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
Personalized Medicine in Infant Population with Cancer: Pharmacogenetic Pilot Study of Polymorphisms Related to Toxicity and Response to Chemotherapy.
Cancers
Urtasun, Andrea A; Olivera, Gladys G GG; Sendra, Luis L; Aliño, Salvador F SF; Berlanga, Pablo P; Gargallo, Pablo P; Hervás, David D; Balaguer, Julia J; Juan-Ribelles, Antonio A; Andrés, María Del Mar MDM; Cañete, Adela A; Herrero, María José MJ
Network expansion of genetic associations defines a pleiotropy map of human cell biology.
Nature Genetics
Barrio-Hernandez, Inigo I; Schwartzentruber, Jeremy J; Shrivastava, Anjali A; Del-Toro, Noemi N; Gonzalez, Asier A; Zhang, Qian Q; Mountjoy, Edward E; Suveges, Daniel D; Ochoa, David D; Ghoussaini, Maya M; Bradley, Glyn G; Hermjakob, Henning H; Orchard, Sandra S; Dunham, Ian I; Anderson, Carl A CA; Porras, Pablo P; Beltrao, Pedro P
Publication Date: 2023-02-23
Variant appearance in text: UMPS: 638G>C; Gly213Ala
Beneficial effects of mifepristone treatment in breast cancer patients selected by the progesterone receptor isoform ratio: Results from the MIPRA trial.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Elía, Andrés A; Saldain, Leo L; Vanzulli, Silvia I SI; Helguero, Luisa A LA; Lamb, Caroline A CA; Fabris, Victoria V; Pataccini, Gabriela G; Martínez-Vazquez, Paula P; Burruchaga, Javier J; Caillet-Bois, Ines I; Spengler, Eunice E; Acosta Haab, Gabriela G; Liguori, Marcos M; Castets, Alejandra A; Lovisi, Silvia S; Abascal, María F MF; Novaro, Virginia V; Sánchez, Jana J; Muñoz, Javier J; Belizán, Jose M JM; Abba, Martín C MC; Gass, Hugo H; Rojas, Paola P; Lanari, Claudia C
Publication Date: 2022-10-21
Variant appearance in text: UMPS: 638G>C; Gly213Ala; rs1801019
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
Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Xia, Youli Y; He, Xiaping X; Renshaw, Lorna L; Martinez-Perez, Carlos C; Kay, Charlene C; Gray, Mark M; Meehan, James J; Parker, Joel S JS; Perou, Charles M CM; Carey, Lisa A LA; Dixon, J Michael JM; Turnbull, Arran A
Publication Date: 2022-08-15
Variant appearance in text: UMPS: G213A; rs1801019
Pharmacogenetics implementation in the clinics: information and guidelines for germline variants.
Cancer Drug Resistance (Alhambra, Calif.)
Olivera, Gladys G; Sendra, Luis L; Herrero, María José MJ; Berlanga, Pablo P; Gargallo, Pablo P; Yáñez, Yania Y; Urtasun, Andrea A; de Mora, Jaime Font JF; Castel, Victoria V; Cañete, Adela A; Aliño, Salvador F SF
Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels.
Metabolites
Hysi, Pirro G PG; Mangino, Massimo M; Christofidou, Paraskevi P; Falchi, Mario M; Karoly, Edward D ED; Nihr Bioresource Investigators, ; Mohney, Robert P RP; Valdes, Ana M AM; Spector, Tim D TD; Menni, Cristina C
Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels.
Metabolites
Hysi, Pirro G PG; Mangino, Massimo M; Christofidou, Paraskevi P; Falchi, Mario M; Karoly, Edward D ED; Nihr Bioresource Investigators, ; Mohney, Robert P RP; Valdes, Ana M AM; Spector, Tim D TD; Menni, Cristina C
A case-control study of a combination of single nucleotide polymorphisms and clinical parameters to predict clinically relevant toxicity associated with fluoropyrimidine and platinum-based chemotherapy in gastric cancer.
Bmc Cancer
Cordova-Delgado, Miguel M; Bravo, María Loreto ML; Cumsille, Elisa E; Hill, Charlotte N CN; Muñoz-Medel, Matías M; Pinto, Mauricio P MP; Retamal, Ignacio N IN; Lavanderos, María A MA; Miquel, Juan Francisco JF; Rodriguez-Fernandez, Maria M; Liao, Yuwei Y; Li, Zhiguang Z; Corvalán, Alejandro H AH; Armisén, Ricardo R; Garrido, Marcelo M; Quiñones, Luis A LA; Owen, Gareth I GI
Publication Date: 2021-09-16
Variant appearance in text: UMPS: G213A; rs1801019
Genetic analysis of sinonasal undifferentiated carcinoma discovers recurrent SWI/SNF alterations and a novel PGAP3-SRPK1 fusion gene.
