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
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: PMF1-BGLAP: 224A>G; Gln75Arg; rs1052053
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
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
A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells.
Cell & Bioscience
Riaz, Moeen M; Mattisson, Jonas J; Polekhina, Galina G; Bakshi, Andrew A; Halvardson, Jonatan J; Danielsson, Marcus M; Ameur, Adam A; McNeil, John J; Forsberg, Lars A LA; Lacaze, Paul P
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: PMF1: 224A>G; Q75R; rs1052053
Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells.
Npj Systems Biology And Applications
Immanuel, Selva Rupa Christinal SRC; Ghanate, Avinash D AD; Parmar, Dharmeshkumar S DS; Yadav, Ritu R; Uthup, Riya R; Panchagnula, Venkateswarlu V; Raghunathan, Anu A
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; ,
Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes.
Communications Biology
Perrino, Peter A PA; Talbot, Lidiya L; Kirkland, Rose R; Hill, Amanda A; Rendall, Amanda R AR; Mountford, Hayley S HS; Taylor, Jenny J; , ; Buscarello, Alexzandrea N AN; Lahiri, Nayana N; Saggar, Anand A; Fitch, R Holly RH; Newbury, Dianne F DF
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
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
Organoids as a new model for improving regenerative medicine and cancer personalized therapy in renal diseases.
Cell Death & Disease
Grassi, Ludovica L; Alfonsi, Romina R; Francescangeli, Federica F; Signore, Michele M; De Angelis, Maria Laura ML; Addario, Antonio A; Costantini, Manuela M; Flex, Elisabetta E; Ciolfi, Andrea A; Pizzi, Simone S; Bruselles, Alessandro A; Pallocca, Matteo M; Simone, Giuseppe G; Haoui, Mustapha M; Falchi, Mario M; Milella, Michele M; Sentinelli, Steno S; Di Matteo, Paola P; Stellacci, Emilia E; Gallucci, Michele M; Muto, Giovanni G; Tartaglia, Marco M; De Maria, Ruggero R; Bonci, Désirée D
Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.
Nature Genetics
Malik, Rainer R; Chauhan, Ganesh G; Traylor, Matthew M; Sargurupremraj, Muralidharan M; Okada, Yukinori Y; Mishra, Aniket A; Rutten-Jacobs, Loes L; Giese, Anne-Katrin AK; van der Laan, Sander W SW; Gretarsdottir, Solveig S; Anderson, Christopher D CD; Chong, Michael M; Adams, Hieab H H HHH; Ago, Tetsuro T; Almgren, Peter P; Amouyel, Philippe P; Ay, Hakan H; Bartz, Traci M TM; Benavente, Oscar R OR; Bevan, Steve S; Boncoraglio, Giorgio B GB; Brown, Robert D RD; Butterworth, Adam S AS; Carrera, Caty C; Carty, Cara L CL; Chasman, Daniel I DI; Chen, Wei-Min WM; Cole, John W JW; Correa, Adolfo A; Cotlarciuc, Ioana I; Cruchaga, Carlos C; Danesh, John J; de Bakker, Paul I W PIW; DeStefano, Anita L AL; den Hoed, Marcel M; Duan, Qing Q; Engelter, Stefan T ST; Falcone, Guido J GJ; Gottesman, Rebecca F RF; Grewal, Raji P RP; Gudnason, Vilmundur V; Gustafsson, Stefan S; Haessler, Jeffrey J; Harris, Tamara B TB; Hassan, Ahamad A; Havulinna, Aki S AS; Heckbert, Susan