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
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
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: VPS33B: G514S; rs11073964
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
Publication Date: 2022-01-21
Variant appearance in text: VPS33B: G514S; rs11073964
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: VPS33B: 1540G>A; G514S; rs11073964
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
Publication Date: 2021-01-08
Variant appearance in text: VPS33B: 1540G>A; G514S; rs11073964
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
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: VPS33B: 1540G>A; Gly514Ser
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: VPS33B: G514S; rs11073964
Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls.
Nature
Flannick, Jason J; Mercader, Josep M JM; Fuchsberger, Christian C; Udler, Miriam S MS; Mahajan, Anubha A; Wessel, Jennifer J; Teslovich, Tanya M TM; Caulkins, Lizz L; Koesterer, Ryan R; Barajas-Olmos, Francisco F; Blackwell, Thomas W TW; Boerwinkle, Eric E; Brody, Jennifer A JA; Centeno-Cruz, Federico F; Chen, Ling L; Chen, Siying S; Contreras-Cubas, Cecilia C; Córdova, Emilio E; Correa, Adolfo A; Cortes, Maria M; DeFronzo, Ralph A RA; Dolan, Lawrence L; Drews, Kimberly L KL; Elliott, Amanda A; Floyd, James S JS; Gabriel, Stacey S; Garay-Sevilla, Maria Eugenia ME; García-Ortiz, Humberto H; Gross, Myron M; Han, Sohee S; Heard-Costa, Nancy L NL; Jackson, Anne U AU; Jørgensen, Marit E ME; Kang, Hyun Min HM; Kelsey, Megan M; Kim, Bong-Jo BJ; Koistinen, Heikki A HA; Kuusisto, Johanna J; Leader, Joseph B JB; Linneberg, Allan A; Liu, Ching-Ti CT; Liu, Jianjun J; Lyssenko, Valeriya V; Manning, Alisa K AK; Marcketta, Anthony A; Malacara-Hernandez, Juan Manuel JM; Martínez-Hernández, Angélica A; Matsuo, Karen K; Mayer-Davis, Elizabeth E; Mendoza-Caamal, Elvia E; Mohlke, Karen L KL; Morrison, Alanna C AC; Ndungu, Anne A; Ng, Maggie C Y MCY; O'Dushlaine, Colm C; Payne, Anthony J AJ; Pihoker, Catherine C; , ; Post, Wendy S WS; Preuss, Michael M; Psaty, Bruce M BM; Vasan, Ramachandran S RS; Rayner, N William NW; Reiner, Alexander P AP; Revilla-Monsalve, Cristina C; Robertson, Neil R NR; Santoro, Nicola N; Schurmann, Claudia C; So, Wing Yee WY; Soberón, Xavier X; Stringham, Heather M HM; Strom, Tim M TM; Tam, Claudia H T CHT; Thameem, Farook F; Tomlinson, Brian B; Torres, Jason M JM; Tracy, Russell P RP; van Dam, Rob M RM; Vujkovic, Marijana M; Wang, Shuai S; Welch, Ryan P RP; Witte, Daniel R DR; Wong, Tien-Yin TY; Atzmon, Gil G; Barzilai, Nir N; Blangero, John J; Bonnycastle, Lori L LL; Bowden, Donald W DW; Chambers, John C JC; Chan, Edmund E; Cheng, Ching-Yu CY; Cho, Yoon Shin YS; Collins, Francis S FS; de Vries, Paul S PS; Duggirala, Ravindranath R; Glaser, Benjamin B; Gonzalez, Clicerio C; Gonzalez, Ma Elena ME; Groop, Leif L; Kooner, Jaspal Singh JS; Kwak, Soo Heon SH; Laakso, Markku M; Lehman, Donna M DM; Nilsson, Peter P; Spector, Timothy D TD; Tai, E Shyong ES; Tuomi, Tiinamaija T; Tuomilehto, Jaakko J; Wilson, James G JG; Aguilar-Salinas, Carlos A CA; Bottinger, Erwin E; Burke, Brian B; Carey, David J DJ; Chan, Juliana C N JCN; Dupuis, Josée J; Frossard, Philippe P; Heckbert, Susan R SR; Hwang, Mi Yeong MY; Kim, Young Jin YJ; Kirchner, H Lester HL; Lee, Jong-Young JY; Lee, Juyoung J; Loos, Ruth J F RJF; Ma, Ronald C W RCW; Morris, Andrew D AD; O'Donnell, Christopher J CJ; Palmer, Colin N A CNA; Pankow, James