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: FAT1: Q2933L

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 3
• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 2

View BVdb publication page

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Integrated Whole-Exome and Transcriptome Sequencing Indicated Dysregulation of Cholesterol Metabolism in Eyelid Sebaceous Gland Carcinoma.

Translational Vision Science & Technology

Wang, Yuchuan Y; Li, Jun J; Hao, Peng P; Li, Jing J; Han, Ruifang R; Lin, Jinyong J; Li, Xuan X

Publication Date: 2023-02-01

Variant appearance in text: FAT1: Q2933L

PubMed Link: 36735267

Variant Present in the following documents:

• tvst-12-2-4_s004.xls, sheet 5

View BVdb publication page

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Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma.

Frontiers In Oncology

Block, Timothy T; Zezulinski, Daniel D; Kaplan, David E DE; Lu, Jingqiao J; Zanine, Samantha S; Zhan, Tingting T; Doria, Cataldo C; Sayeed, Aejaz A

Publication Date: 2022

Variant appearance in text: rs1280098

PubMed Link: 36582804

Variant Present in the following documents:

• Table_6.xlsx, sheet 1

View BVdb publication page

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High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer.

Nature Communications

Palafox, Marta M; Monserrat, Laia L; Bellet, Meritxell M; Villacampa, Guillermo G; Gonzalez-Perez, Abel A; Oliveira, Mafalda M; Brasó-Maristany, Fara F; Ibrahimi, Nusaibah N; Kannan, Srinivasaraghavan S; Mina, Leonardo L; Herrera-Abreu, Maria Teresa MT; Òdena, Andreu A; Sánchez-Guixé, Mònica M; Capelán, Marta M; Azaro, Analía A; Bruna, Alejandra A; Rodríguez, Olga O; Guzmán, Marta M; Grueso, Judit J; Viaplana, Cristina C; Hernández, Javier J; Su, Faye F; Lin, Kui K; Clarke, Robert B RB; Caldas, Carlos C; Arribas, Joaquín J; Michiels, Stefan S; García-Sanz, Alicia A; Turner, Nicholas C NC; Prat, Aleix A; Nuciforo, Paolo P; Dienstmann, Rodrigo R; Verma, Chandra S CS; Lopez-Bigas, Nuria N; Scaltriti, Maurizio M; Arnedos, Monica M; Saura, Cristina C; Serra, Violeta V

Publication Date: 2022-09-07

Variant appearance in text: FAT1: 8798A>T; Q2933L

PubMed Link: 36071033

Variant Present in the following documents:

• 41467_2022_32828_MOESM4_ESM.xlsx, sheet 3

View BVdb publication page

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Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition.

Molecular & Cellular Proteomics : Mcp

Schmitt, Marisa M; Sinnberg, Tobias T; Bratl, Katrin K; Zittlau, Katharina K; Garbe, Claus C; Macek, Boris B; Nalpas, Nicolas C NC

Publication Date: 2021-10-19

Variant appearance in text: FAT1: Q2933L

PubMed Link: 34673281

Variant Present in the following documents:

• mmc2.xlsx, sheet 11
• mmc2.xlsx, sheet 4
• mmc2.xlsx, sheet 6
• mmc2.xlsx, sheet 9

View BVdb publication page

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Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition.

Molecular & Cellular Proteomics : Mcp

Schmitt, Marisa M; Sinnberg, Tobias T; Bratl, Katrin K; Zittlau, Katharina K; Garbe, Claus C; Macek, Boris B; Nalpas, Nicolas C NC

Publication Date: 2021

Variant appearance in text: FAT1: Q2933L

PubMed Link: 34673281

Variant Present in the following documents:

• mmc2.xlsx, sheet 9
• mmc2.xlsx, sheet 4
• mmc2.xlsx, sheet 6
• mmc2.xlsx, sheet 11

View BVdb publication page

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Integrative genome-wide analyses reveal the transcriptional aberrations in Japanese esophageal squamous cell carcinoma.

