;
- Marra, Marco A.;
- Huntsman, David G.;
- Hirst, Martin;
- Aparicio, Sam;
- Shah, Sohrab;
- Creighton, Chad
Publication type:
Article
Identifying Sources of Stress Across Years of General Surgery Residency.
Published in:
Hawai'i Journal of Health & Social Welfare, 2020, v. 79, n. 3, p. 75
By:
- Ha, Gavin Q.;
- Go, Joseph T.;
- Murayama, Kenric M.;
- Steinemann, Susan
Publication type:
Article
Genomic and immune profiling of pre-invasive lung adenocarcinoma.
Published in:
Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-13460-3
By:
- Chen, Haiquan;
- Carrot-Zhang, Jian;
- Zhao, Yue;
- Hu, Haichuan;
- Freeman, Samuel S.;
- Yu, Su;
- Ha, Gavin;
- Taylor, Alison M.;
- Berger, Ashton C.;
- Westlake, Lindsay;
- Zheng, Yuanting;
- Zhang, Jiyang;
- Ramachandran, Aruna;
- Zheng, Qiang;
- Pan, Yunjian;
- Zheng, Difan;
- Zheng, Shanbo;
- Cheng, Chao;
- Kuang, Muyu;
- Zhou, Xiaoyan
Publication type:
Article
Circulating Cell-Free DNA as Biomarker of Taxane Resistance in Metastatic Castration-Resistant Prostate Cancer.
Published in:
Cancers, 2021, v. 13, n. 16, p. 4055, doi. 10.3390/cancers13164055
By:
- Francini, Edoardo;
- Ou, Fang-Shu;
- Rhoades, Justin;
- Wolfe, Eric G.;
- O'Connor, Edward P.;
- Ha, Gavin;
- Gydush, Gregory;
- Kelleher, Kaitlin M.;
- Bhatt, Rupal S.;
- Balk, Steven P.;
- Sweeney, Christopher J.;
- Adalsteinsson, Viktor A.;
- Taplin, Mary-Ellen;
- Choudhury, Atish D.
Publication type:
Article
Assessment of TROP2, CEACAM5 and DLL3 in metastatic prostate cancer: Expression landscape and molecular correlates.
Published in:
NPJ Precision Oncology, 2024, v. 8, n. 1, p. 1, doi. 10.1038/s41698-024-00599-6
By:
- Ajkunic, Azra;
- Sayar, Erolcan;
- Roudier, Martine P.;
- Patel, Radhika A.;
- Coleman, Ilsa M.;
- De Sarkar, Navonil;
- Hanratty, Brian;
- Adil, Mohamed;
- Zhao, Jimmy;
- Zaidi, Samir;
- True, Lawrence D.;
- Sperger, Jamie M.;
- Cheng, Heather H.;
- Yu, Evan Y.;
- Montgomery, Robert B.;
- Hawley, Jessica E.;
- Ha, Gavin;
- Persse, Thomas;
- Galipeau, Patricia;
- Lee, John K.
Publication type:
Article
GENE-07. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL-FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE.
Published in:
Neuro-Oncology, 2019, v. 21, p. ii82, doi. 10.1093/neuonc/noz036.078
By:
- Pagès, Mélanie;
- Rotem, Denisse;
- Gydush, Gregory;
- Reed, Sarah;
- Rhoades, Justin;
- Ha, Gavin;
- Lo, Chris;
- Tracy, Adam;
- Jones, Robert;
- Becker, Sarah;
- Haller, Michaela;
- Chi, Susan;
- Kieran, Mark;
- Goumnerova, Liliana;
- Love, Christopher;
- Ligon, Keith;
- Wright, Karen;
- Adalsteinsson, Viktor;
- Beroukhim, Rameen;
- Bandopadhayay, Pratiti
Publication type:
Article
INNV-22. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE.
Published in:
Neuro-Oncology, 2018, v. 20, p. vi142, doi. 10.1093/neuonc/noy148.595
By:
- Pages, Mélanie;
- Rotem, Denisse;
- Gydush, Gregory;
- Reed, Sarah;
- Rhoades, Justin;
- Ha, Gavin;
- Lo, Chris;
- Tracy, Adam;
- Jones, Robert;
- Becker, Sarah
Publication type:
Article
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data.
