Publications:

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Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues.

Nature Communications

Abelin, Jennifer G JG; Bergstrom, Erik J EJ; Rivera, Keith D KD; Taylor, Hannah B HB; Klaeger, Susan S; Xu, Charles C; Verzani, Eva K EK; Jackson White, C C; Woldemichael, Hilina B HB; Virshup, Maya M; Olive, Meagan E ME; Maynard, Myranda M; Vartany, Stephanie A SA; Allen, Joseph D JD; Phulphagar, Kshiti K; Harry Kane, M M; Rachimi, Suzanna S; Mani, D R DR; Gillette, Michael A MA; Satpathy, Shankha S; Clauser, Karl R KR; Udeshi, Namrata D ND; Carr, Steven A SA

Publication Date: 2023-04-03

Variant appearance in text: POLE: A11N

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 2

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Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer.

Cell Systems

Ciani, Yari Y; Fedrizzi, Tarcisio T; Prandi, Davide D; Lorenzin, Francesca F; Locallo, Alessio A; Gasperini, Paola P; Franceschini, Gian Marco GM; Benelli, Matteo M; Elemento, Olivier O; Fava, Luca L LL; Inga, Alberto A; Demichelis, Francesca F

Publication Date: 2022-02-16

Variant appearance in text: POLE: A11N

PubMed Link: 34731645

Variant Present in the following documents:

• mmc2.xlsx, sheet 1

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POLE/POLD1 mutation in non-exonuclease domain matters for predicting efficacy of immune-checkpoint-inhibitor therapy.

Clinical And Translational Medicine

Chen, Yan-Xing YX; Wang, Zi-Xian ZX; Yuan, Shu-Qiang SQ; Jiang, Teng-Jia TJ; Huang, You-Sheng YS; Xu, Rui-Hua RH; Wang, Feng F; Zhao, Qi Q

Publication Date: 2021-09

Variant appearance in text: POLE: A11N

PubMed Link: 34586735

Variant Present in the following documents:

• CTM2-11-e524-s001.xlsx, sheet 2

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Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations.

Computational And Structural Biotechnology Journal

Fedrizzi, Tarcisio T; Ciani, Yari Y; Lorenzin, Francesca F; Cantore, Thomas T; Gasperini, Paola P; Demichelis, Francesca F

Publication Date: 2021

Variant appearance in text: POLE: A11N

PubMed Link: 34429855

Variant Present in the following documents:

• mmc2.xlsx, sheet 2

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A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases.

Scientific Reports

Magraner-Pardo, Lorena L; Laskowski, Roman A RA; Pons, Tirso T; Thornton, Janet M JM

Publication Date: 2021-07-12

Variant appearance in text: POLE: A11N

PubMed Link: 34253785

Variant Present in the following documents:

• 41598_2021_93715_MOESM2_ESM.xlsx, sheet 10

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Elevated expression of LPCAT1 predicts a poor prognosis and is correlated with the tumour microenvironment in endometrial cancer.

Cancer Cell International

Zhao, Tianyi T; Zhang, Yifang Y; Ma, Xiaohong X; Wei, Lina L; Hou, Yixin Y; Sun, Rui R; Jiang, Jie J

Publication Date: 2021-05-20

Variant appearance in text: POLE: A11N

PubMed Link: 34016103

Variant Present in the following documents:

• 12935_2021_1965_MOESM4_ESM.xlsx, sheet 1

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Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability.

Plos Genetics

Raynaud, Franck F; Mina, Marco M; Tavernari, Daniele D; Ciriello, Giovanni G

Publication Date: 2018-09

Variant appearance in text: POLE: A11N

PubMed Link: 30212491

Variant Present in the following documents:

• pgen.1007669.s008.xlsx, sheet 1

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Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair.

Nature Communications

Haradhvala, N J NJ; Kim, J J; Maruvka, Y E YE; Polak, P P; Rosebrock, D D; Livitz, D D; Hess, J M JM; Leshchiner, I I; Kamburov, A A; Mouw, K W KW; Lawrence, M S MS; Getz, G G

Publication Date: 2018-05-01

Variant appearance in text: POLE: A11N

PubMed Link: 29717118

Variant Present in the following documents:

• 41467_2018_4002_MOESM1_ESM.pdf

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Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Cell Reports

Way, Gregory P GP; Sanchez-Vega, Francisco F; La, Konnor K; Armenia, Joshua J; Chatila, Walid K WK; Luna, Augustin A; Sander, Chris C; Cherniack, Andrew D AD; Mina, Marco M; Ciriello, Giovanni G; Schultz, Nikolaus N; , ; Sanchez, Yolanda Y; Greene, Casey S CS

Publication Date: 2018-04-03

Variant appearance in text: POLE: A11N

PubMed Link: 29617658

Variant Present in the following documents:

• NIHMS958974-supplement-3.xlsx, sheet 1

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Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response.