R SR; Holliday, Elizabeth G EG; Howard, George G; Hsu, Fang-Chi FC; Hyacinth, Hyacinth I HI; Ikram, M Arfan MA; Ingelsson, Erik E; Irvin, Marguerite R MR; Jian, Xueqiu X; Jiménez-Conde, Jordi J; Johnson, Julie A JA; Jukema, J Wouter JW; Kanai, Masahiro M; Keene, Keith L KL; Kissela, Brett M BM; Kleindorfer, Dawn O DO; Kooperberg, Charles C; Kubo, Michiaki M; Lange, Leslie A LA; Langefeld, Carl D CD; Langenberg, Claudia C; Launer, Lenore J LJ; Lee, Jin-Moo JM; Lemmens, Robin R; Leys, Didier D; Lewis, Cathryn M CM; Lin, Wei-Yu WY; Lindgren, Arne G AG; Lorentzen, Erik E; Magnusson, Patrik K PK; Maguire, Jane J; Manichaikul, Ani A; McArdle, Patrick F PF; Meschia, James F JF; Mitchell, Braxton D BD; Mosley, Thomas H TH; Nalls, Michael A MA; Ninomiya, Toshiharu T; O'Donnell, Martin J MJ; Psaty, Bruce M BM; Pulit, Sara L SL; Rannikmäe, Kristiina K; Reiner, Alexander P AP; Rexrode, Kathryn M KM; Rice, Kenneth K; Rich, Stephen S SS; Ridker, Paul M PM; Rost, Natalia S NS; Rothwell, Peter M PM; Rotter, Jerome I JI; Rundek, Tatjana T; Sacco, Ralph L RL; Sakaue, Saori S; Sale, Michele M MM; Salomaa, Veikko V; Sapkota, Bishwa R BR; Schmidt, Reinhold R; Schmidt, Carsten O CO; Schminke, Ulf U; Sharma, Pankaj P; Slowik, Agnieszka A; Sudlow, Cathie L M CLM; Tanislav, Christian C; Tatlisumak, Turgut T; Taylor, Kent D KD; Thijs, Vincent N S VNS; Thorleifsson, Gudmar G; Thorsteinsdottir, Unnur U; Tiedt, Steffen S; Trompet, Stella S; Tzourio, Christophe C; van Duijn, Cornelia M CM; Walters, Matthew M; Wareham, Nicholas J NJ; Wassertheil-Smoller, Sylvia S; Wilson, James G JG; Wiggins, Kerri L KL; Yang, Qiong Q; Yusuf, Salim S; , ; , ; , ; , ; , ; Bis, Joshua C JC; Pastinen, Tomi T; Ruusalepp, Arno A; Schadt, Eric E EE; Koplev, Simon S; Björkegren, Johan L M JLM; Codoni, Veronica V; Civelek, Mete M; Smith, Nicholas L NL; Trégouët, David A DA; Christophersen, Ingrid E IE; Roselli, Carolina C; Lubitz, Steven A SA; Ellinor, Patrick T PT; Tai, E Shyong ES; Kooner, Jaspal S JS; Kato, Norihiro N; He, Jiang J; van der Harst, Pim P; Elliott, Paul P; Chambers, John C JC; Takeuchi, Fumihiko F; Johnson, Andrew D AD; , ; , ; , ; , ; , ; , ; , ; , ; , ; , ; Sanghera, Dharambir K DK; Melander, Olle O; Jern, Christina C; Strbian, Daniel D; Fernandez-Cadenas, Israel I; Longstreth, W T WT; Rolfs, Arndt A; Hata, Jun J; Woo, Daniel D; Rosand, Jonathan J; Pare, Guillaume G; Hopewell, Jemma C JC; Saleheen, Danish D; Stefansson, Kari K; Worrall, Bradford B BB; Kittner, Steven J SJ; Seshadri, Sudha S; Fornage, Myriam M; Markus, Hugh S HS; Howson, Joanna M M JMM; Kamatani, Yoichiro Y; Debette, Stephanie S; Dichgans, Martin M
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.
Nature Communications
Zhu, Yafeng Y; Orre, Lukas M LM; Johansson, Henrik J HJ; Huss, Mikael M; Boekel, Jorrit J; Vesterlund, Mattias M; Fernandez-Woodbridge, Alejandro A; Branca, Rui M M RMM; Lehtiö, Janne J
Genetic variants associated with mosaic Y chromosome loss highlight cell cycle genes and overlap with cancer susceptibility.
