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: RPA1: T351A

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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SMAP is a pipeline for sample matching in proteogenomics.

Nature Communications

Li, Ling L; Niu, Mingming M; Erickson, Alyssa A; Luo, Jie J; Rowbotham, Kincaid K; Guo, Kai K; Huang, He H; Li, Yuxin Y; Jiang, Yi Y; Hur, Junguk J; Liu, Chunyu C; Peng, Junmin J; Wang, Xusheng X

Publication Date: 2022-02-08

Variant appearance in text: RPA1: T351A

PubMed Link: 35136070

Variant Present in the following documents:

• 41467_2022_28411_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

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Validation of Genetic Markers Associated with Survival in Colorectal Cancer Patients Treated with Oxaliplatin-Based Chemotherapy.

Cancer Epidemiology, Biomarkers & Prevention : A Publication Of The American Association For Cancer Research, Cosponsored By The American Society Of Preventive Oncology

Park, Hanla A HA; Seibold, Petra P; Edelmann, Dominic D; Benner, Axel A; Canzian, Federico F; Alwers, Elizabeth E; Jansen, Lina L; Schneider, Martin M; Hoffmeister, Michael M; Brenner, Hermann H; Chang-Claude, Jenny J

Publication Date: 2022-02

Variant appearance in text: rs5030755

PubMed Link: 34862210

Variant Present in the following documents:

• Main text
• 268527_2_supp_7525223_r2sknd.pdf
• 352.pdf

View BVdb publication page

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Polygenic basis and biomedical consequences of telomere length variation.

Nature Genetics

Codd, Veryan V; Wang, Qingning Q; Allara, Elias E; Musicha, Crispin C; Kaptoge, Stephen S; Stoma, Svetlana S; Jiang, Tao T; Hamby, Stephen E SE; Braund, Peter S PS; Bountziouka, Vasiliki V; Budgeon, Charley A CA; Denniff, Matthew M; Swinfield, Chloe C; Papakonstantinou, Manolo M; Sheth, Shilpi S; Nanus, Dominika E DE; Warner, Sophie C SC; Wang, Minxian M; Khera, Amit V AV; Eales, James J; Ouwehand, Willem H WH; Thompson, John R JR; Di Angelantonio, Emanuele E; Wood, Angela M AM; Butterworth, Adam S AS; Danesh, John N JN; Nelson, Christopher P CP; Samani, Nilesh J NJ

Publication Date: 2021-10

Variant appearance in text: rs5030755

PubMed Link: 34611362

Variant Present in the following documents:

• 41588_2021_944_MOESM3_ESM.pdf

View BVdb publication page

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Polygenic basis and biomedical consequences of telomere length variation.

Nature Genetics

Codd, Veryan V; Wang, Qingning Q; Allara, Elias E; Musicha, Crispin C; Kaptoge, Stephen S; Stoma, Svetlana S; Jiang, Tao T; Hamby, Stephen E SE; Braund, Peter S PS; Bountziouka, Vasiliki V; Budgeon, Charley A CA; Denniff, Matthew M; Swinfield, Chloe C; Papakonstantinou, Manolo M; Sheth, Shilpi S; Nanus, Dominika E DE; Warner, Sophie C SC; Wang, Minxian M; Khera, Amit V AV; Eales, James J; Ouwehand, Willem H WH; Thompson, John R JR; Di Angelantonio, Emanuele E; Wood, Angela M AM; Butterworth, Adam S AS; Danesh, John N JN; Nelson, Christopher P CP; Samani, Nilesh J NJ

Publication Date: 2021-10

Variant appearance in text: rs5030755

PubMed Link: 34611362

Variant Present in the following documents:

• 41588_2021_944_MOESM3_ESM.pdf

View BVdb publication page

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Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Cell

Krug, Karsten K; Jaehnig, Eric J EJ; Satpathy, Shankha S; Blumenberg, Lili L; Karpova, Alla A; Anurag, Meenakshi M; Miles, George G; Mertins, Philipp P; Geffen, Yifat Y; Tang, Lauren C LC; Heiman, David I DI; Cao, Song S; Maruvka, Yosef E YE; Lei, Jonathan T JT; Huang, Chen C; Kothadia, Ramani B RB; Colaprico, Antonio A; Birger, Chet C; Wang, Jarey J; Dou, Yongchao Y; Wen, Bo B; Shi, Zhiao Z; Liao, Yuxing Y; Wiznerowicz, Maciej M; Wyczalkowski, Matthew A MA; Chen, Xi Steven XS; Kennedy, Jacob J JJ; Paulovich, Amanda G AG; Thiagarajan, Mathangi M; Kinsinger, Christopher R CR; Hiltke, Tara T; Boja, Emily S ES; Mesri, Mehdi M; Robles, Ana I AI; Rodriguez, Henry H; Westbrook, Thomas F TF; Ding, Li L; Getz, Gad G; Clauser, Karl R KR; Fenyö, David D; Ruggles, Kelly V KV; Zhang, Bing B; Mani, D R DR; Carr, Steven A SA; Ellis, Matthew J MJ; Gillette, Michael A MA; ,

Publication Date: 2020-11-25

Variant appearance in text: RPA1: T351A

PubMed Link: 33212010

Variant Present in the following documents:

• NIHMS1687926-supplement-Supplemental_Table_3.xlsx, sheet 5

View BVdb publication page

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Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities.

