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: ALK: F921L

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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A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy.

Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research

Jang, H Josh HJ; Hostetter, Galen G; MacFarlane, Alexander W AW; Madaj, Zachary Z; Ross, Eric A EA; Hinoue, Toshinori T; Kulchycki, Justin R JR; Burgos, Ryan S RS; Tafseer, Mahvish M; Alpaugh, R Katherine RK; Schwebel, Candice L CL; Kokate, Rutika R; Geynisman, Daniel M DM; Zibelman, Matthew R MR; Ghatalia, Pooja P; Nichols, Peter W PW; Chung, Woonbok W; Madzo, Jozef J; Hahn, Noah M NM; Quinn, David I DI; Issa, Jean-Pierre J JJ; Topper, Michael J MJ; Baylin, Stephen B SB; Shen, Hui H; Campbell, Kerry S KS; Jones, Peter A PA; Plimack, Elizabeth R ER

Publication Date: 2023-03-16

Variant appearance in text: ALK: F921L

PubMed Link: 36928921

Variant Present in the following documents:

• ccr-22-3642_supplementary_tables_1_suppts1.xlsx, sheet 3

View BVdb publication page

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Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria.

American Journal Of Human Genetics

Pejaver, Vikas V; Byrne, Alicia B AB; Feng, Bing-Jian BJ; Pagel, Kymberleigh A KA; Mooney, Sean D SD; Karchin, Rachel R; O'Donnell-Luria, Anne A; Harrison, Steven M SM; Tavtigian, Sean V SV; Greenblatt, Marc S MS; Biesecker, Leslie G LG; Radivojac, Predrag P; Brenner, Steven E SE; ,

Publication Date: 2022-12-01

Variant appearance in text: ALK: F921L; rs201042802

PubMed Link: 36413997

Variant Present in the following documents:

• mmc3.xlsx, sheet 1

View BVdb publication page

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Investigating the Retained Inhibitory Effect of Cobimetinib against p.P124L Mutated MEK1: A Combined Liquid Biopsy and in Silico Approach.

Cancers

Catoni, Cristina C; Poggiana, Cristina C; Facchinetti, Antonella A; Pigozzo, Jacopo J; Piccin, Luisa L; Chiarion-Sileni, Vanna V; Rosato, Antonio A; Minervini, Giovanni G; Scaini, Maria Chiara MC

Publication Date: 2022-08-27

Variant appearance in text: ALK: 2763C>G; F921L

PubMed Link: 36077693

Variant Present in the following documents:

• cancers-14-04153.pdf

View BVdb publication page

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Single-cell sequencing reveals CD133+CD44--originating evolution and novel stemness related variants in human colorectal cancer.

Ebiomedicine

Zhang, Xiaoyan X; Yang, Ling L; Lei, Wanjun W; Hou, Qiang Q; Huang, Ming M; Zhou, Rongjing R; Enver, Tariq T; Wu, Shixiu S

Publication Date: 2022-08

Variant appearance in text: ALK: F921L

PubMed Link: 35785618

Variant Present in the following documents:

• mmc1.xlsx, sheet 2

View BVdb publication page

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Case Report: Molecular Characterization of Aggressive Malignant Retroperitoneal Solitary Fibrous Tumor: A Case Study.

Frontiers In Oncology

Nonaka, Haruna H; Kandori, Shuya S; Nitta, Satoshi S; Shiga, Masanobu M; Nagumo, Yoshiyuki Y; Kimura, Tomokazu T; Kawahara, Takashi T; Negoro, Hiromitsu H; Hoshi, Akio A; Kojima, Takahiro T; Kawai, Koji K; Mathis, Bryan J BJ; Tamura, Takuro T; Sato, Taka-Aki TA; Yamato, Mariko M; Noguchi, Masayuki M; Nishiyama, Hiroyuki H

Publication Date: 2021

Variant appearance in text: ALK: Phe921Leu

PubMed Link: 35004271

Variant Present in the following documents:

• Table_3.xlsx, sheet 1
• Table_4.xlsx, sheet 1

View BVdb publication page

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Case Report: A Variant Non-ketotic Hyperglycinemia With GLRX5 Mutations: Manifestation of Deficiency of Activities of the Respiratory Chain Enzymes.

