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: KRAS: 108A>G; Ile36Met
Spatially interacting phosphorylation sites and mutations in cancer.
Nature Communications
Huang, Kuan-Lin KL; Scott, Adam D AD; Zhou, Daniel Cui DC; Wang, Liang-Bo LB; Weerasinghe, Amila A; Elmas, Abdulkadir A; Liu, Ruiyang R; Wu, Yige Y; Wendl, Michael C MC; Wyczalkowski, Matthew A MA; Baral, Jessika J; Sengupta, Sohini S; Lai, Chin-Wen CW; Ruggles, Kelly K; Payne, Samuel H SH; Raphael, Benjamin B; Fenyö, David D; Chen, Ken K; Mills, Gordon G; Ding, Li L
EZH2 inactivation in RAS-driven myeloid neoplasms hyperactivates RAS-signaling and increases MEK inhibitor sensitivity.
Leukemia
Berg, Johannes Lorenz JL; Perfler, Bianca B; Hatzl, Stefan S; Uhl, Barbara B; Reinisch, Andreas A; Pregartner, Gudrun G; Berghold, Andrea A; Penz, Thomas T; Schuster, Michael M; Geissler, Klaus K; Prokesch, Andreas A; Müller-Tidow, Carsten C; Hoefler, Gerald G; Kashofer, Karl K; Wölfler, Albert A; Sill, Heinz H; Caraffini, Veronica V; Zebisch, Armin A
Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival.
Nature Communications
Zaidi, Syed H SH; Harrison, Tabitha A TA; Phipps, Amanda I AI; Steinfelder, Robert R; Trinh, Quang M QM; Qu, Conghui C; Banbury, Barbara L BL; Georgeson, Peter P; Grasso, Catherine S CS; Giannakis, Marios M; Adams, Jeremy B JB; Alwers, Elizabeth E; Amitay, Efrat L EL; Barfield, Richard T RT; Berndt, Sonja I SI; Borozan, Ivan I; Brenner, Hermann H; Brezina, Stefanie S; Buchanan, Daniel D DD; Cao, Yin Y; Chan, Andrew T AT; Chang-Claude, Jenny J; Connolly, Charles M CM; Drew, David A DA; Farris, Alton Brad AB; Figueiredo, Jane C JC; French, Amy J AJ; Fuchs, Charles S CS; Garraway, Levi A LA; Gruber, Steve S; Guinter, Mark A MA; Hamilton, Stanley R SR; Harlid, Sophia S; Heisler, Lawrence E LE; Hidaka, Akihisa A; Hopper, John L JL; Huang, Wen-Yi WY; Huyghe, Jeroen R JR; Jenkins, Mark A MA; Krzyzanowski, Paul M PM; Lemire, Mathieu M; Lin, Yi Y; Luo, Xuemei X; Mardis, Elaine R ER; McPherson, John D JD; Miller, Jessica K JK; Moreno, Victor V; Mu, Xinmeng Jasmine XJ; Nishihara, Reiko R; Papadopoulos, Nickolas N; Pasternack, Danielle D; Quist, Michael J MJ; Rafikova, Adilya A; Reid, Emma E G EEG; Shinbrot, Eve E; Shirts, Brian H BH; Stein, Lincoln D LD; Teney, Cherie D CD; Timms, Lee L; Um, Caroline Y CY; Van Guelpen, Bethany B; Van Tassel, Megan M; Wang, Xiaolong X; Wheeler, David A DA; Yung, Christina K CK; Hsu, Li L; Ogino, Shuji S; Gsur, Andrea A; Newcomb, Polly A PA; Gallinger, Steven S; Hoffmeister, Michael M; Campbell, Peter T PT; Thibodeau, Stephen N SN; Sun, Wei W; Hudson, Thomas J TJ; Peters, Ulrike U
mTOR Signaling and SREBP Activity Increase FADS2 Expression and Can Activate Sapienate Biosynthesis.
Cell Reports
Triki, Mouna M; Rinaldi, Gianmarco G; Planque, Melanie M; Broekaert, Dorien D; Winkelkotte, Alina M AM; Maier, Carina R CR; Janaki Raman, Sudha S; Vandekeere, Anke A; Van Elsen, Joke J; Orth, Martin F MF; Grünewald, Thomas G P TGP; Schulze, Almut A; Fendt, Sarah-Maria SM
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants.
Nature Medicine
Razavi, Pedram P; Li, Bob T BT; Brown, David N DN; Jung, Byoungsok B; Hubbell, Earl E; Shen, Ronglai R; Abida, Wassim W; Juluru, Krishna K; De Bruijn, Ino I; Hou, Chenlu C; Venn, Oliver O; Lim, Raymond R; Anand, Aseem A; Maddala, Tara T; Gnerre, Sante S; Vijaya Satya, Ravi R; Liu, Qinwen Q; Shen, Ling L; Eattock, Nicholas N; Yue, Jeanne J; Blocker, Alexander W AW; Lee, Mark M; Sehnert, Amy A; Xu, Hui H; Hall, Megan P MP; Santiago-Zayas, Angie A; Novotny, William F WF; Isbell, James M JM; Rusch, Valerie W VW; Plitas, George G; Heerdt, Alexandra S AS; Ladanyi, Marc M; Hyman, David M DM; Jones, David R DR; Morrow, Monica M; Riely, Gregory J GJ; Scher, Howard I HI; Rudin, Charles M CM; Robson, Mark E ME; Diaz, Luis A LA; Solit, David B DB; Aravanis, Alexander M AM; Reis-Filho, Jorge S JS
Publication Date: 2019-12
Variant appearance in text: KRAS: 108A>G; I36M; rs727503109
Assessing the Pathogenicity, Penetrance, and Expressivity of Putative Disease-Causing Variants in a Population Setting.
