Publications:

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Integration of deep learning with Ramachandran plot molecular dynamics simulation for genetic variant classification.

Iscience

Tam, Benjamin B; Qin, Zixin Z; Zhao, Bojin B; Wang, San Ming SM; Lei, Chon Lok CL

Publication Date: 2023-03-17

Variant appearance in text: TP53: 493C>A; Q165K

PubMed Link: 36879825

Variant Present in the following documents:

• mmc4.xlsx, sheet 1
• mmc3.xlsx, sheet 1
• mmc2.xlsx, sheet 1

View BVdb publication page

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A new intronic quantitative PCR method led to the discovery of transformation from human ascites to murine malignancy in a mouse model.

Frontiers In Oncology

Jin, Jiankang J; Huo, Longfei L; Fan, Yibo Y; Wang, Ruiping R; Scott, Ailing W AW; Pizzi, Melissa Pool MP; Yao, Xiaodan X; Shao, Shan S; Ma, Lang L; Da Silva, Matheus S MS; Yamashita, Kohei K; Yoshimura, Katsuhiro K; Zhang, Boyu B; Wu, Jingjing J; Wang, Linghua L; Song, Shumei S; Ajani, Jaffer A JA

Publication Date: 2023

Variant appearance in text: TP53: Q165K

PubMed Link: 36865791

Variant Present in the following documents:

• Main text
• fonc-13-1062424.pdf

View BVdb publication page

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Evolutionary route of nasopharyngeal carcinoma metastasis and its clinical significance.

Nature Communications

Lin, Mei M; Zhang, Xiao-Long XL; You, Rui R; Liu, You-Ping YP; Cai, Hong-Min HM; Liu, Li-Zhi LZ; Liu, Xue-Fei XF; Zou, Xiong X; Xie, Yu-Long YL; Zou, Ru-Hai RH; Zhang, Yi-Nuan YN; Sun, Rui R; Feng, Wei-Yi WY; Wang, Hai-Yan HY; Tao, Gui-Hua GH; Li, Hao-Jiang HJ; Huang, Wen-Jie WJ; Zhang, Chao C; Huang, Pei-Yu PY; Wang, Jin J; Zhao, Qi Q; Yang, Qi Q; Zhang, Hong-Wan HW; Liu, Ting T; Li, Hui-Feng HF; Jiang, Xiao-Bing XB; Tang, Jun J; Gu, Yang-Kui YK; Yu, Tao T; Wang, Zhi-Qiang ZQ; Feng, Lin L; Kang, Tie-Bang TB; Zuo, Zhi-Xiang ZX; Chen, Ming-Yuan MY

Publication Date: 2023-02-04

Variant appearance in text: TP53: 493C>A

PubMed Link: 36739462

Variant Present in the following documents:

• 41467_2023_35995_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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ESR1 gene amplification and MAP3K mutations are selected during adjuvant endocrine therapies in relapsing Hormone Receptor-positive, HER2-negative breast cancer (HR+ HER2- BC).

Plos Genetics

Ferrando, Lorenzo L; Vingiani, Andrea A; Garuti, Anna A; Vernieri, Claudio C; Belfiore, Antonino A; Agnelli, Luca L; Dagrada, Gianpaolo G; Ivanoiu, Diana D; Bonizzi, Giuseppina G; Munzone, Elisabetta E; Lippolis, Luana L; Dameri, Martina M; Ravera, Francesco F; Colleoni, Marco M; Viale, Giuseppe G; Magnani, Luca L; Ballestrero, Alberto A; Zoppoli, Gabriele G; Pruneri, Giancarlo G

Publication Date: 2023-01-03

Variant appearance in text: rs730882001

PubMed Link: 36595552

Variant Present in the following documents:

• pgen.1010563.s004.xlsx, sheet 1

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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: TP53: Q165K

PubMed Link: 36413997

Variant Present in the following documents:

• mmc2.xlsx, sheet 1

View BVdb publication page

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Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery.

Nature Communications

Havugimana, Pierre C PC; Goel, Raghuveera Kumar RK; Phanse, Sadhna S; Youssef, Ahmed A; Padhorny, Dzmitry D; Kotelnikov, Sergei S; Kozakov, Dima D; Emili, Andrew A

Publication Date: 2022-07-13

Variant appearance in text: TP53: 493C>A; His165Asn

PubMed Link: 35831314

Variant Present in the following documents:

• 41467_2022_31809_MOESM8_ESM.xlsx, sheet 3

View BVdb publication page

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Comprehensive Identification of Deleterious TP53 Missense VUS Variants Based on Their Impact on TP53 Structural Stability.

