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: PTEN: F238L

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 2

View BVdb publication page

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Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types.

Genome Medicine

Bao, Riyue R; Stapor, Daniel D; Luke, Jason J JJ

Publication Date: 2020-10-27

Variant appearance in text: PTEN: F238L

PubMed Link: 33106165

Variant Present in the following documents:

• 13073_2020_787_MOESM1_ESM.xlsx, sheet 9

View BVdb publication page

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High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants.

Nature Medicine

Razavi, Pedram P; Li, Bob T BT; Brown, David N DN; Jung, Byoungsok B; Hubbell, Earl E; Shen, Ronglai R; Abida, Wassim W; Juluru, Krishna K; De Bruijn, Ino I; Hou, Chenlu C; Venn, Oliver O; Lim, Raymond R; Anand, Aseem A; Maddala, Tara T; Gnerre, Sante S; Vijaya Satya, Ravi R; Liu, Qinwen Q; Shen, Ling L; Eattock, Nicholas N; Yue, Jeanne J; Blocker, Alexander W AW; Lee, Mark M; Sehnert, Amy A; Xu, Hui H; Hall, Megan P MP; Santiago-Zayas, Angie A; Novotny, William F WF; Isbell, James M JM; Rusch, Valerie W VW; Plitas, George G; Heerdt, Alexandra S AS; Ladanyi, Marc M; Hyman, David M DM; Jones, David R DR; Morrow, Monica M; Riely, Gregory J GJ; Scher, Howard I HI; Rudin, Charles M CM; Robson, Mark E ME; Diaz, Luis A LA; Solit, David B DB; Aravanis, Alexander M AM; Reis-Filho, Jorge S JS

Publication Date: 2019-12

Variant appearance in text: PTEN: Phe238Leu

PubMed Link: 31768066

Variant Present in the following documents:

• NIHMS1541314-supplement-1541314_Sup_Tab.xlsx, sheet 4

View BVdb publication page

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Resectable lung lesions malignancy assessment and cancer detection by ultra-deep sequencing of targeted gene mutations in plasma cell-free DNA.

Journal Of Medical Genetics

Peng, Muyun M; Xie, Yuancai Y; Li, Xiaohua X; Qian, Youhui Y; Tu, Xiaonian X; Yao, Xumei X; Cheng, Fangsheng F; Xu, Feiyue F; Kong, Deju D; He, Bing B; Liu, Chaoyu C; Cao, Fengjun F; Yang, Haoxian H; Yu, Fenglei F; Xu, Chuanbo C; Tian, Geng G

Publication Date: 2019-10

Variant appearance in text: PTEN: 714C>A

PubMed Link: 30981987

Variant Present in the following documents:

• jmedgenet-2018-105825supp002.xlsx, sheet 4

View BVdb publication page

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Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.

Plos One

Prentice, Leah M LM; Miller, Ruth R RR; Knaggs, Jeff J; Mazloomian, Alborz A; Aguirre Hernandez, Rosalia R; Franchini, Patrick P; Parsa, Kourosh K; Tessier-Cloutier, Basile B; Lapuk, Anna A; Huntsman, David D; Schaeffer, David F DF; Sheffield, Brandon S BS

Publication Date: 2018

Variant appearance in text: PTEN: F238L

PubMed Link: 29698444

Variant Present in the following documents:

• pone.0196434.s001.xlsx, sheet 1
• pone.0196434.s001.xlsx, sheet 3
• pone.0196434.s001.xlsx, sheet 2

View BVdb publication page

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Amplicon sequencing of colorectal cancer: variant calling in frozen and formalin-fixed samples.

Plos One

Betge, Johannes J; Kerr, Grainne G; Miersch, Thilo T; Leible, Svenja S; Erdmann, Gerrit G; Galata, Christian L CL; Zhan, Tianzuo T; Gaiser, Timo T; Post, Stefan S; Ebert, Matthias P MP; Horisberger, Karoline K; Boutros, Michael M

Publication Date: 2015

Variant appearance in text: PTEN: F238L

PubMed Link: 26010451

Variant Present in the following documents:

• pone.0127146.s013.xlsx, sheet 3
• pone.0127146.s014.xlsx, sheet 3

View BVdb publication page

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Predicting the functional impact of protein mutations: application to cancer genomics.

Nucleic Acids Research

Reva, Boris B; Antipin, Yevgeniy Y; Sander, Chris C

Publication Date: 2011-09-01

Variant appearance in text: PTEN: F238L

PubMed Link: 21727090

Variant Present in the following documents:

• supp_gkr407_Supplement2_Table_SM1_COSMIC_mutations.xls, sheet 1

View BVdb publication page

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