The Journal Of Pathology

Temko, Daniel D; Van Gool, Inge C IC; Rayner, Emily E; Glaire, Mark M; Makino, Seiko S; Brown, Matthew M; Chegwidden, Laura L; Palles, Claire C; Depreeuw, Jeroen J; Beggs, Andrew A; Stathopoulou, Chaido C; Mason, John J; Baker, Ann-Marie AM; Williams, Marc M; Cerundolo, Vincenzo V; Rei, Margarida M; Taylor, Jenny C JC; Schuh, Anna A; Ahmed, Ahmed A; Amant, Frédéric F; Lambrechts, Diether D; Smit, Vincent Thbm VT; Bosse, Tjalling T; Graham, Trevor A TA; Church, David N DN; Tomlinson, Ian I

Publication Date: 2018-07

Variant appearance in text: POLE: A11N

PubMed Link: 29604063

Variant Present in the following documents:

• PATH-245-283-s006.pdf
• PATH-245-283-s004.pdf

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Ornithine decarboxylase as a therapeutic target for endometrial cancer.

Plos One

Kim, Hong Im HI; Schultz, Chad R CR; Buras, Andrea L AL; Friedman, Elizabeth E; Fedorko, Alyssa A; Seamon, Leigh L; Chandramouli, Gadisetti V R GVR; Maxwell, G Larry GL; Bachmann, André S AS; Risinger, John I JI

Publication Date: 2017

Variant appearance in text: POLE: A11N

PubMed Link: 29240775

Variant Present in the following documents:

• pone.0189044.s004.xlsx, sheet 3

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Mutation Clusters from Cancer Exome.

Genes

Kakushadze, Zura Z; Yu, Willie W

Publication Date: 2017-08-15

Variant appearance in text: POLE: A11N

PubMed Link: 28809811

Variant Present in the following documents:

• Main text

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The somatic POLE P286R mutation defines a unique subclass of colorectal cancer featuring hypermutation, representing a potential genomic biomarker for immunotherapy.

Oncotarget

Ahn, Sung-Min SM; Ansari, Adnan Ahmad AA; Kim, Jihun J; Kim, Deokhoon D; Chun, Sung-Min SM; Kim, Jiyun J; Kim, Tae Won TW; Park, Inja I; Yu, Chang-Sik CS; Jang, Se Jin SJ

Publication Date: 2016-10-18

Variant appearance in text: POLE: A11N

PubMed Link: 27612425

Variant Present in the following documents:

• oncotarget-07-68638-s005.xlsx, sheet 1

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Long non-coding RNA profiling links subgroup classification of endometrioid endometrial carcinomas with trithorax and polycomb complex aberrations.

Oncotarget

Jiang, Yunyun Y; Malouf, Gabriel G GG; Zhang, Jianping J; Zheng, Xiaofeng X; Chen, Yunxin Y; Thompson, Erika J EJ; Weinstein, John N JN; Yuan, Ying Y; Spano, Jean-Philippe JP; Broaddus, Russell R; Tannir, Nizar M NM; Khayat, David D; Lu, Karen H KH; Su, Xiaoping X

Publication Date: 2015-11-24

Variant appearance in text: POLE: A11N

PubMed Link: 26431491

Variant Present in the following documents:

• oncotarget-06-39865-s002.xlsx, sheet 11

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Age-related mutations associated with clonal hematopoietic expansion and malignancies.

Nature Medicine

Xie, Mingchao M; Lu, Charles C; Wang, Jiayin J; McLellan, Michael D MD; Johnson, Kimberly J KJ; Wendl, Michael C MC; McMichael, Joshua F JF; Schmidt, Heather K HK; Yellapantula, Venkata V; Miller, Christopher A CA; Ozenberger, Bradley A BA; Welch, John S JS; Link, Daniel C DC; Walter, Matthew J MJ; Mardis, Elaine R ER; Dipersio, John F JF; Chen, Feng F; Wilson, Richard K RK; Ley, Timothy J TJ; Ding, Li L

Publication Date: 2014-12

Variant appearance in text: POLE: A11N

PubMed Link: 25326804

Variant Present in the following documents:

• NIHMS630249-supplement-5.xlsx, sheet 1

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A TrkB-STAT3-miR-204-5p regulatory circuitry controls proliferation and invasion of endometrial carcinoma cells.

Molecular Cancer

Bao, Wei W; Wang, Hui-Hui HH; Tian, Fu-Ju FJ; He, Xiao-Ying XY; Qiu, Mei-Ting MT; Wang, Jing-Yun JY; Zhang, Hui-Juan HJ; Wang, Li-Hua LH; Wan, Xiao-Ping XP

Publication Date: 2013-12-09

Variant appearance in text: POLE: A11N

PubMed Link: 24321270

Variant Present in the following documents:

• 1476-4598-12-155-S5.xls, sheet 4
• 1476-4598-12-155-S5.xls, sheet 5

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DNA polymerase ε and δ exonuclease domain mutations in endometrial cancer.

Human Molecular Genetics

Church, David N DN; Briggs, Sarah E W SE; Palles, Claire C; Domingo, Enric E; Kearsey, Stephen J SJ; Grimes, Jonathon M JM; Gorman, Maggie M; Martin, Lynn L; Howarth, Kimberley M KM; Hodgson, Shirley V SV; , ; Kaur, Kulvinder K; Taylor, Jenny J; Tomlinson, Ian P M IP

Publication Date: 2013-07-15

Variant appearance in text: POLE: A11N

PubMed Link: 23528559

Variant Present in the following documents:

• supp_ddt131_ddt131supp.pdf

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