Cancer Science

Takemoto, Akira A; Tanimoto, Kousuke K; Mori, Seiichi S; Inoue, Jun J; Fujiwara, Naoto N; Noda, Tetsuo T; Inazawa, Johji J

Publication Date: 2021-10

Variant appearance in text: FAT1: Q2933L

PubMed Link: 34263978

Variant Present in the following documents:

• CAS-112-4377-s006.pdf

View BVdb publication page

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The Gain-of-Function p53 R248W Mutant Promotes Migration by STAT3 Deregulation in Human Pancreatic Cancer Cells.

Frontiers In Oncology

Klemke, Luisa L; Fehlau, Clara F CF; Winkler, Nadine N; Toboll, Felicia F; Singh, Shiv K SK; Moll, Ute M UM; Schulz-Heddergott, Ramona R

Publication Date: 2021

Variant appearance in text: FAT1: 8798A>T; Gln2933Leu; rs1280098

PubMed Link: 34178628

Variant Present in the following documents:

• DataSheet_1.pdf

View BVdb publication page

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Pan-cancer circulating tumor DNA detection in over 10,000 Chinese patients.

Nature Communications

Zhang, Yongliang Y; Yao, Yu Y; Xu, Yaping Y; Li, Lifeng L; Gong, Yan Y; Zhang, Kai K; Zhang, Meng M; Guan, Yanfang Y; Chang, Lianpeng L; Xia, Xuefeng X; Li, Lin L; Jia, Shuqin S; Zeng, Qiang Q

Publication Date: 2021-01-04

Variant appearance in text: FAT1: 8798A>T; Q2933L

PubMed Link: 33397889

Variant Present in the following documents:

• 41467_2020_20162_MOESM6_ESM.xlsx, sheet 1

View BVdb publication page

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Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes.

Communications Biology

Perrino, Peter A PA; Talbot, Lidiya L; Kirkland, Rose R; Hill, Amanda A; Rendall, Amanda R AR; Mountford, Hayley S HS; Taylor, Jenny J; , ; Buscarello, Alexzandrea N AN; Lahiri, Nayana N; Saggar, Anand A; Fitch, R Holly RH; Newbury, Dianne F DF

Publication Date: 2020-04-20

Variant appearance in text: rs1280098

PubMed Link: 32313182

Variant Present in the following documents:

• 42003_2020_885_MOESM2_ESM.xlsx, sheet 1

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: FAT1: 8798A>T; Gln2933Leu

PubMed Link: 32277576

Variant Present in the following documents:

• JCMM-24-4931-s010.xlsx, sheet 1

View BVdb publication page

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Activating mutations in CSF1R and additional receptor tyrosine kinases in histiocytic neoplasms.

Nature Medicine

Durham, Benjamin H BH; Lopez Rodrigo, Estibaliz E; Picarsic, Jennifer J; Abramson, David D; Rotemberg, Veronica V; De Munck, Steven S; Pannecoucke, Erwin E; Lu, Sydney X SX; Pastore, Alessandro A; Yoshimi, Akihide A; Mandelker, Diana D; Ceyhan-Birsoy, Ozge O; Ulaner, Gary A GA; Walsh, Michael M; Yabe, Mariko M; Petrova-Drus, Kseniya K; Arcila, Maria E ME; Ladanyi, Marc M; Solit, David B DB; Berger, Michael F MF; Hyman, David M DM; Lacouture, Mario E ME; Erickson, Caroline C; Saganty, Ruth R; Ki, Michelle M; Dunkel, Ira J IJ; Santa-María López, Vicente V; Mora, Jaume J; Haroche, Julien J; Emile, Jean-Francois JF; Decaux, Olivier O; Geissmann, Frederic F; Savvides, Savvas N SN; Drilon, Alexander A; Diamond, Eli L EL; Abdel-Wahab, Omar O

Publication Date: 2019-12

Variant appearance in text: FAT1: 8798A>T; Q2933L

PubMed Link: 31768065

Variant Present in the following documents:

• NIHMS1541330-supplement-1.pdf

View BVdb publication page

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Distinctive mutational spectrum and karyotype disruption in long-term cisplatin-treated urothelial carcinoma cell lines.