International Journal Of Molecular Sciences

Tam, Benjamin B; Sinha, Siddharth S; Qin, Zixin Z; Wang, San Ming SM

Publication Date: 2021-10-20

Variant appearance in text: TP53: Q165K

PubMed Link: 34768775

Variant Present in the following documents:

• Main text
• ijms-22-11345.pdf

View BVdb publication page

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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: TP53: 493C>A; Gln165Lys

PubMed Link: 34253785

Variant Present in the following documents:

• 41598_2021_93715_MOESM2_ESM.xlsx, sheet 6

View BVdb publication page

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Next-generation sequencing revealed synchronous double primary lung squamous carcinoma: a case report.

The Journal Of International Medical Research

Yang, De-Song DS; Huang, Kai K; Su, Min M; Wang, Ting-Ting TT; Liu, Si-Si SS; Xu, Yang Y; Wang, Wen-Xiang WX

Publication Date: 2021-05

Variant appearance in text: TP53: 493C>A

PubMed Link: 34038210

Variant Present in the following documents:

• 10.1177_03000605211018575.pdf

View BVdb publication page

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Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model.

Computational And Structural Biotechnology Journal

Tam, Benjamin B; Sinha, Siddharth S; Wang, San Ming SM

Publication Date: 2020

Variant appearance in text: TP53: 493C>A; Q165K

PubMed Link: 33363700

Variant Present in the following documents:

• mmc1.xlsx, sheet 1

View BVdb publication page

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Cancer-Related Mutations Are Not Enriched in Naive Human Pluripotent Stem Cells.

Cell Stem Cell

Stirparo, Giuliano Giuseppe GG; Smith, Austin A; Guo, Ge G

Publication Date: 2021-01-07

Variant appearance in text: TP53: Q165K

PubMed Link: 33321074

Variant Present in the following documents:

• mmc4.pdf

View BVdb publication page

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Fitness Landscape of Clonal Hematopoiesis Under Selective Pressure of Immune Checkpoint Blockade.

Jco Precision Oncology

Miller, Peter G PG; Gibson, Christopher J CJ; Mehta, Arnav A; Sperling, Adam S AS; Frederick, Dennie T DT; Manos, Michael P MP; Miao, Benchun B; Hacohen, Nir N; Hodi, F Stephen FS; Boland, Genevieve M GM; Ebert, Benjamin L BL

Publication Date: 2020

Variant appearance in text: TP53: Q165K

PubMed Link: 33015529

Variant Present in the following documents:

• Main text

View BVdb publication page

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Mutation profiling of cancer drivers in Brazilian colorectal cancer.

Scientific Reports

Dos Santos, Wellington W; Sobanski, Thais T; de Carvalho, Ana Carolina AC; Evangelista, Adriane Feijó AF; Matsushita, Marcus M; Berardinelli, Gustavo Nóriz GN; de Oliveira, Marco Antonio MA; Reis, Rui Manuel RM; Guimarães, Denise Peixoto DP

Publication Date: 2019-09-23

Variant appearance in text: rs730882001

PubMed Link: 31548566

Variant Present in the following documents:

• 41598_2019_49611_MOESM1_ESM.pdf

View BVdb publication page

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From uncertainty to pathogenicity: clinical and functional interrogation of a rare TP53 in-frame deletion.

Cold Spring Harbor Molecular Case Studies

Quinn, Emily A EA; Maciaszek, Jamie L JL; Pinto, Emilia M EM; Phillips, Aaron H AH; Berdy, David D; Khandwala, Mohammad M; Upadhyaya, Santhosh A SA; Zambetti, Gerard P GP; Kriwacki, Richard W RW; Ellison, David W DW; Nichols, Kim E KE; Kesserwan, Chimene C

Publication Date: 2019-08

Variant appearance in text: TP53: 493C>A; Gln165Lys

PubMed Link: 30886117

Variant Present in the following documents:

• supp_mcs.a003921_Supplemental_Table_1a.xlsx, sheet 1

View BVdb publication page

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appreci8: a pipeline for precise variant calling integrating 8 tools.

Bioinformatics (Oxford, England)

Sandmann, Sarah S; Karimi, Mohsen M; de Graaf, Aniek O AO; Rohde, Christian C; Göllner, Stefanie S; Varghese, Julian J; Ernsting, Jan J; Walldin, Gunilla G; van der Reijden, Bert A BA; Müller-Tidow, Carsten C; Malcovati, Luca L; Hellström-Lindberg, Eva E; Jansen, Joop H JH; Dugas, Martin M

Publication Date: 2018-12-15

Variant appearance in text: TP53: 493C>A; Gln165Lys

PubMed Link: 29945233

Variant Present in the following documents:

• bty518_supplementary_data_s4.xlsx, sheet 9

View BVdb publication page

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Expression of cell cycle regulators and frequency of TP53 mutations in high risk gastrointestinal stromal tumors prior to adjuvant imatinib treatment.

