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
A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy.
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Jang, H Josh HJ; Hostetter, Galen G; MacFarlane, Alexander W AW; Madaj, Zachary Z; Ross, Eric A EA; Hinoue, Toshinori T; Kulchycki, Justin R JR; Burgos, Ryan S RS; Tafseer, Mahvish M; Alpaugh, R Katherine RK; Schwebel, Candice L CL; Kokate, Rutika R; Geynisman, Daniel M DM; Zibelman, Matthew R MR; Ghatalia, Pooja P; Nichols, Peter W PW; Chung, Woonbok W; Madzo, Jozef J; Hahn, Noah M NM; Quinn, David I DI; Issa, Jean-Pierre J JJ; Topper, Michael J MJ; Baylin, Stephen B SB; Shen, Hui H; Campbell, Kerry S KS; Jones, Peter A PA; Plimack, Elizabeth R ER
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
A genome-wide meta-analysis identifies 50 genetic loci associated with carpal tunnel syndrome.
Nature Communications
Skuladottir, Astros Th AT; Bjornsdottir, Gyda G; Ferkingstad, Egil E; Einarsson, Gudmundur G; Stefansdottir, Lilja L; Nawaz, Muhammad Sulaman MS; Oddsson, Asmundur A; Olafsdottir, Thorunn A TA; Saevarsdottir, Saedis S; Walters, G Bragi GB; Magnusson, Sigurdur H SH; Bjornsdottir, Anna A; Sveinsson, Olafur A OA; Vikingsson, Arnor A; Hansen, Thomas Folkmann TF; Jacobsen, Rikke Louise RL; Erikstrup, Christian C; Schwinn, Michael M; Brunak, Søren S; Banasik, Karina K; Ostrowski, Sisse Rye SR; Troelsen, Anders A; Henkel, Cecilie C; Pedersen, Ole Birger OB; , ; Jonsdottir, Ingileif I; Gudbjartsson, Daniel F DF; Sulem, Patrick P; Thorgeirsson, Thorgeir E TE; Stefansson, Hreinn H; Stefansson, Kari K
Neoadjuvant PD-1 Blockade Combined With Chemotherapy Followed by Concurrent Immunoradiotherapy in Locally Advanced Anal Canal Squamous Cell Carcinoma Patients: Antitumor Efficacy, Safety and Biomarker Analysis.
Frontiers In Immunology
Xiao, WeiWei W; Yuan, Yan Y; Wang, SuiHai S; Liao, Zhidong Z; Cai, PeiQiang P; Chen, BaoQing B; Zhang, Rong R; Wang, Fang F; Zeng, ZhiFan Z; Gao, YuanHong Y
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; ,
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: ITIH1: Q595R; rs1042779
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
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
Bivariate genome-wide association analyses of the broad depression phenotype combined with major depressive disorder, bipolar disorder or schizophrenia reveal eight novel genetic loci for depression.
Molecular Psychiatry
Amare, Azmeraw T AT; Vaez, Ahmad A; Hsu, Yi-Hsiang YH; Direk, Nese N; Kamali, Zoha Z; Howard, David M DM; McIntosh, Andrew M AM; Tiemeier, Henning H; Bültmann, Ute U; Snieder, Harold H; Hartman, Catharina A CA
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: ITIH1: Q595R; rs1042779
Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia.
Genome Research
Bhattacharya, Sanchita S; Li, Jian J; Sockell, Alexandra A; Kan, Matthew J MJ; Bava, Felice A FA; Chen, Shann-Ching SC; Ávila-Arcos, María C MC; Ji, Xuhuai X; Smith, Emery E; Asadi, Narges B NB; Lachman, Ralph S RS; Lam, Hugo Y K HYK; Bustamante, Carlos D CD; Butte, Atul J AJ; Nolan, Garry P GP
Publication Date: 2018-04
Variant appearance in text: ITIH1: Q595R; rs1042779
PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.
Nature Methods
Ting, Ying S YS; Egertson, Jarrett D JD; Bollinger, James G JG; Searle, Brian C BC; Payne, Samuel H SH; Noble, William Stafford WS; MacCoss, Michael J MJ
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
Publication Date: 2015-12-08
Variant appearance in text: ITIH1: Q595R; rs1042779
JEPEG: a summary statistics based tool for gene-level joint testing of functional variants.
Bioinformatics (Oxford, England)
Lee, Donghyung D; Williamson, Vernell S VS; Bigdeli, T Bernard TB; Riley, Brien P BP; Fanous, Ayman H AH; Vladimirov, Vladimir I VI; Bacanu, Silviu-Alin SA
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: ITIH1: Q595R; rs1042779
Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data.