Published in:
PLoS Computational Biology, 2011, v. 7, n. 5, p. 1, doi. 10.1371/journal.pcbi.1001138
By:
- McPherson, Andrew;
- Hormozdiari, Fereydoun;
- Zayed, Abdalnasser;
- Giuliany, Ryan;
- Ha, Gavin;
- Sun, Mark G. F.;
- Griffith, Malachi;
- Moussavi, Alireza Heravi;
- Janine6Senz;
- Melnyk, Nataliya;
- Pacheco, Marina;
- Marra, Marco A.;
- Hirst, Martin;
- Nielsen, Torsten O.;
- Sahinalp, S. Cenk;
- Huntsman, David;
- Shah, Sohrab P.
Publication type:
Article
The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis.
Published in:
Nature Communications, 2016, v. 7, n. 7, p. 12160, doi. 10.1038/ncomms12160
By:
- Ben-David, Uri;
- Ha, Gavin;
- Khadka, Prasidda;
- Jin, Xin;
- Wong, Bang;
- Franke, Lude;
- Golub, Todd R.
Publication type:
Article
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
Published in:
Nature Communications, 2015, v. 6, n. 10, p. 8554, doi. 10.1038/ncomms9554
By:
- Ding, Jiarui;
- McConechy, Melissa K.;
- Horlings, Hugo M.;
- Ha, Gavin;
- Chun Chan, Fong;
- Funnell, Tyler;
- Mullaly, Sarah C.;
- Reimand, Jüri;
- Bashashati, Ali;
- Bader, Gary D.;
- Huntsman, David;
- Aparicio, Samuel;
- Condon, Anne;
- Shah, Sohrab P.
Publication type:
Article
Genetic interrogation of circulating multiple myeloma cells at single-cell resolution.
Published in:
Science Translational Medicine, 2016, v. 8, n. 363, p. 1, doi. 10.1126/scitranslmed.aac7037
By:
- Lohr, Jens G.;
- Sora Kim;
- Gould, Joshua;
- Knoechel, Birgit;
- Drier, Yotam;
- Cotton, Matthew J.;
- Gray, Daniel;
- Birrer, Nicole;
- Bang Wong;
- Gavin Ha;
- Cheng-Zhong Zhang;
- Guangwu Guo;
- Meyerson, Matthew;
- Yee, Andrew J.;
- Boehm, Jesse S.;
- Raje, Noopur;
- Golub, Todd R.
Publication type:
Article
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
Published in:
Genome Biology, 2012, v. 13, n. 12, p. 1, doi. 10.1186/gb-2012-13-12-r124
By:
- Bashashati, Ali;
- Haffari, Gholamreza;
- Ding, Jiarui;
- Ha, Gavin;
- Lui, Kenneth;
- Rosner, Jamie;
- Huntsman, David G.;
- Caldas, Carlos;
- Aparicio, Samuel A.;
- Shah, Sohrab P.
Publication type:
Article
Correction: Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group.
Published in:
2019
By:
- Shulman, David S.;
- Klega, Kelly;
- Imamovic-Tuco, Alma;
- Clapp, Andrea;
- Nag, Anwesha;
- Thorner, Aaron R.;
- Van Allen, Eliezer;
- Ha, Gavin;
- Lessnick, Stephen L.;
- Gorlick, Richard;
- Janeway, Katherine A.;
- Leavey, Patrick J.;
- Mascarenhas, Leo;
- London, Wendy B.;
- Vo, Kieuhoa T.;
- Stegmaier, Kimberly;
- Hall, David;
- Krailo, Mark D.;
- Barkauskas, Donald A.;
- DuBois, Steven G.
Publication type:
corrected article
Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children’s Oncology Group.
Published in:
British Journal of Cancer, 2018, v. 119, n. 5, p. 615, doi. 10.1038/s41416-018-0212-9
By:
- Shulman, David S.;
- Klega, Kelly;
- Imamovic-Tuco, Alma;
- Clapp, Andrea;
- Nag, Anwesha;
- Thorner, Aaron R.;
- Van Allen, Eliezer;
- Ha, Gavin;
- Lessnick, Stephen L.;
- Gorlick, Richard;
- Janeway, Katherine A.;
- Leavey, Patrick J.;
- Mascarenhas, Leo;
- London, Wendy B.;
- Vo, Kieuhoa T.;
- Stegmaier, Kimberly;
- Hall, David;
- Krailo, Mark D.;
- Barkauskas, Donald A.;
- DuBois, Steven G.