Nature Genetics
Wright, Daniel J DJ; Day, Felix R FR; Kerrison, Nicola D ND; Zink, Florian F; Cardona, Alexia A; Sulem, Patrick P; Thompson, Deborah J DJ; Sigurjonsdottir, Svanhvit S; Gudbjartsson, Daniel F DF; Helgason, Agnar A; Chapman, J Ross JR; Jackson, Steve P SP; Langenberg, Claudia C; Wareham, Nicholas J NJ; Scott, Robert A RA; Thorsteindottir, Unnur U; Ong, Ken K KK; Stefansson, Kari K; Perry, John R B JRB
Integrated genomic analyses of de novo pathways underlying atypical meningiomas.
Nature Communications
Harmancı, Akdes Serin AS; Youngblood, Mark W MW; Clark, Victoria E VE; Coşkun, Süleyman S; Henegariu, Octavian O; Duran, Daniel D; Erson-Omay, E Zeynep EZ; Kaulen, Leon D LD; Lee, Tong Ihn TI; Abraham, Brian J BJ; Simon, Matthias M; Krischek, Boris B; Timmer, Marco M; Goldbrunner, Roland R; Omay, S Bülent SB; Baranoski, Jacob J; Baran, Burçin B; Carrión-Grant, Geneive G; Bai, Hanwen H; Mishra-Gorur, Ketu K; Schramm, Johannes J; Moliterno, Jennifer J; Vortmeyer, Alexander O AO; Bilgüvar, Kaya K; Yasuno, Katsuhito K; Young, Richard A RA; Günel, Murat M
Publication Date: 2017-02-14
Variant appearance in text: PMF1: 224A>G; Gln75Arg; rs1052053
Clonal relationships between lobular carcinoma in situ and other breast malignancies.
Breast Cancer Research : Bcr
Begg, Colin B CB; Ostrovnaya, Irina I; Carniello, Jose V Scarpa JV; Sakr, Rita A RA; Giri, Dilip D; Towers, Russell R; Schizas, Michail M; De Brot, Marina M; Andrade, Victor P VP; Mauguen, Audrey A; Seshan, Venkatraman E VE; King, Tari A TA
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; ,
Generation of a High Number of Healthy Erythroid Cells from Gene-Edited Pyruvate Kinase Deficiency Patient-Specific Induced Pluripotent Stem Cells.
Stem Cell Reports
Garate, Zita Z; Quintana-Bustamante, Oscar O; Crane, Ana M AM; Olivier, Emmanuel E; Poirot, Laurent L; Galetto, Roman R; Kosinski, Penelope P; Hill, Collin C; Kung, Charles C; Agirre, Xabi X; Orman, Israel I; Cerrato, Laura L; Alberquilla, Omaira O; Rodriguez-Fornes, Fatima F; Fusaki, Noemi N; Garcia-Sanchez, Felix F; Maia, Tabita M TM; Ribeiro, Maria L ML; Sevilla, Julian J; Prosper, Felipe F; Jin, Shengfang S; Mountford, Joanne J; Guenechea, Guillermo G; Gouble, Agnes A; Bueren, Juan A JA; Davis, Brian R BR; Segovia, Jose C JC
Genes from a translational analysis support a multifactorial nature of white matter hyperintensities.
Stroke
Lopez, Lorna M LM; Hill, W David WD; Harris, Sarah E SE; Valdes Hernandez, Maria M; Munoz Maniega, Susana S; Bastin, Mark E ME; Bailey, Emma E; Smith, Colin C; McBride, Martin M; McClure, John J; Graham, Delyth D; Dominiczak, Anna A; Yang, Qiong Q; Fornage, Myriam M; Ikram, M Arfan MA; Debette, Stephanie S; Launer, Lenore L; Bis, Joshua C JC; Schmidt, Reinhold R; Seshadri, Sudha S; Porteous, David J DJ; Starr, John J; Deary, Ian J IJ; Wardlaw, Joanna M JM
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
Meta-analysis of genome-wide association studies identifies 1q22 as a susceptibility locus for intracerebral hemorrhage.