Nature Biotechnology
Denny, Joshua C JC; Bastarache, Lisa L; Ritchie, Marylyn D MD; Carroll, Robert J RJ; Zink, Raquel R; Mosley, Jonathan D JD; Field, Julie R JR; Pulley, Jill M JM; Ramirez, Andrea H AH; Bowton, Erica E; Basford, Melissa A MA; Carrell, David S DS; Peissig, Peggy L PL; Kho, Abel N AN; Pacheco, Jennifer A JA; Rasmussen, Luke V LV; Crosslin, David R DR; Crane, Paul K PK; Pathak, Jyotishman J; Bielinski, Suzette J SJ; Pendergrass, Sarah A SA; Xu, Hua H; Hindorff, Lucia A LA; Li, Rongling R; Manolio, Teri A TA; Chute, Christopher G CG; Chisholm, Rex L RL; Larson, Eric B EB; Jarvik, Gail P GP; Brilliant, Murray H MH; McCarty, Catherine A CA; Kullo, Iftikhar J IJ; Haines, Jonathan L JL; Crawford, Dana C DC; Masys, Daniel R DR; Roden, Dan M DM
A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation.
Biological Psychiatry
, ; , ; Bramon, Elvira E; Pirinen, Matti M; Strange, Amy A; Lin, Kuang K; Freeman, Colin C; Bellenguez, Céline C; Su, Zhan Z; Band, Gavin G; Pearson, Richard R; Vukcevic, Damjan D; Langford, Cordelia C; Deloukas, Panos P; Hunt, Sarah S; Gray, Emma E; Dronov, Serge S; Potter, Simon C SC; Tashakkori-Ghanbaria, Avazeh A; Edkins, Sarah S; Bumpstead, Suzannah J SJ; Arranz, Maria J MJ; Bakker, Steven S; Bender, Stephan S; Bruggeman, Richard R; Cahn, Wiepke W; Chandler, David D; Collier, David A DA; Crespo-Facorro, Benedicto B; Dazzan, Paola P; de Haan, Lieuwe L; Di Forti, Marta M; Dragović, Milan M; Giegling, Ina I; Hall, Jeremy J; Iyegbe, Conrad C; Jablensky, Assen A; Kahn, René S RS; Kalaydjieva, Luba L; Kravariti, Eugenia E; Lawrie, Stephen S; Linszen, Don H DH; Mata, Ignacio I; McDonald, Colm C; McIntosh, Andrew A; Myin-Germeys, Inez I; Ophoff, Roel A RA; Pariante, Carmine M CM; Paunio, Tiina T; Picchioni, Marco M; , ; Ripke, Stephan S; Rujescu, Dan D; Sauer, Heinrich H; Shaikh, Madiha M; Sussmann, Jessika J; Suvisaari, Jaana J; Tosato, Sarah S; Toulopoulou, Timothea T; Van Os, Jim J; Walshe, Muriel M; Weisbrod, Matthias M; Whalley, Heather H; Wiersma, Durk D; Blackwell, Jenefer M JM; Brown, Matthew A MA; Casas, Juan P JP; Corvin, Aiden A; Duncanson, Audrey A; Jankowski, Janusz A Z JA; Markus, Hugh S HS; Mathew, Christopher G CG; Palmer, Colin N A CN; Plomin, Robert R; Rautanen, Anna A; Sawcer, Stephen J SJ; Trembath, Richard C RC; Wood, Nicholas W NW; Barroso, Ines I; Peltonen, Leena L; Lewis, Cathryn M CM; Murray, Robin M RM; Donnelly, Peter P; Powell, John J; Spencer, Chris C A CC
A mega-analysis of genome-wide association studies for major depressive disorder.
