Publications:

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Tissue and liquid biopsy profiling reveal convergent tumor evolution and therapy evasion in breast cancer.

Nature Communications

Sivakumar, Smruthy S; Jin, Dexter X DX; Tukachinsky, Hanna H; Murugesan, Karthikeyan K; McGregor, Kimberly K; Danziger, Natalie N; Pavlick, Dean D; Gjoerup, Ole O; Ross, Jeffrey S JS; Harmon, Robert R; Chung, Jon J; Decker, Brennan B; Dennis, Lucas L; Frampton, Garrett M GM; Molinero, Luciana L; Oesterreich, Steffi S; Venstrom, Jeffrey M JM; Oxnard, Geoffrey R GR; Hegde, Priti S PS; Sokol, Ethan S ES

Publication Date: 2022-12-05

Variant appearance in text: TP53: D228H

PubMed Link: 36470901

Variant Present in the following documents:

• 41467_2022_35245_MOESM4_ESM.xlsx, sheet 17

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CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions.

Iscience

Zhou, Rong R; Tian, Kai K; Huang, Jie J; Duan, Wenjia W; Fu, Hongye H; Feng, Ying Y; Wang, Hui H; Jiang, Yongpeng Y; Li, Yuanjun Y; Wang, Rui R; Hu, Jiazhi J; Ma, Hanhui H; Qi, Zhi Z; Ji, Xiong X

Publication Date: 2022-09-16

Variant appearance in text: p53: 682G>C

PubMed Link: 36117989

Variant Present in the following documents:

• mmc4.xlsx, sheet 1
• mmc5.xlsx, sheet 1

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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: 682G>C; D228H

PubMed Link: 35831314

Variant Present in the following documents:

• 41467_2022_31809_MOESM8_ESM.xlsx, sheet 3

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Loss of Smad4 promotes aggressive lung cancer metastasis by de-repression of PAK3 via miRNA regulation.

Nature Communications

Tan, Xiaohong X; Tong, Lu L; Li, Lin L; Xu, Jinjin J; Xie, Shaofang S; Ji, Lei L; Fu, Junjiang J; Liu, Qingwu Q; Shen, Shihui S; Liu, Yun Y; Xiao, Yanhui Y; Gao, Feiran F; Moses, Robb E RE; Bardeesy, Nabeel N; Wang, Yanxiao Y; Zhang, Jishuai J; Tang, Longying L; Li, Lei L; Wong, Kwok-Kin KK; Song, Dianwen D; Yang, Xiao X; Liu, Jian J; Li, Xiaotao X

Publication Date: 2021-08-11

Variant appearance in text: TP53: D228H

PubMed Link: 34381046

Variant Present in the following documents:

• 41467_2021_24898_MOESM10_ESM.xlsx, sheet 1

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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: 682G>C; D228H

PubMed Link: 34253785

Variant Present in the following documents:

• 41598_2021_93715_MOESM2_ESM.xlsx, sheet 9
• 41598_2021_93715_MOESM2_ESM.xlsx, sheet 10

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Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer.

Nature Communications

Vandekerkhove, Gillian G; Lavoie, Jean-Michel JM; Annala, Matti M; Murtha, Andrew J AJ; Sundahl, Nora N; Walz, Simon S; Sano, Takeshi T; Taavitsainen, Sinja S; Ritch, Elie E; Fazli, Ladan L; Hurtado-Coll, Antonio A; Wang, Gang G; Nykter, Matti M; Black, Peter C PC; Todenhöfer, Tilman T; Ost, Piet P; Gibb, Ewan A EA; Chi, Kim N KN; Eigl, Bernhard J BJ; Wyatt, Alexander W AW

Publication Date: 2021-01-08

Variant appearance in text: TP53: D228H

PubMed Link: 33420073

Variant Present in the following documents:

• 41467_2020_20493_MOESM3_ESM.xlsx, sheet 4
• 41467_2020_20493_MOESM3_ESM.xlsx, sheet 7

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Defining relative mutational difficulty to understand cancer formation.

Cell Discovery

Shan, Lin L; Yu, Jiao J; He, Zhengjin Z; Chen, Shishuang S; Liu, Mingxian M; Ding, Hongyu H; Xu, Liang L; Zhao, Jie J; Yang, Ailing A; Jiang, Hai H

Publication Date: 2020

Variant appearance in text: p53: D228H

PubMed Link: 32704382

Variant Present in the following documents:

• 41421_2020_177_MOESM4_ESM.xlsx, sheet 1

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Phase and context shape the function of composite oncogenic mutations.

Nature

Gorelick, Alexander N AN; Sánchez-Rivera, Francisco J FJ; Cai, Yanyan Y; Bielski, Craig M CM; Biederstedt, Evan E; Jonsson, Philip P; Richards, Allison L AL; Vasan, Neil N; Penson, Alexander V AV; Friedman, Noah D ND; Ho, Yu-Jui YJ; Baslan, Timour T; Bandlamudi, Chaitanya C; Scaltriti, Maurizio M; Schultz, Nikolaus N; Lowe, Scott W SW; Reznik, Ed E; Taylor, Barry S BS

Publication Date: 2020-06

Variant appearance in text: TP53: D228H

PubMed Link: 32461694

Variant Present in the following documents:

• NIHMS1582596-supplement-1582596_Supp_Tab1-5.xlsx, sheet 2

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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: TP53: 682G>C; D228H

PubMed Link: 31768066

Variant Present in the following documents:

• NIHMS1541314-supplement-1541314_Sup_Tab.xlsx, sheet 4
• NIHMS1541314-supplement-1541314_Sup_Tab.xlsx, sheet 6

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Finding driver mutations in cancer: Elucidating the role of background mutational processes.