Nature Communications

Nichols, Caitlin A CA; Gibson, William J WJ; Brown, Meredith S MS; Kosmicki, Jack A JA; Busanovich, John P JP; Wei, Hope H; Urbanski, Laura M LM; Curimjee, Naomi N; Berger, Ashton C AC; Gao, Galen F GF; Cherniack, Andrew D AD; Dhe-Paganon, Sirano S; Paolella, Brenton R BR; Beroukhim, Rameen R

Publication Date: 2020-05-20

Variant appearance in text: RPA1: 1051A>G; Thr351Ala; rs5030755

PubMed Link: 32433464

Variant Present in the following documents:

• 41467_2020_16399_MOESM7_ESM.xlsx, sheet 1
• 41467_2020_16399_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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Somatic mutations in the DNA repairome in prostate cancers in African Americans and Caucasians.

Oncogene

Yadav, Santosh S; Anbalagan, Muralidharan M; Baddoo, Melody M; Chellamuthu, Vinodh K VK; Mukhopadhyay, Sudurika S; Woods, Carol C; Jiang, Wei W; Moroz, Krzysztof K; Flemington, Erik K EK; Makridakis, Nick N

Publication Date: 2020-05

Variant appearance in text: RPA1: T351A; rs5030755

PubMed Link: 32300177

Variant Present in the following documents:

• 41388_2020_1280_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.

Nature Communications

Wen, Bo B; Li, Kai K; Zhang, Yun Y; Zhang, Bing B

Publication Date: 2020-04-09

Variant appearance in text: RPA1: T351A

PubMed Link: 32273506

Variant Present in the following documents:

• 41467_2020_15456_MOESM6_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: RPA1: T351A; rs5030755

PubMed Link: 30894629

Variant Present in the following documents:

• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 4
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 3
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 6

View BVdb publication page

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Functional Polymorphisms in DNA Repair Genes Are Associated with Sporadic Colorectal Cancer Susceptibility and Clinical Outcome.

International Journal Of Molecular Sciences

Jiraskova, Katerina K; Hughes, David J DJ; Brezina, Stefanie S; Gumpenberger, Tanja T; Veskrnova, Veronika V; Buchler, Tomas T; Schneiderova, Michaela M; Levy, Miroslav M; Liska, Vaclav V; Vodenkova, Sona S; Di Gaetano, Cornelia C; Naccarati, Alessio A; Pardini, Barbara B; Vymetalkova, Veronika V; Gsur, Andrea A; Vodicka, Pavel P

Publication Date: 2018-12-27

Variant appearance in text: RPA1: Thr351Ala; rs5030755

PubMed Link: 30591675

Variant Present in the following documents:

• Main text
• ijms-20-00097.pdf

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: RPA1: T351A; rs5030755

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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Multi-OMICS analyses unveil STAT1 as a potential modifier gene in mevalonate kinase deficiency.

Annals Of The Rheumatic Diseases

Carapito, Raphael R; Carapito, Christine C; Morlon, Aurore A; Paul, Nicodème N; Vaca Jacome, Alvaro Sebastian AS; Alsaleh, Ghada G; Rolli, Véronique V; Tahar, Ouria O; Aouadi, Ismail I; Rompais, Magali M; Delalande, François F; Pichot, Angélique A; Georgel, Philippe P; Messer, Laurent L; Sibilia, Jean J; Cianferani, Sarah S; Van Dorsselaer, Alain A; Bahram, Seiamak S

Publication Date: 2018-11

Variant appearance in text: RPA1: T351A; rs5030755

PubMed Link: 30030262

Variant Present in the following documents:

• annrheumdis-2018-213524supp002.xlsx, sheet 1

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: RPA1: T351A; rs5030755

PubMed Link: 29254223

Variant Present in the following documents:

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

View BVdb publication page

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Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.

Oncotarget

Ma, Shiyong S; Menon, Ranjeeta R; Poulos, Rebecca C RC; Wong, Jason W H JWH

Publication Date: 2017-11-10

Variant appearance in text: RPA1: T351A; rs5030755

PubMed Link: 29221171

Variant Present in the following documents:

• oncotarget-08-95841-s002.xlsx, sheet 1
• oncotarget-08-95841-s002.xlsx, sheet 4

View BVdb publication page

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Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines.

Genome Medicine

Alfaro, Javier A JA; Ignatchenko, Alexandr A; Ignatchenko, Vladimir V; Sinha, Ankit A; Boutros, Paul C PC; Kislinger, Thomas T

Publication Date: 2017-07-18

Variant appearance in text: RPA1: T351A; rs5030755

PubMed Link: 28716134

Variant Present in the following documents:

• 13073_2017_454_MOESM7_ESM.xlsx, sheet 1
• 13073_2017_454_MOESM6_ESM.xlsx, sheet 1

View BVdb publication page

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Proteogenomics connects somatic mutations to signalling in breast cancer.

