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: PRX: P1083R

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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Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes.

Nature Communications

Li, Lingling L; Jiang, Dongxian D; Liu, Hui H; Guo, Chunmei C; Zhao, Rui R; Zhang, Qiao Q; Xu, Chen C; Qin, Zhaoyu Z; Feng, Jinwen J; Liu, Yang Y; Wang, Haixing H; Chen, Weijie W; Zhang, Xue X; Li, Bin B; Bai, Lin L; Tian, Sha S; Tan, Subei S; Yu, Zixiang Z; Chen, Lingli L; Huang, Jie J; Zhao, Jian-Yuan JY; Hou, Yingyong Y; Ding, Chen C

Publication Date: 2023-03-29

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 36991000

Variant Present in the following documents:

• 41467_2023_37221_MOESM5_ESM.xlsx, sheet 3

View BVdb publication page

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Next-generation whole exome sequencing to delineate the genetic basis of primary congenital glaucoma.

Scientific Reports

Rauf, Bushra B; Khan, Shahid Y SY; Jiao, Xiaodong X; Irum, Bushra B; Ashfaq, Ramla R; Zehra, Mubashra M; Khan, Asma A AA; Naeem, Muhammad Asif MA; Shahzad, Mohsin M; Riazuddin, Sheikh S; Hejtmancik, J Fielding JF; Riazuddin, S Amer SA

Publication Date: 2022-10-14

Variant appearance in text: PRX: P1083R

PubMed Link: 36241656

Variant Present in the following documents:

• 41598_2022_20939_MOESM6_ESM.xlsx, sheet 2
• 41598_2022_20939_MOESM12_ESM.xlsx, sheet 2
• 41598_2022_20939_MOESM13_ESM.xlsx, sheet 2

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A genomic deletion encompassing CRYBB2-CRYBB2P1 is responsible for autosomal recessive congenital cataracts.

Human Genome Variation

Irum, Bushra B; Kabir, Firoz F; Shoshany, Nadav N; Khan, Shahid Y SY; Rauf, Bushra B; Naeem, Muhammad Asif MA; Qaiser, Tanveer A TA; Riazuddin, Sheikh S; Hejtmancik, J Fielding JF; Riazuddin, S Amer SA

Publication Date: 2022-09-08

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 36075891

Variant Present in the following documents:

• 41439_2022_208_MOESM5_ESM.xlsx, sheet 2

View BVdb publication page

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Genomic, transcriptomic, and metabolomic profiles of hiPSC-derived dopamine neurons from clinically discordant brothers with identical PRKN deletions.

Npj Parkinson'S Disease

Cukier, Holly N HN; Kim, Hyunjin H; Griswold, Anthony J AJ; Codreanu, Simona G SG; Prince, Lisa M LM; Sherrod, Stacy D SD; McLean, John A JA; Dykxhoorn, Derek M DM; Ess, Kevin C KC; Hedera, Peter P; Bowman, Aaron B AB; Neely, M Diana MD

Publication Date: 2022-06-29

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 35768426

Variant Present in the following documents:

• 41531_2022_346_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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Correction: Raasakka, A.; Kursula, P. Flexible Players within the Sheaths: The Intrinsically Disordered Proteins of Myelin in Health and Disease. Cells 2020, 9, 470.

Cells

Raasakka, Arne A; Kursula, Petri P

Publication Date: 2022-02-14

Variant appearance in text: PRX: P1083R

PubMed Link: 35203407

Variant Present in the following documents:

• Main text
• cells-11-00662.pdf

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: PRX: P1083R; rs3745202

PubMed Link: 34673281

Variant Present in the following documents:

• mmc2.xlsx, sheet 11
• mmc2.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

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 34673281

Variant Present in the following documents:

• mmc2.xlsx, sheet 3
• mmc2.xlsx, sheet 11

View BVdb publication page

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Case Report: A Variant Non-ketotic Hyperglycinemia With GLRX5 Mutations: Manifestation of Deficiency of Activities of the Respiratory Chain Enzymes.

Frontiers In Genetics

Feng, Wei-Xing WX; Zhuo, Xiu-Wei XW; Liu, Zhi-Mei ZM; Li, Jiu-Wei JW; Zhang, Wei-Hua WH; Wu, Yun Y; Han, Tong-Li TL; Fang, Fang F

Publication Date: 2021

Variant appearance in text: PRX: 3248C>G; P1083R; rs3745202

PubMed Link: 34054912

Variant Present in the following documents:

• Table_2.xlsx, sheet 1

View BVdb publication page

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Prioritization of candidate genes for a South African family with Parkinson's disease using in-silico tools.

