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
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
Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry.
Iscience
Bateman, Nicholas W NW; Tarney, Christopher M CM; Abulez, Tamara S TS; Hood, Brian L BL; Conrads, Kelly A KA; Zhou, Ming M; Soltis, Anthony R AR; Teng, Pang-Ning PN; Jackson, Amanda A; Tian, Chunqiao C; Dalgard, Clifton L CL; Wilkerson, Matthew D MD; Kessler, Michael D MD; Goecker, Zachary Z; Loffredo, Jeremy J; Shriver, Craig D CD; Hu, Hai H; Cote, Michele M; Parker, Glendon J GJ; Segars, James J; Al-Hendy, Ayman A; Risinger, John I JI; Phippen, Neil T NT; Casablanca, Yovanni Y; Darcy, Kathleen M KM; Maxwell, G Larry GL; Conrads, Thomas P TP; O'Connor, Timothy D TD
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
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: TP53BP1: D358E; rs560191
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
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: TP53BP1: D358E; rs560191
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
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: TP53BP1: D358E; rs560191
Interactions Between Genetic Variants and Environmental Factors Affect Risk of Esophageal Adenocarcinoma and Barrett's Esophagus.
Clinical Gastroenterology And Hepatology : The Official Clinical Practice Journal Of The American Gastroenterological Association
Dong, Jing J; Levine, David M DM; Buas, Matthew F MF; Zhang, Rui R; Onstad, Lynn L; Fitzgerald, Rebecca C RC; , ; Corley, Douglas A DA; Shaheen, Nicholas J NJ; Lagergren, Jesper J; Hardie, Laura J LJ; Reid, Brian J BJ; Iyer, Prasad G PG; Risch, Harvey A HA; Caldas, Carlos C; Caldas, Isabel I; Pharoah, Paul D PD; Liu, Geoffrey G; Gammon, Marilie D MD; Chow, Wong-Ho WH; Bernstein, Leslie L; Bird, Nigel C NC; Ye, Weimin W; Wu, Anna H AH; Anderson, Lesley A LA; MacGregor, Stuart S; Whiteman, David C DC; Vaughan, Thomas L TL; Thrift, Aaron P AP
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 predisposition to lung cancer: comprehensive literature integration, meta-analysis, and multiple evidence assessment of candidate-gene association studies.
Scientific Reports
Wang, Junjun J; Liu, Qingyun Q; Yuan, Shuai S; Xie, Weijia W; Liu, Yuan Y; Xiang, Ying Y; Wu, Na N; Wu, Long L; Ma, Xiangyu X; Cai, Tongjian T; Zhang, Yao Y; Sun, Zhifu Z; Li, Yafei Y
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: TP53BP1: D358E; rs560191
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
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: TP53BP1: D358E; rs560191
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: TP53BP1: D358E; rs560191
Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations.
Human Genomics
Zhang, Guojie G; Pei, Zhang Z; Ball, Edward V EV; Mort, Matthew M; Kehrer-Sawatzki, Hildegard H; Cooper, David N DN
Genome-wide significant association between a sequence variant at 15q15.2 and lung cancer risk.
Cancer Research
Rafnar, Thorunn T; Sulem, Patrick P; Besenbacher, Soren S; Gudbjartsson, Daniel F DF; Zanon, Carlo C; Gudmundsson, Julius J; Stacey, Simon N SN; Kostic, Jelena P JP; Thorgeirsson, Thorgeir E TE; Thorleifsson, Gudmar G; Bjarnason, Hjordis H; Skuladottir, Halla H; Gudbjartsson, Tomas T; Isaksson, Helgi J HJ; Isla, Dolores D; Murillo, Laura L; García-Prats, Maria D MD; Panadero, Angeles A; Aben, Katja K H KK; Vermeulen, Sita H SH; van der Heijden, Henricus F M HF; Feser, William J WJ; Miller, York E YE; Bunn, Paul A PA; Kong, Augustine A; Wolf, Holly J HJ; Franklin, Wilbur A WA; Mayordomo, Jose I JI; Kiemeney, Lambertus A LA; Jonsson, Steinn S; Thorsteinsdottir, Unnur U; Stefansson, Kari K
Interactions between genetic polymorphisms in the apoptotic pathway and environmental factors on esophageal adenocarcinoma risk.