Publication type:
Article
Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group.
Published in:
2018
By:
- Shulman, David S;
- Klega, Kelly;
- Imamovic-Tuco, Alma;
- Clapp, Andrea;
- Nag, Anwesha;
- Thorner, Aaron R;
- Van Allen, Eliezer;
- Ha, Gavin;
- Lessnick, Stephen L;
- Gorlick, Richard;
- Janeway, Katherine A;
- Leavey, Patrick J;
- Mascarenhas, Leo;
- London, Wendy B;
- Vo, Kieuhoa T;
- Stegmaier, Kimberly;
- Hall, David;
- Krailo, Mark D;
- Barkauskas, Donald A;
- DuBois, Steven G
Publication type:
journal article
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.
Published in:
Nature, 2015, v. 518, n. 7539, p. 422, doi. 10.1038/nature13952
By:
- Eirew, Peter;
- Steif, Adi;
- Khattra, Jaswinder;
- Ha, Gavin;
- Yap, Damian;
- Farahani, Hossein;
- Gelmon, Karen;
- Chia, Stephen;
- Mar, Colin;
- Wan, Adrian;
- Laks, Emma;
- Biele, Justina;
- Shumansky, Karey;
- Rosner, Jamie;
- McPherson, Andrew;
- Nielsen, Cydney;
- Roth, Andrew J. L.;
- Lefebvre, Calvin;
- Bashashati, Ali;
- de Souza, Camila
Publication type:
Article
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
Published in:
Nature, 2012, v. 486, n. 7403, p. 346, doi. 10.1038/nature10983
By:
- Curtis, Christina;
- Shah, Sohrab P.;
- Chin, Suet-Feung;
- Turashvili, Gulisa;
- Rueda, Oscar M.;
- Dunning, Mark J.;
- Speed, Doug;
- Lynch, Andy G.;
- Samarajiwa, Shamith;
- Yuan, Yinyin;
- Gräf, Stefan;
- Ha, Gavin;
- Haffari, Gholamreza;
- Bashashati, Ali;
- Russell, Roslin;
- McKinney, Steven;
- Caldas, Carlos;
- Aparicio, Samuel;
- Curtis†, Christina;
- Brenton, James D.
Publication type:
Article
The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
Published in:
Nature, 2012, v. 486, n. 7403, p. 395, doi. 10.1038/nature10933
By:
- Shah, Sohrab P.;
- Roth, Andrew;
- Goya, Rodrigo;
- Oloumi, Arusha;
- Ha, Gavin;
- Zhao, Yongjun;
- Turashvili, Gulisa;
- Ding, Jiarui;
- Tse, Kane;
- Haffari, Gholamreza;
- Bashashati, Ali;
- Prentice, Leah M.;
- Khattra, Jaswinder;
- Burleigh, Angela;
- Yap, Damian;
- Bernard, Virginie;
- McPherson, Andrew;
- Shumansky, Karey;
- Crisan, Anamaria;
- Giuliany, Ryan
Publication type:
Article
Publisher Correction: DNA-based copy number analysis confirms genomic evolution of PDX models.
Published in:
2022
By:
- Hoge, Anna C. H.;
- Getz, Michal;
- Zimmer, Anat;
- Ko, Minjeong;
- Raz, Linoy;
- Beroukhim, Rameen;
- Golub, Todd R.;
- Ha, Gavin;
- Ben-David, Uri
Publication type:
Correction Notice
DNA-based copy number analysis confirms genomic evolution of PDX models.
Published in:
NPJ Precision Oncology, 2022, v. 6, n. 1, p. 1, doi. 10.1038/s41698-022-00268-6
By:
- Hoge, Anna C. H.;
- Getz, Michal;
- Zimmer, Anat;
- Ko, Minjeong;
- Raz, Linoy;
- Beroukhim, Rameen;
- Golub, Todd R.;
- Ha, Gavin;
- David, Uri Ben
Publication type:
Article
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.
