Publications:

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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: RET: A641T; rs377767411

PubMed Link: 36413997

Variant Present in the following documents:

• mmc3.xlsx, sheet 1

View BVdb publication page

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Construction and validation of an immunoediting-based optimized neoantigen load (ioTNL) model to predict the response and prognosis of immune checkpoint therapy in various cancers.

Aging

Su, Xiaofan X; Jin, Haoxuan H; Wang, Jiaqian J; Lu, Huiping H; Gu, Tiantian T; Gao, Zhibo Z; Li, Manxiang M

Publication Date: 2022-05-25

Variant appearance in text: RET: 1921G>A; A641T

PubMed Link: 35613927

Variant Present in the following documents:

• aging-14-204101-s004.xlsx, sheet 1

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: RET: 1921G>A; A641T

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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Cas9 activates the p53 pathway and selects for p53-inactivating mutations.

Nature Genetics

Enache, Oana M OM; Rendo, Veronica V; Abdusamad, Mai M; Lam, Daniel D; Davison, Desiree D; Pal, Sangita S; Currimjee, Naomi N; Hess, Julian J; Pantel, Sasha S; Nag, Anwesha A; Thorner, Aaron R AR; Doench, John G JG; Vazquez, Francisca F; Beroukhim, Rameen R; Golub, Todd R TR; Ben-David, Uri U

Publication Date: 2020-07

Variant appearance in text: RET: 1921G>A; A641T

PubMed Link: 32424350

Variant Present in the following documents:

• NIHMS1581982-supplement-1581982_Supp_Dataset1-7.xlsx, sheet 7

View BVdb publication page

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Oncogenic and drug-sensitive RET mutations in human epithelial ovarian cancer.

Journal Of Experimental & Clinical Cancer Research : Cr

Guan, Luyao L; Li, Zhang Z; Xie, Feifei F; Pang, Yuzhi Y; Zhang, Chenyun C; Tang, Haosha H; Zhang, Hao H; Chen, Chun C; Zhan, Yaying Y; Zhao, Ting T; Jiang, Hongyuan H; Jia, Xiaona X; Wang, Yuexiang Y; Lu, Yuan Y

Publication Date: 2020-03-23

Variant appearance in text: RET: A641T

PubMed Link: 32293499

Variant Present in the following documents:

• Main text
• 13046_2020_Article_1557.pdf
• 13046_2020_1557_MOESM2_ESM.xls, sheet 3

View BVdb publication page

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Targeted Exome Sequencing Provided Comprehensive Genetic Diagnosis of Congenital Anomalies of the Kidney and Urinary Tract.

Journal Of Clinical Medicine

Ahn, Yo Han YH; Lee, Chung C; Kim, Nayoung K D NKD; Park, Eujin E; Kang, Hee Gyung HG; Ha, Il-Soo IS; Park, Woong-Yang WY; Cheong, Hae Il HI

Publication Date: 2020-03-10

Variant appearance in text: RET: 1921G>A; Ala641Thr

PubMed Link: 32164334

Variant Present in the following documents:

• jcm-09-00751-s001.pdf

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: RET: A641T

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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Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.

Cell Reports

Way, Gregory P GP; Sanchez-Vega, Francisco F; La, Konnor K; Armenia, Joshua J; Chatila, Walid K WK; Luna, Augustin A; Sander, Chris C; Cherniack, Andrew D AD; Mina, Marco M; Ciriello, Giovanni G; Schultz, Nikolaus N; , ; Sanchez, Yolanda Y; Greene, Casey S CS

Publication Date: 2018-04-03

Variant appearance in text: RET: 1921G>A

PubMed Link: 29617658

Variant Present in the following documents:

• NIHMS958974-supplement-5.xlsx, sheet 1
• NIHMS958974-supplement-6.xlsx, sheet 1

View BVdb publication page

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The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine.

Genome Medicine

Garofalo, Andrea A; Sholl, Lynette L; Reardon, Brendan B; Taylor-Weiner, Amaro A; Amin-Mansour, Ali A; Miao, Diana D; Liu, David D; Oliver, Nelly N; MacConaill, Laura L; Ducar, Matthew M; Rojas-Rudilla, Vanesa V; Giannakis, Marios M; Ghazani, Arezou A; Gray, Stacy S; Janne, Pasi P; Garber, Judy J; Joffe, Steve S; Lindeman, Neal N; Wagle, Nikhil N; Garraway, Levi A LA; Van Allen, Eliezer M EM

Publication Date: 2016-07-26

Variant appearance in text: RET: 1921G>A

PubMed Link: 27460824

Variant Present in the following documents:

• 13073_2016_333_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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A Landscape of Pharmacogenomic Interactions in Cancer.

Cell

Iorio, Francesco F; Knijnenburg, Theo A TA; Vis, Daniel J DJ; Bignell, Graham R GR; Menden, Michael P MP; Schubert, Michael M; Aben, Nanne N; Gonçalves, Emanuel E; Barthorpe, Syd S; Lightfoot, Howard H; Cokelaer, Thomas T; Greninger, Patricia P; van Dyk, Ewald E; Chang, Han H; de Silva, Heshani H; Heyn, Holger H; Deng, Xianming X; Egan, Regina K RK; Liu, Qingsong Q; Mironenko, Tatiana T; Mitropoulos, Xeni X; Richardson, Laura L; Wang, Jinhua J; Zhang, Tinghu T; Moran, Sebastian S; Sayols, Sergi S; Soleimani, Maryam M; Tamborero, David D; Lopez-Bigas, Nuria N; Ross-Macdonald, Petra P; Esteller, Manel M; Gray, Nathanael S NS; Haber, Daniel A DA; Stratton, Michael R MR; Benes, Cyril H CH; Wessels, Lodewyk F A LFA; Saez-Rodriguez, Julio J; McDermott, Ultan U; Garnett, Mathew J MJ

Publication Date: 2016-07-28

Variant appearance in text: RET: 1921G>A; A641T

PubMed Link: 27397505

Variant Present in the following documents:

• mmc3.xlsx, sheet 3

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: RET: A641T

PubMed Link: 27270441

Variant Present in the following documents:

• onc2016172x3.xls, sheet 3

View BVdb publication page

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High-throughput sequencing and copy number variation detection using formalin fixed embedded tissue in metastatic gastric cancer.

Plos One

Kim, Seokhwi S; Lee, Jeeyun J; Hong, Min Eui ME; Do, In-Gu IG; Kang, So Young SY; Ha, Sang Yun SY; Kim, Seung Tae ST; Park, Se Hoon SH; Kang, Won Ki WK; Choi, Min-Gew MG; Lee, Jun Ho JH; Sohn, Tae Sung TS; Bae, Jae Moon JM; Kim, Sung S; Kim, Duk-Hwan DH; Kim, Kyoung-Mee KM

Publication Date: 2014

Variant appearance in text: RET: A641T

PubMed Link: 25372287

Variant Present in the following documents:

• Main text
• pone.0111693.pdf

View BVdb publication page

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