J; Park, Kyong Soo KS; Rasheed, Asif A; Saleheen, Danish D; Sim, Xueling X; Small, Kerrin S KS; Teo, Yik Ying YY; Haiman, Christopher C; Hanis, Craig L CL; Henderson, Brian E BE; Orozco, Lorena L; Tusié-Luna, Teresa T; Dewey, Frederick E FE; Baras, Aris A; Gieger, Christian C; Meitinger, Thomas T; Strauch, Konstantin K; Lange, Leslie L; Grarup, Niels N; Hansen, Torben T; Pedersen, Oluf O; Zeitler, Philip P; Dabelea, Dana D; Abecasis, Goncalo G; Bell, Graeme I GI; Cox, Nancy J NJ; Seielstad, Mark M; Sladek, Rob R; Meigs, James B JB; Rich, Steve S SS; Rotter, Jerome I JI; , ; , ; , ; , ; , ; , ; , ; , ; , ; Altshuler, David D; Burtt, Noël P NP; Scott, Laura J LJ; Morris, Andrew P AP; Florez, Jose C JC; McCarthy, Mark I MI; Boehnke, Michael M
Publication Date: 2019-06
Variant appearance in text: VPS33B: Gly514Ser; rs11073964
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: VPS33B: 1540G>A; G514S; rs11073964
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: VPS33B: G514S; rs11073964
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
Publication Date: 2019-02-27
Variant appearance in text: VPS33B: 1540G>A; Gly514Ser; rs11073964
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: VPS33B: G514S; rs11073964
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.
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: VPS33B: G514S; rs11073964
Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes.
Nature Communications
Bonàs-Guarch, Sílvia S; Guindo-Martínez, Marta M; Miguel-Escalada, Irene I; Grarup, Niels N; Sebastian, David D; Rodriguez-Fos, Elias E; Sánchez, Friman F; Planas-Fèlix, Mercè M; Cortes-Sánchez, Paula P; González, Santi S; Timshel, Pascal P; Pers, Tune H TH; Morgan, Claire C CC; Moran, Ignasi I; Atla, Goutham G; González, Juan R JR; Puiggros, Montserrat M; Martí, Jonathan J; Andersson, Ehm A EA; Díaz, Carlos C; Badia, Rosa M RM; Udler, Miriam M; Leong, Aaron A; Kaur, Varindepal V; Flannick, Jason J; Jørgensen, Torben T; Linneberg, Allan A; Jørgensen, Marit E ME; Witte, Daniel R DR; Christensen, Cramer C; Brandslund, Ivan I; Appel, Emil V EV; Scott, Robert A RA; Luan, Jian'an J; Langenberg, Claudia C; Wareham, Nicholas J NJ; Pedersen, Oluf O; Zorzano, Antonio A; Florez, Jose C JC; Hansen, Torben T; Ferrer, Jorge J; Mercader, Josep Maria JM; Torrents, David D
Publication Date: 2018-01-22
Variant appearance in text: VPS33B: Gly514Ser; rs11073964
Three-dimensional modelling identifies novel genetic dependencies associated with breast cancer progression in the isogenic MCF10 model.
The Journal Of Pathology
Maguire, Sarah L SL; Peck, Barrie B; Wai, Patty T PT; Campbell, James J; Barker, Holly H; Gulati, Aditi A; Daley, Frances F; Vyse, Simon S; Huang, Paul P; Lord, Christopher J CJ; Farnie, Gillian G; Brennan, Keith K; Natrajan, Rachael R
Publication Date: 2016-11
Variant appearance in text: VPS33B: G514S; rs11073964
Deleterious coding variants in multi-case families with non-syndromic cleft lip and/or palate phenotypes.
Scientific Reports
Pengelly, Reuben J RJ; Arias, Liliana L; Martínez, Julio J; Upstill-Goddard, Rosanna R; Seaby, Eleanor G EG; Gibson, Jane J; Ennis, Sarah S; Collins, Andrew A; Briceño, Ignacio I
Publication Date: 2016-07-26
Variant appearance in text: VPS33B: G514S; rs11073964
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; ,
Publication Date: 2016-06-02
Variant appearance in text: VPS33B: G514S; rs11073964
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: VPS33B: G514S; rs11073964