Plos One

Sebate, Boiketlo B; Cuttler, Katelyn K; Cloete, Ruben R; Britz, Marcell M; Christoffels, Alan A; Williams, Monique M; Carr, Jonathan J; Bardien, Soraya S

Publication Date: 2021

Variant appearance in text: PRX: 3248C>G; P1083R; rs3745202

PubMed Link: 33770142

Variant Present in the following documents:

• pone.0249324.s003.xlsx, sheet 3

View BVdb publication page

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Identification of a nonsense mutation in TNNI3K associated with cardiac conduction disease.

Journal Of Clinical Laboratory Analysis

Liu, Jiang J; Liu, Da D; Li, Muzheng M; Wu, Keke K; Liu, Na N; Zhao, Chenyu C; Shi, Xiaoliu X; Liu, Qiming Q

Publication Date: 2020-09

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 32529721

Variant Present in the following documents:

• JCLA-34-e23418-s003.xls, sheet 1

View BVdb publication page

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Flexible Players within the Sheaths: The Intrinsically Disordered Proteins of Myelin in Health and Disease.

Cells

Raasakka, Arne A; Kursula, Petri P

Publication Date: 2020-02-18

Variant appearance in text: PRX: P1083R

PubMed Link: 32085570

Variant Present in the following documents:

• Main text
• cells-09-00470.pdf

View BVdb publication page

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YAP1 mediates survival of ALK-rearranged lung cancer cells treated with alectinib via pro-apoptotic protein regulation.

Nature Communications

Tsuji, Takahiro T; Ozasa, Hiroaki H; Aoki, Wataru W; Aburaya, Shunsuke S; Yamamoto Funazo, Tomoko T; Furugaki, Koh K; Yoshimura, Yasushi Y; Yamazoe, Masatoshi M; Ajimizu, Hitomi H; Yasuda, Yuto Y; Nomizo, Takashi T; Yoshida, Hironori H; Sakamori, Yuichi Y; Wake, Hiroaki H; Ueda, Mitsuyoshi M; Kim, Young Hak YH; Hirai, Toyohiro T

Publication Date: 2020-01-03

Variant appearance in text: PRX: P1083R

PubMed Link: 31900393

Variant Present in the following documents:

• 41467_2019_13771_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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Genome landscapes of rectal cancer before and after preoperative chemoradiotherapy.

Theranostics

Yang, Jie J; Lin, Yuan Y; Huang, Ying Y; Jin, Jing J; Zou, Shuangmei S; Zhang, Xiaolong X; Li, Hongmin H; Feng, Ting T; Chen, Jinna J; Zuo, Zhixiang Z; Zheng, Jian J; Li, Yexiong Y; Gao, Ge G; Wu, Chen C; Tan, Wen W; Lin, Dongxin D

Publication Date: 2019

Variant appearance in text: PRX: P1083R

PubMed Link: 31660073

Variant Present in the following documents:

• thnov09p6856s2.xlsx, sheet 7

View BVdb publication page

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PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations.

Genome Biology

Zhang, Chao C; Gao, Yang Y; Ning, Zhilin Z; Lu, Yan Y; Zhang, Xiaoxi X; Liu, Jiaojiao J; Xie, Bo B; Xue, Zhe Z; Wang, Xiaoji X; Yuan, Kai K; Ge, Xueling X; Pan, Yuwen Y; Liu, Chang C; Tian, Lei L; Wang, Yuchen Y; Lu, Dongsheng D; Hoh, Boon-Peng BP; Xu, Shuhua S

Publication Date: 2019-10-22

Variant appearance in text: PRX: 3248C>G; Pro1083Arg; rs3745202

PubMed Link: 31640808

Variant Present in the following documents:

• 13059_2019_1838_MOESM3_ESM.xlsx, sheet 1

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: PRX: P1083R; rs3745202

PubMed Link: 31597922

Variant Present in the following documents:

• 41598_2019_50891_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Database : The Journal Of Biological Databases And Curation

Famiglietti, M L ML; Estreicher, A A; Breuza, L L; Poux, S S; Redaschi, N N; Xenarios, I I; Bridge, A A; ,

Publication Date: 2019-01-01

Variant appearance in text: PRX: 3248C>G; Pro1083Arg

PubMed Link: 30937429

Variant Present in the following documents:

• famiglietti_supplementarytables1_rev_baz040.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: PRX: P1083R; rs3745202

PubMed Link: 30894629

Variant Present in the following documents:

• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 9
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 11
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 13
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 5

View BVdb publication page

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Multiple genetic mutations caused by NKX6.3 depletion contribute to gastric tumorigenesis.