Bmc Cancer
Heft Neal, Molly E ME; Birkeland, Andrew C AC; Bhangale, Apurva D AD; Zhai, Jingyi J; Kulkarni, Aditi A; Foltin, Susan K SK; Jewell, Brittany M BM; Ludwig, Megan L ML; Pinatti, Lisa L; Jiang, Hui H; McHugh, Jonathan B JB; Marentette, Lawence L; McKean, Erin L EL; Brenner, J Chad JC
Publication Date: 2021-05-29
Variant appearance in text: UMPS: 638G>C; Gly213Ala; rs1801019
Polymorphisms in the CYP2A6 and ABCC4 genes are associated with a protective effect on chronic myeloid leukemia in the Brazilian Amazon population.
Molecular Genetics & Genomic Medicine
Monte, Natasha N; Pantoja, Karla B C C KBCC; Rodrigues, Juliana C G JCG; de Carvalho, Darlen C DC; Azevedo, Tereza C B TCB; Pereira, Esdras E B EEB; de Assumpção, Paulo P PP; Dos Santos, Sidney E B SEB; Fernandes, Marianne R MR; Dos Santos, Ney P C NPC
Polymorphisms in the CYP2A6 and ABCC4 genes are associated with a protective effect on chronic myeloid leukemia in the Brazilian Amazon population.
Molecular Genetics & Genomic Medicine
Monte, Natasha N; Pantoja, Karla B C C KBCC; Rodrigues, Juliana C G JCG; de Carvalho, Darlen C DC; Azevedo, Tereza C B TCB; Pereira, Esdras E B EEB; de Assumpção, Paulo P PP; Dos Santos, Sidney E B SEB; Fernandes, Marianne R MR; Dos Santos, Ney P C NPC
Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity.
Scientific Reports
Phung, Tanya N TN; Webster, Timothy H TH; Lenkiewicz, Elizabeth E; Malasi, Smriti S; Andreozzi, Mariacarla M; McCullough, Ann E AE; Anderson, Karen S KS; Pockaj, Barbara A BA; Wilson, Melissa A MA; Barrett, Michael T MT
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: UMPS: 638G>C; G213A; rs1801019
Drug-Drug Interactions and Pharmacogenomic Evaluation in Colorectal Cancer Patients: The New Drug-PIN® System Comprehensive Approach.
Pharmaceuticals (Basel, Switzerland)
Roberto, Michela M; Rossi, Alessandro A; Panebianco, Martina M; Pomes, Leda Marina LM; Arrivi, Giulia G; Ierinò, Debora D; Simmaco, Maurizio M; Marchetti, Paolo P; Mazzuca, Federica F
Publication Date: 2021-01-15
Variant appearance in text: UMPS: G213A; rs1801019
Polymorphisms of xenobiotic-metabolizing and transporter genes, and the risk of gastric and colorectal cancer in an admixed population from the Brazilian Amazon.
American Journal Of Translational Research
de Castro, Amanda Nazaré Cohen Lima ANCL; Fernandes, Marianne Rodrigues MR; de Carvalho, Darlen Cardoso DC; de Souza, Tatiane Piedade TP; Rodrigues, Juliana Carla Gomes JCG; Andrade, Roberta Borges RB; Modesto, Antonio Andre Conde AAC; Santos, Sidney S; Assumpção, Paulo Pimentel PP; Dos Santos, Ney Pereira Carneiro NPC
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: UMPS: 638G>C; Gly213Ala; rs1801019
The Identification of Admixture Patterns Could Refine Pharmacogenetic Counseling: Analysis of a Population-Based Sample in Mexico.
Frontiers In Pharmacology
Martínez-Magaña, José Jaime JJ; Genis-Mendoza, Alma Delia AD; Villatoro Velázquez, Jorge Ameth JA; Camarena, Beatriz B; Martín Del Campo Sanchez, Raul R; Fleiz Bautista, Clara C; Bustos Gamiño, Marycarmen M; Reséndiz, Esbehidy E; Aguilar, Alejandro A; Medina-Mora, María Elena ME; Nicolini, Humberto H
Publication Date: 2020
Variant appearance in text: UMPS: G213A; rs1801019
The role of myoglobin in epithelial cancers: Insights from transcriptomics.
International Journal Of Molecular Medicine
Bicker, Anne A; Nauth, Theresa T; Gerst, Daniela D; Aboouf, Mostafa Ahmed MA; Fandrey, Joachim J; Kristiansen, Glen G; Gorr, Thomas Alexander TA; Hankeln, Thomas T
Publication Date: 2020-02
Variant appearance in text: UMPS: 638G>C; Gly213Ala
Introducing the first whole genomes of nationals from the United Arab Emirates.