American Journal Of Human Genetics
Woo, Daniel D; Falcone, Guido J GJ; Devan, William J WJ; Brown, W Mark WM; Biffi, Alessandro A; Howard, Timothy D TD; Anderson, Christopher D CD; Brouwers, H Bart HB; Valant, Valerie V; Battey, Thomas W K TW; Radmanesh, Farid F; Raffeld, Miriam R MR; Baedorf-Kassis, Sylvia S; Deka, Ranjan R; Woo, Jessica G JG; Martin, Lisa J LJ; Haverbusch, Mary M; Moomaw, Charles J CJ; Sun, Guangyun G; Broderick, Joseph P JP; Flaherty, Matthew L ML; Martini, Sharyl R SR; Kleindorfer, Dawn O DO; Kissela, Brett B; Comeau, Mary E ME; Jagiella, Jeremiasz M JM; Schmidt, Helena H; Freudenberger, Paul P; Pichler, Alexander A; Enzinger, Christian C; Hansen, Björn M BM; Norrving, Bo B; Jimenez-Conde, Jordi J; Giralt-Steinhauer, Eva E; Elosua, Roberto R; Cuadrado-Godia, Elisa E; Soriano, Carolina C; Roquer, Jaume J; Kraft, Peter P; Ayres, Alison M AM; Schwab, Kristin K; McCauley, Jacob L JL; Pera, Joanna J; Urbanik, Andrzej A; Rost, Natalia S NS; Goldstein, Joshua N JN; Viswanathan, Anand A; Stögerer, Eva-Maria EM; Tirschwell, David L DL; Selim, Magdy M; Brown, Devin L DL; Silliman, Scott L SL; Worrall, Bradford B BB; Meschia, James F JF; Kidwell, Chelsea S CS; Montaner, Joan J; Fernandez-Cadenas, Israel I; Delgado, Pilar P; Malik, Rainer R; Dichgans, Martin M; Greenberg, Steven M SM; Rothwell, Peter M PM; Lindgren, Arne A; Slowik, Agnieszka A; Schmidt, Reinhold R; Langefeld, Carl D CD; Rosand, Jonathan J; ,
Genome-wide association studies of cerebral white matter lesion burden: the CHARGE consortium.
Annals Of Neurology
Fornage, Myriam M; Debette, Stephanie S; Bis, Joshua C JC; Schmidt, Helena H; Ikram, M Arfan MA; Dufouil, Carole C; Sigurdsson, Sigurdur S; Lumley, Thomas T; DeStefano, Anita L AL; Fazekas, Franz F; Vrooman, Henri A HA; Shibata, Dean K DK; Maillard, Pauline P; Zijdenbos, Alex A; Smith, Albert V AV; Gudnason, Haukur H; de Boer, Renske R; Cushman, Mary M; Mazoyer, Bernard B; Heiss, Gerardo G; Vernooij, Meike W MW; Enzinger, Christian C; Glazer, Nicole L NL; Beiser, Alexa A; Knopman, David S DS; Cavalieri, Margherita M; Niessen, Wiro J WJ; Harris, Tamara B TB; Petrovic, Katja K; Lopez, Oscar L OL; Au, Rhoda R; Lambert, Jean-Charles JC; Hofman, Albert A; Gottesman, Rebecca F RF; Garcia, Melissa M; Heckbert, Susan R SR; Atwood, Larry D LD; Catellier, Diane J DJ; Uitterlinden, Andre G AG; Yang, Qiong Q; Smith, Nicholas L NL; Aspelund, Thor T; Romero, Jose R JR; Rice, Kenneth K; Taylor, Kent D KD; Nalls, Michael A MA; Rotter, Jerome I JI; Sharrett, Richey R; van Duijn, Cornelia M CM; Amouyel, Philippe P; Wolf, Philip A PA; Gudnason, Vilmundur V; van der Lugt, Aad A; Boerwinkle, Eric E; Psaty, Bruce M BM; Seshadri, Sudha S; Tzourio, Christophe C; Breteler, Monique M B MM; Mosley, Thomas H TH; Schmidt, Reinhold R; Longstreth, W T WT; DeCarli, Charles C; Launer, Lenore J LJ