Scientific Reports

Yoon, Jung Hwan JH; Kim, Olga O; Eun, Jung Woo JW; Choi, Sung Sook SS; Ashktorab, Hassan H; Smoot, Duane T DT; Nam, Suk Woo SW; Park, Won Sang WS

Publication Date: 2018-12-04

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 30514953

Variant Present in the following documents:

• 41598_2018_35733_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family.

Scientific Reports

Khan, Muhammad Jaseem MJ; Pollock, Nijole N; Jiang, Huaiyang H; Castro, Carlos C; Nazli, Rubina R; Ahmed, Jawad J; Basit, Sulman S; Rajkovic, Aleksandar A; Yatsenko, Alexander N AN

Publication Date: 2018-11-02

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 30389958

Variant Present in the following documents:

• 41598_2018_34262_MOESM2_ESM.xlsx, sheet 2

View BVdb publication page

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Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants.

Oncotarget

Miller, Eirwen M EM; Patterson, Nicole E NE; Zechmeister, Jenna Marcus JM; Bejerano-Sagie, Michal M; Delio, Maria M; Patel, Kunjan K; Ravi, Nivedita N; Quispe-Tintaya, Wilber W; Maslov, Alexander A; Simmons, Nichelle N; Castaldi, Maria M; Vijg, Jan J; Karabakhtsian, Rouzan G RG; Greally, John M JM; Kuo, Dennis Y S DYS; Montagna, Cristina C

Publication Date: 2017-11-24

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 29254223

Variant Present in the following documents:

• oncotarget-08-102033-s003.xlsx, sheet 1

View BVdb publication page

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Sources of discordance among germ-line variant classifications in ClinVar.

Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Yang, Shan S; Lincoln, Stephen E SE; Kobayashi, Yuya Y; Nykamp, Keith K; Nussbaum, Robert L RL; Topper, Scott S

Publication Date: 2017-10

Variant appearance in text: PRX: 3248C>G; Pro1083Arg

PubMed Link: 28569743

Variant Present in the following documents:

• gim201760x7.xlsx, sheet 2

View BVdb publication page

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Three-dimensional modelling identifies novel genetic dependencies associated with breast cancer progression in the isogenic MCF10 model.

The Journal Of Pathology

Maguire, Sarah L SL; Peck, Barrie B; Wai, Patty T PT; Campbell, James J; Barker, Holly H; Gulati, Aditi A; Daley, Frances F; Vyse, Simon S; Huang, Paul P; Lord, Christopher J CJ; Farnie, Gillian G; Brennan, Keith K; Natrajan, Rachael R

Publication Date: 2016-11

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 27512948

Variant Present in the following documents:

• PATH-240-315-s015.xlsx, sheet 1

View BVdb publication page

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Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations.

Plos One

Holehouse, Alex S AS; Naegle, Kristen M KM

Publication Date: 2015

Variant appearance in text: rs3745202

PubMed Link: 26659599

Variant Present in the following documents:

• pone.0144692.s002.xlsx, sheet 1

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: PRX: P1083R; rs3745202

PubMed Link: 25944692

Variant Present in the following documents:

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

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: PRX: P1083R; rs3745202

PubMed Link: 25390934

Variant Present in the following documents:

• pone.0112430.s004.xlsx, sheet 1

View BVdb publication page

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NCI-60 whole exome sequencing and pharmacological CellMiner analyses.

Plos One

Reinhold, William C WC; Varma, Sudhir S; Sousa, Fabricio F; Sunshine, Margot M; Abaan, Ogan D OD; Davis, Sean R SR; Reinhold, Spencer W SW; Kohn, Kurt W KW; Morris, Joel J; Meltzer, Paul S PS; Doroshow, James H JH; Pommier, Yves Y

Publication Date: 2014

Variant appearance in text: rs3745202

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

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Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases.

Nucleic Acids Research

Ryu, Gil-Mi GM; Song, Pamela P; Kim, Kyu-Won KW; Oh, Kyung-Soo KS; Park, Keun-Joon KJ; Kim, Jong Hun JH

Publication Date: 2009-03

Variant appearance in text: PRX: P1083R; rs3745202

PubMed Link: 19139070

Variant Present in the following documents:

• gkn1008_nar-01723-s-2008-File009.xls, sheet 5

View BVdb publication page

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Periaxin mutations cause recessive Dejerine-Sottas neuropathy.

American Journal Of Human Genetics

Boerkoel, C F CF; Takashima, H H; Stankiewicz, P P; Garcia, C A CA; Leber, S M SM; Rhee-Morris, L L; Lupski, J R JR

Publication Date: 2001-02

Variant appearance in text: PRX: P1083R

PubMed Link: 11133365

Variant Present in the following documents:

• Main text

View BVdb publication page

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