Scientific Reports

Skowron, Margaretha A MA; Petzsch, Patrick P; Hardt, Karin K; Wagner, Nicholas N; Beier, Manfred M; Stepanow, Stefanie S; Drechsler, Matthias M; Rieder, Harald H; Köhrer, Karl K; Niegisch, Günter G; Hoffmann, Michèle J MJ; Schulz, Wolfgang A WA

Publication Date: 2019-10-09

Variant appearance in text: FAT1: Q2933L; rs1280098

PubMed Link: 31597922

Variant Present in the following documents:

• 41598_2019_50891_MOESM5_ESM.xlsx, sheet 1
• 41598_2019_50891_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

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Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy.

Nature Communications

Takata, Atsushi A; Nakashima, Mitsuko M; Saitsu, Hirotomo H; Mizuguchi, Takeshi T; Mitsuhashi, Satomi S; Takahashi, Yukitoshi Y; Okamoto, Nobuhiko N; Osaka, Hitoshi H; Nakamura, Kazuyuki K; Tohyama, Jun J; Haginoya, Kazuhiro K; Takeshita, Saoko S; Kuki, Ichiro I; Okanishi, Tohru T; Goto, Tomohide T; Sasaki, Masayuki M; Sakai, Yasunari Y; Miyake, Noriko N; Miyatake, Satoko S; Tsuchida, Naomi N; Iwama, Kazuhiro K; Minase, Gaku G; Sekiguchi, Futoshi F; Fujita, Atsushi A; Imagawa, Eri E; Koshimizu, Eriko E; Uchiyama, Yuri Y; Hamanaka, Kohei K; Ohba, Chihiro C; Itai, Toshiyuki T; Aoi, Hiromi H; Saida, Ken K; Sakaguchi, Tomohiro T; Den, Kouhei K; Takahashi, Rina R; Ikeda, Hiroko H; Yamaguchi, Tokito T; Tsukamoto, Kazuki K; Yoshitomi, Shinsaku S; Oboshi, Taikan T; Imai, Katsumi K; Kimizu, Tomokazu T; Kobayashi, Yu Y; Kubota, Masaya M; Kashii, Hirofumi H; Baba, Shimpei S; Iai, Mizue M; Kira, Ryutaro R; Hara, Munetsugu M; Ohta, Masayasu M; Miyata, Yohane Y; Miyata, Rie R; Takanashi, Jun-Ichi JI; Matsui, Jun J; Yokochi, Kenji K; Shimono, Masayuki M; Amamoto, Masano M; Takayama, Rumiko R; Hirabayashi, Shinichi S; Aiba, Kaori K; Matsumoto, Hiroshi H; Nabatame, Shin S; Shiihara, Takashi T; Kato, Mitsuhiro M; Matsumoto, Naomichi N

Publication Date: 2019-06-07

Variant appearance in text: FAT1: 8798A>T; Gln2933Leu

PubMed Link: 31175295

Variant Present in the following documents:

• 41467_2019_10482_MOESM8_ESM.xlsx, sheet 1

View BVdb publication page

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A reference collection of patient-derived cell line and xenograft models of proneural, classical and mesenchymal glioblastoma.

Scientific Reports

Stringer, Brett W BW; Day, Bryan W BW; D'Souza, Rochelle C J RCJ; Jamieson, Paul R PR; Ensbey, Kathleen S KS; Bruce, Zara C ZC; Lim, Yi Chieh YC; Goasdoué, Kate K; Offenhäuser, Carolin C; Akgül, Seçkin S; Allan, Suzanne S; Robertson, Thomas T; Lucas, Peter P; Tollesson, Gert G; Campbell, Scott S; Winter, Craig C; Do, Hongdo H; Dobrovic, Alexander A; Inglis, Po-Ling PL; Jeffree, Rosalind L RL; Johns, Terrance G TG; Boyd, Andrew W AW

Publication Date: 2019-03-20

Variant appearance in text: FAT1: Q2933L; rs1280098

PubMed Link: 30894629

Variant Present in the following documents:

• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 11

View BVdb publication page

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Organoids as a new model for improving regenerative medicine and cancer personalized therapy in renal diseases.