Published in:
Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-00965-y
By:
- Adalsteinsson, Viktor A.;
- Ha, Gavin;
- Freeman, Samuel S.;
- Choudhury, Atish D.;
- Stover, Daniel G.;
- Parsons, Heather A.;
- Gydush, Gregory;
- Reed, Sarah C.;
- Rotem, Denisse;
- Rhoades, Justin;
- Loginov, Denis;
- Livitz, Dimitri;
- Rosebrock, Daniel;
- Leshchiner, Ignaty;
- Kim, Jaegil;
- Stewart, Chip;
- Rosenberg, Mara;
- Francis, Joshua M.;
- Cheng-Zhong Zhang;
- Cohen, Ofir
Publication type:
Article
ReMixT: clone-specific genomic structure estimation in cancer.
Published in:
Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1267-2
By:
- McPherson, Andrew W.;
- Roth, Andrew;
- Ha, Gavin;
- Chauve, Cedric;
- Steif, Adi;
- de Souza, Camila P. E.;
- Eirew, Peter;
- Bouchard-Côté, Alexandre;
- Aparicio, Sam;
- Sahinalp, S. Cenk;
- Shah, Sohrab P.
Publication type:
Article
Implementation of a prostate cancer‐specific targeted sequencing panel for credentialing of patient‐derived cell lines and genomic characterization of patient samples.
Published in:
Prostate, 2022, v. 82, n. 5, p. 584, doi. 10.1002/pros.24305
By:
- Stover, Elizabeth H.;
- Oh, Coyin;
- Keskula, Paula;
- Choudhury, Atish D.;
- Tseng, Yuen‐Yi;
- Adalsteinsson, Viktor A.;
- Lohr, Jens G.;
- Thorner, Aaron R.;
- Ducar, Matthew;
- Kryukov, Gregory V.;
- Ha, Gavin;
- Rosenberg, Mara;
- Freeman, Samuel S.;
- Zhang, Zhenwei;
- Wu, Xiaoyun;
- Van Allen, Eliezer M.;
- Takeda, David Y.;
- Loda, Massimo;
- Wu, Chin‐Lee;
- Taplin, Mary‐Ellen
Publication type:
Article
Liquid biopsy detection of genomic alterations in pediatric brain tumors from cell-free DNA in peripheral blood, CSF, and urine.
Published in:
Neuro-Oncology, 2022, v. 24, n. 8, p. 1352, doi. 10.1093/neuonc/noab299
By:
- Pagès, Mélanie;
- Rotem, Denisse;
- Gydush, Gregory;
- Reed, Sarah;
- Rhoades, Justin;
- Ha, Gavin;
- Lo, Christopher;
- Fleharty, Mark;
- Duran, Madeleine;
- Jones, Robert;
- Becker, Sarah;
- Haller, Michaela;
- Sinai, Claire E;
- Goumnerova, Liliana;
- Golub, Todd R;
- Love, J Christopher;
- Ligon, Keith L;
- Wright, Karen D;
- Adalsteinsson, Viktor A;
- Beroukhim, Rameen
Publication type:
Article
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
Published in:
Bioinformatics, 2012, v. 28, n. 7, p. 907, doi. 10.1093/bioinformatics/bts053
By:
- Roth, Andrew;
- Ding, Jiarui;
- Morin, Ryan;
- Crisan, Anamaria;
- Ha, Gavin;
- Giuliany, Ryan;
- Bashashati, Ali;
- Hirst, Martin;
- Turashvili, Gulisa;
- Oloumi, Arusha;
- Marra, Marco A.;
- Aparicio, Samuel;
- Shah, Sohrab P.
Publication type:
Article
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
Published in:
Bioinformatics, 2010, v. 26, n. 6, p. 730, doi. 10.1093/bioinformatics/btq040
By:
- Goya, Rodrigo;
- Sun, Mark G. F.;
- Morin, Ryan D.;
- Leung, Gillian;
- Ha, Gavin;
- Wiegand, Kimberley C.;
- Senz, Janine;
- Crisan, Anamaria;
- Marra, Marco A.;
- Hirst, Martin;
- Huntsman, David;
- Murphy, Kevin P.;
- Aparicio, Sam;
- Shah, Sohrab P.
Publication type:
Article

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