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: KMT2C: T316S

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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Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma.

Nature Communications

Gounder, Mrinal M MM; Agaram, Narasimhan P NP; Trabucco, Sally E SE; Robinson, Victoria V; Ferraro, Richard A RA; Millis, Sherri Z SZ; Krishnan, Anita A; Lee, Jessica J; Attia, Steven S; Abida, Wassim W; Drilon, Alexander A; Chi, Ping P; Angelo, Sandra P D' SP; Dickson, Mark A MA; Keohan, Mary Lou ML; Kelly, Ciara M CM; Agulnik, Mark M; Chawla, Sant P SP; Choy, Edwin E; Chugh, Rashmi R; Meyer, Christian F CF; Myer, Parvathi A PA; Moore, Jessica L JL; Okimoto, Ross A RA; Pollock, Raphael E RE; Ravi, Vinod V; Singh, Arun S AS; Somaiah, Neeta N; Wagner, Andrew J AJ; Healey, John H JH; Frampton, Garrett M GM; Venstrom, Jeffrey M JM; Ross, Jeffrey S JS; Ladanyi, Marc M; Singer, Samuel S; Brennan, Murray F MF; Schwartz, Gary K GK; Lazar, Alexander J AJ; Thomas, David M DM; Maki, Robert G RG; Tap, William D WD; Ali, Siraj M SM; Jin, Dexter X DX

Publication Date: 2022-06-15

Variant appearance in text: KMT2C: T316S

PubMed Link: 35705558

Variant Present in the following documents:

• 41467_2022_30496_MOESM2_ESM.xls, sheet 1

View BVdb publication page

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Multiomics Landscape Uncovers the Molecular Mechanism of the Malignant Evolution of Lung Adenocarcinoma Cells to Chronic Low Dose Cadmium Exposure.

Frontiers In Oncology

Dai, Shun-Dong SD; Wang, Shuang S; Qin, Ya-Nan YN; Zhu, Jin-Chao JC

Publication Date: 2021

Variant appearance in text: MLL3: T316S

PubMed Link: 34858801

Variant Present in the following documents:

• Table_1.xls, sheet 1

View BVdb publication page

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2-kupl: mapping-free variant detection from DNA-seq data of matched samples.

Bmc Bioinformatics

Wang, Yunfeng Y; Xue, Haoliang H; Pourcel, Christine C; Du, Yang Y; Gautheret, Daniel D

Publication Date: 2021-06-05

Variant appearance in text: KMT2C: T316S

PubMed Link: 34090332

Variant Present in the following documents:

• 12859_2021_4185_MOESM3_ESM.xlsx, sheet 2

View BVdb publication page

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Clinicopathologic and molecular analysis of embryonal rhabdomyosarcoma of the genitourinary tract: evidence for a distinct DICER1-associated subgroup.

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

Kommoss, Felix K F FKF; Stichel, Damian D; Mora, Jaume J; Esteller, Manel M; Jones, David T W DTW; Pfister, Stefan M SM; Brack, Eva E; Wachtel, Marco M; Bode, Peter Karl PK; Sinn, Hans-Peter HP; Schmidt, Dietmar D; Mentzel, Thomas T; Kommoss, Friedrich F; Sahm, Felix F; von Deimling, Andreas A; Koelsche, Christian C

Publication Date: 2021-08

Variant appearance in text: KMT2C: T316S

PubMed Link: 33846547

Variant Present in the following documents:

• 41379_2021_804_MOESM1_ESM.pdf

View BVdb publication page

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Primary peritoneal clear cell carcinoma. A case report and literature review.

Gynecologic Oncology Reports

Peiro, Gloria G; Silva-Ortega, Sandra S; Garcia-Espasa, Cristina C; Sala-Ferichola, Manuela M; Perez-Vicente, Sandra S; Castellon-Molla, Elena E; Marcos-Sanmartin, Josefa J

Publication Date: 2020-05

Variant appearance in text: KMT2C: T316S

PubMed Link: 32140530

Variant Present in the following documents:

• Main text
• main.pdf

View BVdb publication page

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Somatic mutation driven codon transition bias in human cancer.

Scientific Reports

Son, Hyeonju H; Kang, Hyundeok H; Kim, Hyun Seok HS; Kim, Sangwoo S

Publication Date: 2017-10-27

Variant appearance in text: MLL3: T316S

PubMed Link: 29079855

Variant Present in the following documents:

• Main text
• 41598_2017_Article_14543.pdf

View BVdb publication page

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Codon-level co-occurrences of germline variants and somatic mutations in cancer are rare but often lead to incorrect variant annotation and underestimated impact prediction.

Plos One

Koire, Amanda A; Kim, Young Won YW; Wang, Jarey J; Katsonis, Panagiotis P; Jin, Haijing H; Lichtarge, Olivier O

Publication Date: 2017

Variant appearance in text: MLL3: T316S

PubMed Link: 28350864

Variant Present in the following documents:

• Main text
• pone.0174766.s004.xlsx, sheet 1
• pone.0174766.pdf

View BVdb publication page

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NF1-mutated melanoma tumors harbor distinct clinical and biological characteristics.