Cell Death & Disease

Grassi, Ludovica L; Alfonsi, Romina R; Francescangeli, Federica F; Signore, Michele M; De Angelis, Maria Laura ML; Addario, Antonio A; Costantini, Manuela M; Flex, Elisabetta E; Ciolfi, Andrea A; Pizzi, Simone S; Bruselles, Alessandro A; Pallocca, Matteo M; Simone, Giuseppe G; Haoui, Mustapha M; Falchi, Mario M; Milella, Michele M; Sentinelli, Steno S; Di Matteo, Paola P; Stellacci, Emilia E; Gallucci, Michele M; Muto, Giovanni G; Tartaglia, Marco M; De Maria, Ruggero R; Bonci, Désirée D

Publication Date: 2019-02-27

Variant appearance in text: rs1280098

PubMed Link: 30814510

Variant Present in the following documents:

• 41419_2019_1453_MOESM27_ESM.xlsx, sheet 2
• 41419_2019_1453_MOESM27_ESM.xlsx, sheet 1

View BVdb publication page

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Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma.

Bmc Cancer

Lu, Hongyang H; Yang, Shifeng S; Zhu, Huineng H; Tong, Xiaoling X; Xie, Fajun F; Qin, Jing J; Han, Na N; Wu, Xue X; Fan, Yun Y; Shao, Yang W YW; Mao, Weimin W

Publication Date: 2018-03-05

Variant appearance in text: FAT1: Q2933L

PubMed Link: 29506494

Variant Present in the following documents:

• 12885_2018_4159_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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Whole-exome sequencing analysis of Waardenburg syndrome in a Chinese family.

Human Genome Variation

Chen, Dezhong D; Zhao, Na N; Wang, Jing J; Li, Zhuoyu Z; Wu, Changxin C; Fu, Jie J; Xiao, Han H

Publication Date: 2017

Variant appearance in text: rs1280098

PubMed Link: 28690861

Variant Present in the following documents:

• hgv201727-s1.xls, sheet 1

View BVdb publication page

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Identification of EML4-ALK as an alternative fusion gene in epithelioid inflammatory myofibroblastic sarcoma.

Orphanet Journal Of Rare Diseases

Jiang, Quan Q; Tong, Han-Xing HX; Hou, Ying-Yong YY; Zhang, Yong Y; Li, Jing-Lei JL; Zhou, Yu-Hong YH; Xu, Jing J; Wang, Jiong-Yuan JY; Lu, Wei-Qi WQ

Publication Date: 2017-05-23

Variant appearance in text: N/A

PubMed Link: 28535796

Variant Present in the following documents:

View BVdb publication page

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Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment.

Scientific Reports

Chen, Xiaowei Sylvia XS; Reader, Rose H RH; Hoischen, Alexander A; Veltman, Joris A JA; Simpson, Nuala H NH; Francks, Clyde C; Newbury, Dianne F DF; Fisher, Simon E SE

Publication Date: 2017-04-25

Variant appearance in text: FAT1: Q2933L; rs1280098

PubMed Link: 28440294

Variant Present in the following documents:

• srep46105-s2.xls, sheet 6

View BVdb publication page

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Molecular analysis of urothelial cancer cell lines for modeling tumor biology and drug response.

Oncogene

Nickerson, M L ML; Witte, N N; Im, K M KM; Turan, S S; Owens, C C; Misner, K K; Tsang, S X SX; Cai, Z Z; Wu, S S; Dean, M M; Costello, J C JC; Theodorescu, D D

Publication Date: 2017-01-05

Variant appearance in text: FAT1: Q2933L; rs1280098

PubMed Link: 27270441

Variant Present in the following documents:

• onc2016172x3.xls, sheet 3

View BVdb publication page

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Genomic characterization of a large panel of patient-derived hepatocellular carcinoma xenograft tumor models for preclinical development.