American Journal Of Human Genetics
Wright, Caroline F CF; West, Ben B; Tuke, Marcus M; Jones, Samuel E SE; Patel, Kashyap K; Laver, Thomas W TW; Beaumont, Robin N RN; Tyrrell, Jessica J; Wood, Andrew R AR; Frayling, Timothy M TM; Hattersley, Andrew T AT; Weedon, Michael N MN
appreci8: a pipeline for precise variant calling integrating 8 tools.
Bioinformatics (Oxford, England)
Sandmann, Sarah S; Karimi, Mohsen M; de Graaf, Aniek O AO; Rohde, Christian C; Göllner, Stefanie S; Varghese, Julian J; Ernsting, Jan J; Walldin, Gunilla G; van der Reijden, Bert A BA; Müller-Tidow, Carsten C; Malcovati, Luca L; Hellström-Lindberg, Eva E; Jansen, Joop H JH; Dugas, Martin M
Publication Date: 2018-12-15
Variant appearance in text: KRAS: 108A>G; Ile36Met
Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.
Plos One
Prentice, Leah M LM; Miller, Ruth R RR; Knaggs, Jeff J; Mazloomian, Alborz A; Aguirre Hernandez, Rosalia R; Franchini, Patrick P; Parsa, Kourosh K; Tessier-Cloutier, Basile B; Lapuk, Anna A; Huntsman, David D; Schaeffer, David F DF; Sheffield, Brandon S BS
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas.
Cell Reports
Way, Gregory P GP; Sanchez-Vega, Francisco F; La, Konnor K; Armenia, Joshua J; Chatila, Walid K WK; Luna, Augustin A; Sander, Chris C; Cherniack, Andrew D AD; Mina, Marco M; Ciriello, Giovanni G; Schultz, Nikolaus N; , ; Sanchez, Yolanda Y; Greene, Casey S CS
Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential.
Nature Communications
Wong, Terrence N TN; Miller, Christopher A CA; Jotte, Matthew R M MRM; Bagegni, Nusayba N; Baty, Jack D JD; Schmidt, Amy P AP; Cashen, Amanda F AF; Duncavage, Eric J EJ; Helton, Nichole M NM; Fiala, Mark M; Fulton, Robert S RS; Heath, Sharon E SE; Janke, Megan M; Luber, Kierstin K; Westervelt, Peter P; Vij, Ravi R; DiPersio, John F JF; Welch, John S JS; Graubert, Timothy A TA; Walter, Matthew J MJ; Ley, Timothy J TJ; Link, Daniel C DC
Protein-structure-guided discovery of functional mutations across 19 cancer types.
Nature Genetics
Niu, Beifang B; Scott, Adam D AD; Sengupta, Sohini S; Bailey, Matthew H MH; Batra, Prag P; Ning, Jie J; Wyczalkowski, Matthew A MA; Liang, Wen-Wei WW; Zhang, Qunyuan Q; McLellan, Michael D MD; Sun, Sam Q SQ; Tripathi, Piyush P; Lou, Carolyn C; Ye, Kai K; Mashl, R Jay RJ; Wallis, John J; Wendl, Michael C MC; Chen, Feng F; Ding, Li L
LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer.
Bmc Bioinformatics
Melloni, Giorgio E M GE; de Pretis, Stefano S; Riva, Laura L; Pelizzola, Mattia M; Céol, Arnaud A; Costanza, Jole J; Müller, Heiko H; Zammataro, Luca L
Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B
Age-related mutations associated with clonal hematopoietic expansion and malignancies.
Nature Medicine
Xie, Mingchao M; Lu, Charles C; Wang, Jiayin J; McLellan, Michael D MD; Johnson, Kimberly J KJ; Wendl, Michael C MC; McMichael, Joshua F JF; Schmidt, Heather K HK; Yellapantula, Venkata V; Miller, Christopher A CA; Ozenberger, Bradley A BA; Welch, John S JS; Link, Daniel C DC; Walter, Matthew J MJ; Mardis, Elaine R ER; Dipersio, John F JF; Chen, Feng F; Wilson, Richard K RK; Ley, Timothy J TJ; Ding, Li L
Functional heterogeneity of genetically defined subclones in acute myeloid leukemia.
Cancer Cell
Klco, Jeffery M JM; Spencer, David H DH; Miller, Christopher A CA; Griffith, Malachi M; Lamprecht, Tamara L TL; O'Laughlin, Michelle M; Fronick, Catrina C; Magrini, Vincent V; Demeter, Ryan T RT; Fulton, Robert S RS; Eades, William C WC; Link, Daniel C DC; Graubert, Timothy A TA; Walter, Matthew J MJ; Mardis, Elaine R ER; Dipersio, John F JF; Wilson, Richard K RK; Ley, Timothy J TJ
Biochemical and functional characterization of germ line KRAS mutations.
Molecular And Cellular Biology
Schubbert, Suzanne S; Bollag, Gideon G; Lyubynska, Natalya N; Nguyen, Hoa H; Kratz, Christian P CP; Zenker, Martin M; Niemeyer, Charlotte M CM; Molven, Anders A; Shannon, Kevin K
Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations.
Journal Of Medical Genetics
Zenker, Martin M; Lehmann, Katarina K; Schulz, Anna Leana AL; Barth, Helmut H; Hansmann, Dagmar D; Koenig, Rainer R; Korinthenberg, Rudolf R; Kreiss-Nachtsheim, Martina M; Meinecke, Peter P; Morlot, Susanne S; Mundlos, Stefan S; Quante, Anne S AS; Raskin, Salmo S; Schnabel, Dirk D; Wehner, Lars-Erik LE; Kratz, Christian P CP; Horn, Denise D; Kutsche, Kerstin K