Molecular Oncology

Cirenajwis, Helena H; Lauss, Martin M; Ekedahl, Henrik H; Törngren, Therese T; Kvist, Anders A; Saal, Lao H LH; Olsson, Håkan H; Staaf, Johan J; Carneiro, Ana A; Ingvar, Christian C; Harbst, Katja K; Hayward, Nicholas K NK; Jönsson, Göran G

Publication Date: 2017-04

Variant appearance in text: MLL3: 947C>G

PubMed Link: 28267273

Variant Present in the following documents:

• MOL2-11-438-s003.xls, sheet 1

View BVdb publication page

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Recurrent inactivating RASA2 mutations in melanoma.

Nature Genetics

Arafeh, Rand R; Qutob, Nouar N; Emmanuel, Rafi R; Keren-Paz, Alona A; Madore, Jason J; Elkahloun, Abdel A; Wilmott, James S JS; Gartner, Jared J JJ; Di Pizio, Antonella A; Winograd-Katz, Sabina S; Sindiri, Sivasish S; Rotkopf, Ron R; Dutton-Regester, Ken K; Johansson, Peter P; Pritchard, Antonia L AL; Waddell, Nicola N; Hill, Victoria K VK; Lin, Jimmy C JC; Hevroni, Yael Y; Rosenberg, Steven A SA; Khan, Javed J; Ben-Dor, Shifra S; Niv, Masha Y MY; Ulitsky, Igor I; Mann, Graham J GJ; Scolyer, Richard A RA; Hayward, Nicholas K NK; Samuels, Yardena Y

Publication Date: 2015-12

Variant appearance in text: MLL3: 947C>G

PubMed Link: 26502337

Variant Present in the following documents:

• NIHMS65345-supplement-Supplementary_table_1.xlsx, sheet 1

View BVdb publication page

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Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

Oncotarget

Munchel, Sarah S; Hoang, Yen Y; Zhao, Yue Y; Cottrell, Joseph J; Klotzle, Brandy B; Godwin, Andrew K AK; Koestler, Devin D; Beyerlein, Peter P; Fan, Jian-Bing JB; Bibikova, Marina M; Chien, Jeremy J

Publication Date: 2015-09-22

Variant appearance in text: MLL3: T316S

PubMed Link: 26305677

Variant Present in the following documents:

• Main text
• oncotarget-06-25943.pdf

View BVdb publication page

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Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes.

Oncotarget

Keerthikumar, Shivakumar S; Gangoda, Lahiru L; Liem, Michael M; Fonseka, Pamali P; Atukorala, Ishara I; Ozcitti, Cemil C; Mechler, Adam A; Adda, Christopher G CG; Ang, Ching-Seng CS; Mathivanan, Suresh S

Publication Date: 2015-06-20

Variant appearance in text: MLL3: T316S

PubMed Link: 25944692

Variant Present in the following documents:

• oncotarget-06-15375-s005.xlsx, sheet 2

View BVdb publication page

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XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine.

Plos One

Talukder, Asoke K AK; Ravishankar, Shashidhar S; Sasmal, Krittika K; Gandham, Santhosh S; Prabhukumar, Jyothsna J; Achutharao, Prahalad H PH; Barh, Debmalya D; Blasi, Francesco F

Publication Date: 2015

Variant appearance in text: KMT2C: T316S

PubMed Link: 25905921

Variant Present in the following documents:

• pone.0123569.s008.xls, sheet 5
• pone.0123569.s008.xls, 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: MLL3: T316S

PubMed Link: 25887915

Variant Present in the following documents:

• 12864_2015_1290_MOESM7_ESM.xlsx, sheet 1

View BVdb publication page

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Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS.

Scientific Reports

Steinberg, Karyn Meltz KM; Yu, Bing B; Koboldt, Daniel C DC; Mardis, Elaine R ER; Pamphlett, Roger R

Publication Date: 2015-03-16

Variant appearance in text: MLL3: T316S

PubMed Link: 25773295

Variant Present in the following documents:

• srep09124-s3.xls, sheet 1

View BVdb publication page

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A highly recurrent RPS27 5'UTR mutation in melanoma.

Oncotarget

Dutton-Regester, Ken K; Gartner, Jared J JJ; Emmanuel, Rafi R; Qutob, Nouar N; Davies, Michael A MA; Gershenwald, Jeffrey E JE; Robinson, William W; Robinson, Steven S; Rosenberg, Steven A SA; Scolyer, Richard A RA; Mann, Graham J GJ; Thompson, John F JF; Hayward, Nicholas K NK; Samuels, Yardena Y

Publication Date: 2014-05-30

Variant appearance in text: MLL3: 947C>G

PubMed Link: 24913145

Variant Present in the following documents:

• oncotarget-05-2912-s003.xlsx, sheet 1

View BVdb publication page

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