Plos One

Ihle, Michaela Angelika MA; Huss, Sebastian S; Jeske, Wiebke W; Hartmann, Wolfgang W; Merkelbach-Bruse, Sabine S; Schildhaus, Hans-Ulrich HU; Büttner, Reinhard R; Sihto, Harri H; Sundby Hall, Kirsten K; Eriksson, Mikael M; Reichardt, Peter P; Joensuu, Heikki H; Wardelmann, Eva E

Publication Date: 2018

Variant appearance in text: p53: Q165K

PubMed Link: 29451912

Variant Present in the following documents:

• Main text
• pone.0193048.pdf

View BVdb publication page

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Dual MET and ERBB inhibition overcomes intratumor plasticity in osimertinib-resistant-advanced non-small-cell lung cancer (NSCLC).

Annals Of Oncology : Official Journal Of The European Society For Medical Oncology

Martinez-Marti, A A; Felip, E E; Matito, J J; Mereu, E E; Navarro, A A; Cedrés, S S; Pardo, N N; Martinez de Castro, A A; Remon, J J; Miquel, J M JM; Guillaumet-Adkins, A A; Nadal, E E; Rodriguez-Esteban, G G; Arqués, O O; Fasani, R R; Nuciforo, P P; Heyn, H H; Villanueva, A A; Palmer, H G HG; Vivancos, A A

Publication Date: 2017-10-01

Variant appearance in text: TP53: Q165K

PubMed Link: 28961841

Variant Present in the following documents:

• Main text
• mdx396.pdf

View BVdb publication page

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The whole-genome landscape of medulloblastoma subtypes.

Nature

Northcott, Paul A PA; Buchhalter, Ivo I; Morrissy, A Sorana AS; Hovestadt, Volker V; Weischenfeldt, Joachim J; Ehrenberger, Tobias T; Gröbner, Susanne S; Segura-Wang, Maia M; Zichner, Thomas T; Rudneva, Vasilisa A VA; Warnatz, Hans-Jörg HJ; Sidiropoulos, Nikos N; Phillips, Aaron H AH; Schumacher, Steven S; Kleinheinz, Kortine K; Waszak, Sebastian M SM; Erkek, Serap S; Jones, David T W DTW; Worst, Barbara C BC; Kool, Marcel M; Zapatka, Marc M; Jäger, Natalie N; Chavez, Lukas L; Hutter, Barbara B; Bieg, Matthias M; Paramasivam, Nagarajan N; Heinold, Michael M; Gu, Zuguang Z; Ishaque, Naveed N; Jäger-Schmidt, Christina C; Imbusch, Charles D CD; Jugold, Alke A; Hübschmann, Daniel D; Risch, Thomas T; Amstislavskiy, Vyacheslav V; Gonzalez, Francisco German Rodriguez FGR; Weber, Ursula D UD; Wolf, Stephan S; Robinson, Giles W GW; Zhou, Xin X; Wu, Gang G; Finkelstein, David D; Liu, Yanling Y; Cavalli, Florence M G FMG; Luu, Betty B; Ramaswamy, Vijay V; Wu, Xiaochong X; Koster, Jan J; Ryzhova, Marina M; Cho, Yoon-Jae YJ; Pomeroy, Scott L SL; Herold-Mende, Christel C; Schuhmann, Martin M; Ebinger, Martin M; Liau, Linda M LM; Mora, Jaume J; McLendon, Roger E RE; Jabado, Nada N; Kumabe, Toshihiro T; Chuah, Eric E; Ma, Yussanne Y; Moore, Richard A RA; Mungall, Andrew J AJ; Mungall, Karen L KL; Thiessen, Nina N; Tse, Kane K; Wong, Tina T; Jones, Steven J M SJM; Witt, Olaf O; Milde, Till T; Von Deimling, Andreas A; Capper, David D; Korshunov, Andrey A; Yaspo, Marie-Laure ML; Kriwacki, Richard R; Gajjar, Amar A; Zhang, Jinghui J; Beroukhim, Rameen R; Fraenkel, Ernest E; Korbel, Jan O JO; Brors, Benedikt B; Schlesner, Matthias M; Eils, Roland R; Marra, Marco A MA; Pfister, Stefan M SM; Taylor, Michael D MD; Lichter, Peter P

Publication Date: 2017-07-19

Variant appearance in text: TP53: Q165K

PubMed Link: 28726821

Variant Present in the following documents:

• 41586_2017_Article_BFnature22973.pdf
• 41586_2017_BFnature22973_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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iFish: predicting the pathogenicity of human nonsynonymous variants using gene-specific/family-specific attributes and classifiers.

Scientific Reports

Wang, Meng M; Wei, Liping L

Publication Date: 2016-08-16

Variant appearance in text: TP53: Q165K

PubMed Link: 27527004

Variant Present in the following documents:

• srep31321-s5.xls, sheet 1

View BVdb publication page

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