Carcinogenesis
Wu, I-Chen IC; Zhao, Yang Y; Zhai, Rihong R; Liu, Chen-yu CY; Chen, Feng F; Ter-Minassian, Monica M; Asomaning, Kofi K; Su, Li L; Heist, Rebecca S RS; Kulke, Matthew H MH; Liu, Geoffrey G; Christiani, David C DC
Evaluation of single nucleotide polymorphisms (SNPs) in the p53 binding protein 1 (TP53BP1) gene in breast cancer patients treated with breast-conserving surgery and whole-breast irradiation (BCS + RT).
International Journal Of Radiation Oncology, Biology, Physics
Haffty, Bruce G BG; Goyal, Sharad S; Kulkarni, Diptee D; Green, Camille C; Vazquez, Alexi A; Schiff, Devora D; Moran, Meena S MS; Yang, Qifeng Q; Ganesan, Shridar S; Hirsfield, Kim M KM
Interactions among genetic variants in apoptosis pathway genes, reflux symptoms, body mass index, and smoking indicate two distinct etiologic patterns of esophageal adenocarcinoma.
Journal Of Clinical Oncology : Official Journal Of The American Society Of Clinical Oncology
Zhai, Rihong R; Chen, Feng F; Liu, Geoffrey G; Su, Li L; Kulke, Matthew H MH; Asomaning, Kofi K; Lin, Xihong X; Heist, Rebecca S RS; Nishioka, Norman S NS; Sheu, Chau-Chyun CC; Wain, John C JC; Christiani, David C DC
International Lung Cancer Consortium: coordinated association study of 10 potential lung cancer susceptibility variants.
Carcinogenesis
Truong, Therese T; Sauter, Wiebke W; McKay, James D JD; Hosgood, H Dean HD; Gallagher, Carla C; Amos, Christopher I CI; Spitz, Margaret M; Muscat, Joshua J; Lazarus, Philip P; Illig, Thomas T; Wichmann, H Erich HE; Bickeböller, Heike H; Risch, Angela A; Dienemann, Hendrik H; Zhang, Zuo-Feng ZF; Naeim, Behnaz Pezeshki BP; Yang, Ping P; Zienolddiny, Shanbeh S; Haugen, Aage A; Le Marchand, Loïc L; Hong, Yun-Chul YC; Kim, Jin Hee JH; Duell, Eric J EJ; Andrew, Angeline S AS; Kiyohara, Chikako C; Shen, Hongbing H; Matsuo, Keitaro K; Suzuki, Takeshi T; Seow, Adeline A; Ng, Daniel P K DP; Lan, Qing Q; Zaridze, David D; Szeszenia-Dabrowska, Neonilia N; Lissowska, Jolanta J; Rudnai, Peter P; Fabianova, Eleonora E; Constantinescu, Vali V; Bencko, Vladimir V; Foretova, Lenka L; Janout, Vladimir V; Caporaso, Neil E NE; Albanes, Demetrius D; Thun, Michael M; Landi, Maria Teresa MT; Trubicka, Joanna J; Lener, Marcin M; Lubinski, Jan J; , ; Wang, Ying Y; Chabrier, Amélie A; Boffetta, Paolo P; Brennan, Paul P; Hung, Rayjean J RJ
Variants in the GH-IGF axis confer susceptibility to lung cancer.
Genome Research
Rudd, Matthew F MF; Webb, Emily L EL; Matakidou, Athena A; Sellick, Gabrielle S GS; Williams, Richard D RD; Bridle, Helen H; Eisen, Tim T; Houlston, Richard S RS; ,
TP53-binding protein variants and breast cancer risk: a case-control study.
Breast Cancer Research : Bcr
Frank, Bernd B; Hemminki, Kari K; Bermejo, Justo Lorenzo JL; Klaes, Rüdiger R; Bugert, Peter P; Wappenschmidt, Barbara B; Schmutzler, Rita K RK; Burwinkel, Barbara B