Plos Computational Biology

Brown, Anna-Leigh AL; Li, Minghui M; Goncearenco, Alexander A; Panchenko, Anna R AR

Publication Date: 2019-04

Variant appearance in text: TP53: D228H

PubMed Link: 31034466

Variant Present in the following documents:

• pcbi.1006981.s010.xlsx, sheet 1

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Incidence and distribution of UroSEEK gene panel in a multi-institutional cohort of bladder urothelial carcinoma.

Modern Pathology : An Official Journal Of The United States And Canadian Academy Of Pathology, Inc

Eich, Marie-Lisa ML; Rodriguez Pena, Maria Del Carmen MDC; Springer, Simeon U SU; Taheri, Diana D; Tregnago, Aline C AC; Salles, Daniela C DC; Bezerra, Stephania Martins SM; Cunha, Isabela W IW; Fujita, Kazutoshi K; Ertoy, Dilek D; Bivalacqua, Trinity J TJ; Tomasetti, Cristian C; Papadopoulos, Nickolas N; Kinzler, Ken W KW; Vogelstein, Bert B; Netto, George J GJ

Publication Date: 2019-10

Variant appearance in text: TP53: D228H

PubMed Link: 31028363

Variant Present in the following documents:

• NIHMS1525315-supplement-2.xlsx, sheet 1

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Analysis on GENIE reveals novel recurrent variants that affect molecular diagnosis of sizable number of cancer patients.

Bmc Cancer

Koyama, Takahiko T; Rhrissorrakrai, Kahn K; Parida, Laxmi L

Publication Date: 2019-02-01

Variant appearance in text: TP53: 682G>C; D228H

PubMed Link: 30709382

Variant Present in the following documents:

• 12885_2019_5313_MOESM3_ESM.xlsx, sheet 1

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Single Amino Acid Variant Profiles of Subpopulations in the MCF-7 Breast Cancer Cell Line.

Journal Of Proteome Research

Tan, Zhijing Z; Nie, Song S; McDermott, Sean P SP; Wicha, Max S MS; Lubman, David M DM

Publication Date: 2017-02-03

Variant appearance in text: TP53: D228H

PubMed Link: 28076950

Variant Present in the following documents:

• Main text

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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: D228H

PubMed Link: 27527004

Variant Present in the following documents:

• srep31321-s5.xls, sheet 1

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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: TP53: 682G>C

PubMed Link: 27060149

Variant Present in the following documents:

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

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Towards a Next-Generation Sequencing Diagnostic Service for Tumour Genotyping: A Comparison of Panels and Platforms.

Biomed Research International

Burghel, George J GJ; Hurst, Carolyn D CD; Watson, Christopher M CM; Chambers, Phillip A PA; Dickinson, Helen H; Roberts, Paul P; Knowles, Margaret A MA

Publication Date: 2015

Variant appearance in text: TP53: 682G>C

PubMed Link: 26351634

Variant Present in the following documents:

• Main text
• BMRI2015-478017.pdf

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GESPA: classifying nsSNPs to predict disease association.

Bmc Bioinformatics

Khurana, Jay K JK; Reeder, Jay E JE; Shrimpton, Antony E AE; Thakar, Juilee J

Publication Date: 2015-07-25

Variant appearance in text: TP53: D228H

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 1

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Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.

Genome Biology

Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B

Publication Date: 2014-10-28

Variant appearance in text: TP53: D228H

PubMed Link: 25348012

Variant Present in the following documents:

• 13059_2014_484_MOESM2_ESM.xlsx, sheet 1

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Pepper suppressor of the G2 allele of skp1 interacts with the receptor-like cytoplasmic kinase1 and type III effector AvrBsT and promotes the hypersensitive cell death response in a phosphorylation-dependent manner.

Plant Physiology

Kim, Nak Hyun NH; Kim, Dae Sung DS; Chung, Eui Hwan EH; Hwang, Byung Kook BK

Publication Date: 2014-05

Variant appearance in text: p53: D228H

PubMed Link: 24686111

Variant Present in the following documents:

• Main text

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Frequent inactivating mutations of STAG2 in bladder cancer are associated with low tumour grade and stage and inversely related to chromosomal copy number changes.

Human Molecular Genetics

Taylor, Claire F CF; Platt, Fiona M FM; Hurst, Carolyn D CD; Thygesen, Helene H HH; Knowles, Margaret A MA

Publication Date: 2014-04-15

Variant appearance in text: TP53: D228H

PubMed Link: 24270882

Variant Present in the following documents:

• supp_ddt589_ddt589supp_table1.pdf
• supp_ddt589_ddt589supp_table5.pdf

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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: TP53: D228H

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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