Scientific Reports
AlSafar, Habiba S HS; Al-Ali, Mariam M; Elbait, Gihan Daw GD; Al-Maini, Mustafa H MH; Ruta, Dymitr D; Peramo, Braulio B; Henschel, Andreas A; Tay, Guan K GK
Publication Date: 2019-10-11
Variant appearance in text: UMPS: G213A; rs1801019
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: UMPS: G213A; rs1801019
DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load.
Nature Communications
Jung, Hyunchul H; Kim, Hong Sook HS; Kim, Jeong Yeon JY; Sun, Jong-Mu JM; Ahn, Jin Seok JS; Ahn, Myung-Ju MJ; Park, Keunchil K; Esteller, Manel M; Lee, Se-Hoon SH; Choi, Jung Kyoon JK
Breast cancer quantitative proteome and proteogenomic landscape.
Nature Communications
Johansson, Henrik J HJ; Socciarelli, Fabio F; Vacanti, Nathaniel M NM; Haugen, Mads H MH; Zhu, Yafeng Y; Siavelis, Ioannis I; Fernandez-Woodbridge, Alejandro A; Aure, Miriam R MR; Sennblad, Bengt B; Vesterlund, Mattias M; Branca, Rui M RM; Orre, Lukas M LM; Huss, Mikael M; Fredlund, Erik E; Beraki, Elsa E; Garred, Øystein Ø; Boekel, Jorrit J; Sauer, Torill T; Zhao, Wei W; Nord, Silje S; Höglander, Elen K EK; Jans, Daniel C DC; Brismar, Hjalmar H; Haukaas, Tonje H TH; Bathen, Tone F TF; Schlichting, Ellen E; Naume, Bjørn B; , ; Luders, Torben T; Borgen, Elin E; Kristensen, Vessela N VN; Russnes, Hege G HG; Lingjærde, Ole Christian OC; Mills, Gordon B GB; Sahlberg, Kristine K KK; Børresen-Dale, Anne-Lise AL; Lehtiö, Janne J
Publication Date: 2019-04-08
Variant appearance in text: UMPS: 638G>C; G213A; rs1801019
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: UMPS: G213A; rs1801019
Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.
Cell Reports
Vigilante, Alessandra A; Laddach, Anna A; Moens, Nathalie N; Meleckyte, Ruta R; Leha, Andreas A; Ghahramani, Arsham A; Culley, Oliver J OJ; Kathuria, Annie A; Hurling, Chloe C; Vickers, Alice A; Wiseman, Erika E; Tewary, Mukul M; Zandstra, Peter W PW; , ; Durbin, Richard R; Fraternali, Franca F; Stegle, Oliver O; Birney, Ewan E; Luscombe, Nicholas M NM; Danovi, Davide D; Watt, Fiona M FM
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: UMPS: G213A; rs1801019
A likely pathogenic variant putatively affecting splicing of PIGA identified in a multiple congenital anomalies hypotonia-seizures syndrome 2 (MCAHS2) family pedigree via whole-exome sequencing.
Pharmacogenetic Analysis of the UK MRC (Medical Research Council) MAGIC Trial: Association of Polymorphisms with Toxicity and Survival in Patients Treated with Perioperative Epirubicin, Cisplatin, and 5-fluorouracil (ECF) Chemotherapy.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Smyth, Elizabeth E; Zhang, Shenli S; Cunningham, David D; Wotherspoon, Andrew A; Soong, Richie R; Peckitt, Clare C; Valeri, Nicola N; Fassan, Matteo M; Rugge, Massimo M; Okines, Alicia A; Allum, William W; Stenning, Sally S; Nankivell, Matthew M; Langley, Ruth R; Tan, Patrick P
A phase II study of preoperative chemoradiation with tegafur-uracil plus leucovorin for locally advanced rectal cancer with pharmacogenetic analysis.
Radiation Oncology (London, England)
Kim, Sun Young SY; Baek, Ji Yeon JY; Oh, Jae Hwan JH; Park, Sung Chan SC; Sohn, Dae Kyung DK; Kim, Min Ju MJ; Chang, Hee Jin HJ; Kong, Sun-Young SY; Kim, Dae Yong DY
ABCC2-24C > T polymorphism is associated with the response to platinum/5-Fu-based neoadjuvant chemotherapy and better clinical outcomes in advanced gastric cancer patients.
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: UMPS: G213A; rs1801019
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
Plos Computational Biology
Bendl, Jaroslav J; Musil, Miloš M; Štourač, Jan J; Zendulka, Jaroslav J; Damborský, Jiří J; Brezovský, Jan J