Frontiers In Genetics

Feng, Wei-Xing WX; Zhuo, Xiu-Wei XW; Liu, Zhi-Mei ZM; Li, Jiu-Wei JW; Zhang, Wei-Hua WH; Wu, Yun Y; Han, Tong-Li TL; Fang, Fang F

Publication Date: 2021

Variant appearance in text: ALK: 2763C>G; F921L; rs201042802

PubMed Link: 34054912

Variant Present in the following documents:

• Table_2.xlsx, sheet 1

View BVdb publication page

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Phase II study of apatinib in combination with oral vinorelbine in heavily pretreated HER2-negative metastatic breast cancer and clinical implications of monitoring ctDNA.

Cancer Biology & Medicine

Zhu, Anjie A; Yuan, Peng P; Hu, Nanlin N; Li, Mingzhou M; Wang, Wenmiao W; Wang, Xue X; Yue, Jian J; Wang, Jiayu J; Luo, Yang Y; Ma, Fei F; Zhang, Pin P; Li, Qing Q; Xu, Binghe B; Cao, Shanbo S; Lippi, Giuseppe G; Naito, Yoichi Y; Osman, Mohammed A MA; Marta, Gustavo N GN; Franceschini, Gianluca G; Orlandi, Armando A

Publication Date: 2021-05-26

Variant appearance in text: ALK: F921L

PubMed Link: 34037346

Variant Present in the following documents:

• cbm-18-875-s001.pdf

View BVdb publication page

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Mutational landscape and genetic signatures of cell-free DNA in tumour-induced osteomalacia.

Journal Of Cellular And Molecular Medicine

Wu, Nan N; Zhang, Zhen Z; Zhou, Xi X; Zhao, Hengqiang H; Ming, Yue Y; Wu, Xue X; Zhang, Xian X; Yang, Xin-Zhuang XZ; Zhou, Meng M; Bao, Hua H; Chen, Weisheng W; Wu, Yong Y; Liu, Sen S; Wang, Huizi H; Niu, Yuchen Y; Li, Yalun Y; Zheng, Yu Y; Shao, Yang Y; Gao, Na N; Yang, Ying Y; Liu, Ying Y; Li, Wenli W; Liu, Jia J; Zhang, Na N; Yang, Xu X; Xu, Yuan Y; Li, Mei M; Sun, Yingli Y; Su, Jianzhong J; Zhang, Jianguo J; Xia, Weibo W; Qiu, Guixing G; Liu, Yong Y; Liu, Jiaqi J; Wu, Zhihong Z

Publication Date: 2020-05

Variant appearance in text: ALK: 2763C>G; Phe921Leu

PubMed Link: 32277576

Variant Present in the following documents:

• JCMM-24-4931-s011.xlsx, sheet 1
• JCMM-24-4931-s010.xlsx, sheet 1

View BVdb publication page

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Clonal replacement of tumor-specific T cells following PD-1 blockade.

Nature Medicine

Yost, Kathryn E KE; Satpathy, Ansuman T AT; Wells, Daniel K DK; Qi, Yanyan Y; Wang, Chunlin C; Kageyama, Robin R; McNamara, Katherine L KL; Granja, Jeffrey M JM; Sarin, Kavita Y KY; Brown, Ryanne A RA; Gupta, Rohit K RK; Curtis, Christina C; Bucktrout, Samantha L SL; Davis, Mark M MM; Chang, Anne Lynn S ALS; Chang, Howard Y HY

Publication Date: 2019-08

Variant appearance in text: ALK: 2763C>G; F921L

PubMed Link: 31359002

Variant Present in the following documents:

• NIHMS1531727-supplement-2.xlsx, sheet 2

View BVdb publication page

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TRPV4 and KRAS and FGFR1 gain-of-function mutations drive giant cell lesions of the jaw.