Molecular Psychiatry
, ; Ripke, Stephan S; Wray, Naomi R NR; Lewis, Cathryn M CM; Hamilton, Steven P SP; Weissman, Myrna M MM; Breen, Gerome G; Byrne, Enda M EM; Blackwood, Douglas H R DH; Boomsma, Dorret I DI; Cichon, Sven S; Heath, Andrew C AC; Holsboer, Florian F; Lucae, Susanne S; Madden, Pamela A F PA; Martin, Nicholas G NG; McGuffin, Peter P; Muglia, Pierandrea P; Noethen, Markus M MM; Penninx, Brenda P BP; Pergadia, Michele L ML; Potash, James B JB; Rietschel, Marcella M; Lin, Danyu D; Müller-Myhsok, Bertram B; Shi, Jianxin J; Steinberg, Stacy S; Grabe, Hans J HJ; Lichtenstein, Paul P; Magnusson, Patrik P; Perlis, Roy H RH; Preisig, Martin M; Smoller, Jordan W JW; Stefansson, Kari K; Uher, Rudolf R; Kutalik, Zoltan Z; Tansey, Katherine E KE; Teumer, Alexander A; Viktorin, Alexander A; Barnes, Michael R MR; Bettecken, Thomas T; Binder, Elisabeth B EB; Breuer, René R; Castro, Victor M VM; Churchill, Susanne E SE; Coryell, William H WH; Craddock, Nick N; Craig, Ian W IW; Czamara, Darina D; De Geus, Eco J EJ; Degenhardt, Franziska F; Farmer, Anne E AE; Fava, Maurizio M; Frank, Josef J; Gainer, Vivian S VS; Gallagher, Patience J PJ; Gordon, Scott D SD; Goryachev, Sergey S; Gross, Magdalena M; Guipponi, Michel M; Henders, Anjali K AK; Herms, Stefan S; Hickie, Ian B IB; Hoefels, Susanne S; Hoogendijk, Witte W; Hottenga, Jouke Jan JJ; Iosifescu, Dan V DV; Ising, Marcus M; Jones, Ian I; Jones, Lisa L; Jung-Ying, Tzeng T; Knowles, James A JA; Kohane, Isaac S IS; Kohli, Martin A MA; Korszun, Ania A; Landen, Mikael M; Lawson, William B WB; Lewis, Glyn G; Macintyre, Donald D; Maier, Wolfgang W; Mattheisen, Manuel M; McGrath, Patrick J PJ; McIntosh, Andrew A; McLean, Alan A; Middeldorp, Christel M CM; Middleton, Lefkos L; Montgomery, Grant M GM; Murphy, Shawn N SN; Nauck, Matthias M; Nolen, Willem A WA; Nyholt, Dale R DR; O'Donovan, Michael M; Oskarsson, Högni H; Pedersen, Nancy N; Scheftner, William A WA; Schulz, Andrea A; Schulze, Thomas G TG; Shyn, Stanley I SI; Sigurdsson, Engilbert E; Slager, Susan L SL; Smit, Johannes H JH; Stefansson, Hreinn H; Steffens, Michael M; Thorgeirsson, Thorgeir T; Tozzi, Federica F; Treutlein, Jens J; Uhr, Manfred M; van den Oord, Edwin J C G EJ; Van Grootheest, Gerard G; Völzke, Henry H; Weilburg, Jeffrey B JB; Willemsen, Gonneke G; Zitman, Frans G FG; Neale, Benjamin B; Daly, Mark M; Levinson, Douglas F DF; Sullivan, Patrick F PF
Meta-analysis of genome-wide association data identifies a risk locus for major mood disorders on 3p21.1.
Nature Genetics
McMahon, Francis J FJ; Akula, Nirmala N; Schulze, Thomas G TG; Muglia, Pierandrea P; Tozzi, Federica F; Detera-Wadleigh, Sevilla D SD; Steele, C J M CJ; Breuer, René R; Strohmaier, Jana J; Wendland, Jens R JR; Mattheisen, Manuel M; Mühleisen, Thomas W TW; Maier, Wolfgang W; Nöthen, Markus M MM; Cichon, Sven S; Farmer, Anne A; Vincent, John B JB; Holsboer, Florian F; Preisig, Martin M; Rietschel, Marcella M; ,
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry.
Proceedings Of The National Academy Of Sciences Of The United States Of America
Scott, Laura J LJ; Muglia, Pierandrea P; Kong, Xiangyang Q XQ; Guan, Weihua W; Flickinger, Matthew M; Upmanyu, Ruchi R; Tozzi, Federica F; Li, Jun Z JZ; Burmeister, Margit M; Absher, Devin D; Thompson, Robert C RC; Francks, Clyde C; Meng, Fan F; Antoniades, Athos A; Southwick, Audrey M AM; Schatzberg, Alan F AF; Bunney, William E WE; Barchas, Jack D JD; Jones, Edward G EG; Day, Richard R; Matthews, Keith K; McGuffin, Peter P; Strauss, John S JS; Kennedy, James L JL; Middleton, Lefkos L; Roses, Allen D AD; Watson, Stanley J SJ; Vincent, John B JB; Myers, Richard M RM; Farmer, Ann E AE; Akil, Huda H; Burns, Daniel K DK; Boehnke, Michael M