Oncotarget

Gu, Qingyang Q; Zhang, Bin B; Sun, Hongye H; Xu, Qiang Q; Tan, Yexiong Y; Wang, Guan G; Luo, Qin Q; Xu, Weiguo W; Yang, Shuqun S; Li, Jian J; Fu, Jing J; Chen, Lei L; Yuan, Shengxian S; Liang, Guibai G; Ji, Qunsheng Q; Chen, Shu-Hui SH; Chan, Chi-Chung CC; Zhou, Weiping W; Xu, Xiaowei X; Wang, Hongyang H; Fang, Douglas D DD

Publication Date: 2015-08-21

Variant appearance in text: FAT1: Q2933L; rs1280098

PubMed Link: 26062443

Variant Present in the following documents:

• oncotarget-06-20160-s004.xlsx, sheet 1

View BVdb publication page

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Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.

Bmc Genomics

Ilyas, Muhammad M; Kim, Jong-Soo JS; Cooper, Jesse J; Shin, Young-Ah YA; Kim, Hak-Min HM; Cho, Yun Sung YS; Hwang, Seungwoo S; Kim, Hyunho H; Moon, Jaewoo J; Chung, Oksung O; Jun, JeHoon J; Rastogi, Achal A; Song, Sanghoon S; Ko, Junsu J; Manica, Andrea A; Rahman, Ziaur Z; Husnain, Tayyab T; Bhak, Jong J

Publication Date: 2015-03-12

Variant appearance in text: N/A

PubMed Link: 25887915

Variant Present in the following documents:

View BVdb publication page

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Identification of the PS1 Thr147Ile Variant in a Family with Very Early Onset Dementia and Expressive Aphasia.

Journal Of Alzheimer'S Disease : Jad

Denvir, James J; Neitch, Shirley S; Fan, Jun J; Niles, Richard M RM; Boskovic, Goran G; Schreurs, Bernard G BG; Primerano, Donald A DA; Alkon, Daniel L DL

Publication Date: 2015

Variant appearance in text: rs1280098

PubMed Link: 25812849

Variant Present in the following documents:

View BVdb publication page

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Whole-genome sequencing of the world's oldest people.

Plos One

Gierman, Hinco J HJ; Fortney, Kristen K; Roach, Jared C JC; Coles, Natalie S NS; Li, Hong H; Glusman, Gustavo G; Markov, Glenn J GJ; Smith, Justin D JD; Hood, Leroy L; Coles, L Stephen LS; Kim, Stuart K SK

Publication Date: 2014

Variant appearance in text: N/A

PubMed Link: 25390934

Variant Present in the following documents:

View BVdb publication page

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The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.

Nucleic Acids Research

Tang, Xiaojia X; Baheti, Saurabh S; Shameer, Khader K; Thompson, Kevin J KJ; Wills, Quin Q; Niu, Nifang N; Holcomb, Ilona N IN; Boutet, Stephane C SC; Ramakrishnan, Ramesh R; Kachergus, Jennifer M JM; Kocher, Jean-Pierre A JP; Weinshilboum, Richard M RM; Wang, Liewei L; Thompson, E Aubrey EA; Kalari, Krishna R KR

Publication Date: 2014-12-16

Variant appearance in text: FAT1: Q2933L; rs1280098

PubMed Link: 25352556

Variant Present in the following documents:

• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 9

View BVdb publication page

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Effect of a poly(ADP-ribose) polymerase-1 inhibitor against esophageal squamous cell carcinoma cell lines.

Cancer Science

Nasuno, Tomomitsu T; Mimaki, Sachiyo S; Okamoto, Makito M; Esumi, Hiroyasu H; Tsuchihara, Katsuya K

Publication Date: 2014-02

Variant appearance in text: FAT1: Q2933L; rs1280098

PubMed Link: 24219164

Variant Present in the following documents:

• cas0105-0202-SD2.xlsx, sheet 1

View BVdb publication page

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Assessment of computational methods for predicting the effects of missense mutations in human cancers.

Bmc Genomics

Gnad, Florian F; Baucom, Albion A; Mukhyala, Kiran K; Manning, Gerard G; Zhang, Zemin Z

Publication Date: 2013

Variant appearance in text: rs1280098

PubMed Link: 23819521

Variant Present in the following documents:

• 1471-2164-14-S3-S7-S1.xlsx, sheet 2

View BVdb publication page

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