Nature Communications

Gomes, Carolina Cavalieri CC; Gayden, Tenzin T; Bajic, Andrea A; Harraz, Osama F OF; Pratt, Jonathan J; Nikbakht, Hamid H; Bareke, Eric E; Diniz, Marina Gonçalves MG; Castro, Wagner Henriques WH; St-Onge, Pascal P; Sinnett, Daniel D; Han, HyeRim H; Rivera, Barbara B; Mikael, Leonie G LG; De Jay, Nicolas N; Kleinman, Claudia L CL; Valera, Elvis Terci ET; Bassenden, Angelia V AV; Berghuis, Albert M AM; Majewski, Jacek J; Nelson, Mark T MT; Gomez, Ricardo Santiago RS; Jabado, Nada N

Publication Date: 2018-11-01

Variant appearance in text: ALK: F921L

PubMed Link: 30385747

Variant Present in the following documents:

• 41467_2018_6690_MOESM8_ESM.xlsx, sheet 1

View BVdb publication page

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Molecular characterization and integrative genomic analysis of a panel of newly established penile cancer cell lines.

Cell Death & Disease

Zhou, Qiang-Hua QH; Deng, Chuang-Zhong CZ; Li, Zai-Shang ZS; Chen, Jie-Ping JP; Yao, Kai K; Huang, Kang-Bo KB; Liu, Ting-Yu TY; Liu, Zhuo-Wei ZW; Qin, Zi-Ke ZK; Zhou, Fang-Jian FJ; Huang, Wenlin W; Han, Hui H; Liu, Ran-Yi RY

Publication Date: 2018-06-07

Variant appearance in text: ALK: 2763C>G; F921L

PubMed Link: 29880898

Variant Present in the following documents:

• 41419_2018_736_MOESM6_ESM.xlsx, sheet 1

View BVdb publication page

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The use of whole exome sequencing and murine patient derived xenografts as a method of chemosensitivity testing in sarcoma.

Clinical Sarcoma Research

Calvert, Nicholas N; Wu, Jiansha J; Sneddon, Sophie S; Woodhouse, Jennifer J; Carey-Smith, Richard R; Wood, David D; Ingley, Evan E

Publication Date: 2018

Variant appearance in text: ALK: F921L

PubMed Link: 29541442

Variant Present in the following documents:

• Main text
• 13569_2018_Article_90.pdf

View BVdb publication page

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Next-Generation Sequencing-based genomic profiling of brain metastases of primary ovarian cancer identifies high number of BRCA-mutations.

Journal Of Neuro-Oncology

Balendran, S S; Liebmann-Reindl, S S; Berghoff, A S AS; Reischer, T T; Popitsch, N N; Geier, C B CB; Kenner, L L; Birner, P P; Streubel, B B; Preusser, M M

Publication Date: 2017-07

Variant appearance in text: ALK: 2763C>G; Phe921Leu

PubMed Link: 28497333

Variant Present in the following documents:

• Main text
• 11060_2017_Article_2459.pdf

View BVdb publication page

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VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.

Nucleic Acids Research

Lai, Zhongwu Z; Markovets, Aleksandra A; Ahdesmaki, Miika M; Chapman, Brad B; Hofmann, Oliver O; McEwen, Robert R; Johnson, Justin J; Dougherty, Brian B; Barrett, J Carl JC; Dry, Jonathan R JR

Publication Date: 2016-06-20

Variant appearance in text: ALK: 2763C>G; F921L

PubMed Link: 27060149

Variant Present in the following documents:

• supp_gkw227_nar-03544-met-k-2015-File003.xls, sheet 2

View BVdb publication page

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Whole-genome sequencing in multiplex families with psychoses reveals mutations in the SHANK2 and SMARCA1 genes segregating with illness.

Molecular Psychiatry

Homann, O R OR; Misura, K K; Lamas, E E; Sandrock, R W RW; Nelson, P P; McDonough, S I SI; DeLisi, L E LE

Publication Date: 2016-12

Variant appearance in text: ALK: F921L

PubMed Link: 27001614

Variant Present in the following documents:

• NIHMS753666-supplement-2.xlsx, sheet 7
• NIHMS753666-supplement-2.xlsx, sheet 4
• NIHMS753666-supplement-2.xlsx, sheet 3
• NIHMS753666-supplement-2.xlsx, sheet 9
• NIHMS753666-supplement-2.xlsx, sheet 8

View BVdb publication page

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