Nature

Mertins, Philipp P; Mani, D R DR; Ruggles, Kelly V KV; Gillette, Michael A MA; Clauser, Karl R KR; Wang, Pei P; Wang, Xianlong X; Qiao, Jana W JW; Cao, Song S; Petralia, Francesca F; Kawaler, Emily E; Mundt, Filip F; Krug, Karsten K; Tu, Zhidong Z; Lei, Jonathan T JT; Gatza, Michael L ML; Wilkerson, Matthew M; Perou, Charles M CM; Yellapantula, Venkata V; Huang, Kuan-lin KL; Lin, Chenwei C; McLellan, Michael D MD; Yan, Ping P; Davies, Sherri R SR; Townsend, R Reid RR; Skates, Steven J SJ; Wang, Jing J; Zhang, Bing B; Kinsinger, Christopher R CR; Mesri, Mehdi M; Rodriguez, Henry H; Ding, Li L; Paulovich, Amanda G AG; Fenyö, David D; Ellis, Matthew J MJ; Carr, Steven A SA; ,

Publication Date: 2016-06-02

Variant appearance in text: RPA1: T351A; rs5030755

PubMed Link: 27251275

Variant Present in the following documents:

• NIHMS778057-supplement-supp_table5.xlsx, sheet 2

View BVdb publication page

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A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia.

Cold Spring Harbor Molecular Case Studies

Lu, Charles C; Riedell, Peter P; Miller, Christopher A CA; Hagemann, Ian S IS; Westervelt, Peter P; Ozenberger, Bradley A BA; O'Laughlin, Michelle M; Magrini, Vincent V; Demeter, Ryan T RT; Duncavage, Eric J EJ; Griffith, Malachi M; Griffith, Obi L OL; Wartman, Lukas D LD

Publication Date: 2016-01

Variant appearance in text: RPA1: T351A; rs5030755

PubMed Link: 27148581

Variant Present in the following documents:

• supp_2.1.a000687_Supp_Table_2.xlsx, sheet 1

View BVdb publication page

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Targeted next-generation sequencing of 22 mismatch repair genes identifies Lynch syndrome families.

Cancer Medicine

Talseth-Palmer, Bente A BA; Bauer, Denis C DC; Sjursen, Wenche W; Evans, Tiffany J TJ; McPhillips, Mary M; Proietto, Anthony A; Otton, Geoffrey G; Spigelman, Allan D AD; Scott, Rodney J RJ

Publication Date: 2016-05

Variant appearance in text: RPA1: 1051A>G; Thr351Ala

PubMed Link: 26811195

Variant Present in the following documents:

• Main text
• CAM4-5-929.pdf

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: rs5030755

PubMed Link: 26659599

Variant Present in the following documents:

• pone.0144692.s002.xlsx, sheet 1

View BVdb publication page

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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: RPA1: T351A

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, 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: RPA1: T351A; rs5030755

PubMed Link: 25390934

Variant Present in the following documents:

• pone.0112430.s004.xlsx, sheet 1

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: RPA1: T351A; rs5030755

PubMed Link: 25352556

Variant Present in the following documents:

• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 8
• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 14

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: RPA1: T351A; rs5030755

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

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Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations.

Nature Genetics

Buczkowicz, Pawel P; Hoeman, Christine C; Rakopoulos, Patricia P; Pajovic, Sanja S; Letourneau, Louis L; Dzamba, Misko M; Morrison, Andrew A; Lewis, Peter P; Bouffet, Eric E; Bartels, Ute U; Zuccaro, Jennifer J; Agnihotri, Sameer S; Ryall, Scott S; Barszczyk, Mark M; Chornenkyy, Yevgen Y; Bourgey, Mathieu M; Bourque, Guillaume G; Montpetit, Alexandre A; Cordero, Francisco F; Castelo-Branco, Pedro P; Mangerel, Joshua J; Tabori, Uri U; Ho, King Ching KC; Huang, Annie A; Taylor, Kathryn R KR; Mackay, Alan A; Bendel, Anne E AE; Nazarian, Javad J; Fangusaro, Jason R JR; Karajannis, Matthias A MA; Zagzag, David D; Foreman, Nicholas K NK; Donson, Andrew A; Hegert, Julia V JV; Smith, Amy A; Chan, Jennifer J; Lafay-Cousin, Lucy L; Dunn, Sandra S; Hukin, Juliette J; Dunham, Chris C; Scheinemann, Katrin K; Michaud, Jean J; Zelcer, Shayna S; Ramsay, David D; Cain, Jason J; Brennan, Cameron C; Souweidane, Mark M MM; Jones, Chris C; Allis, C David CD; Brudno, Michael M; Becher, Oren O; Hawkins, Cynthia C

Publication Date: 2014-05

Variant appearance in text: RPA1: T351A

PubMed Link: 24705254

Variant Present in the following documents:

• NIHMS4215-supplement-10.xlsx, sheet 2

View BVdb publication page

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