Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria.
American Journal Of Human Genetics
Pejaver, Vikas V; Byrne, Alicia B AB; Feng, Bing-Jian BJ; Pagel, Kymberleigh A KA; Mooney, Sean D SD; Karchin, Rachel R; O'Donnell-Luria, Anne A; Harrison, Steven M SM; Tavtigian, Sean V SV; Greenblatt, Marc S MS; Biesecker, Leslie G LG; Radivojac, Predrag P; Brenner, Steven E SE; ,
Publication Date: 2022-12-01
Variant appearance in text: EGFR: A743T; rs759256622
Analysis of matched primary and recurrent BRCA1/2 mutation-associated tumors identifies recurrence-specific drivers.
Nature Communications
Shah, Jennifer B JB; Pueschl, Dana D; Wubbenhorst, Bradley B; Fan, Mengyao M; Pluta, John J; D'Andrea, Kurt K; Hubert, Anna P AP; Shilan, Jake S JS; Zhou, Wenting W; Kraya, Adam A AA; Llop Guevara, Alba A; Ruan, Catherine C; Serra, Violeta V; Balmaña, Judith J; Feldman, Michael M; Morin, Pat J PJ; Nayak, Anupma A; Maxwell, Kara N KN; Domchek, Susan M SM; Nathanson, Katherine L KL
Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma.
Nature Communications
Coy, Shannon S; Wang, Shu S; Stopka, Sylwia A SA; Lin, Jia-Ren JR; Yapp, Clarence C; Ritch, Cecily C CC; Salhi, Lisa L; Baker, Gregory J GJ; Rashid, Rumana R; Baquer, Gerard G; Regan, Michael M; Khadka, Prasidda P; Cole, Kristina A KA; Hwang, Jaeho J; Wen, Patrick Y PY; Bandopadhayay, Pratiti P; Santi, Mariarita M; De Raedt, Thomas T; Ligon, Keith L KL; Agar, Nathalie Y R NYR; Sorger, Peter K PK; Touat, Mehdi M; Santagata, Sandro S
Somatic targeted mutation profiling of colorectal cancer precursor lesions.
Bmc Medical Genomics
Dos Santos, Wellington W; Dos Reis, Mariana Bisarro MB; Porto, Jun J; de Carvalho, Ana Carolina AC; Matsushita, Marcus M; Oliveira, Gabriela G; Syrjänen, Kari K; Reis, Rui Manuel RM; Guimarães, Denise Peixoto DP
Publication Date: 2022-06-28
Variant appearance in text: EGFR: Ala743Thr; rs759256622
Profiling diverse sequence tandem repeats in colorectal cancer reveals co-occurrence of microsatellite and chromosomal instability involving Chromosome 8.
Genome Medicine
Shin, GiWon G; Greer, Stephanie U SU; Hopmans, Erik E; Grimes, Susan M SM; Lee, HoJoon H; Zhao, Lan L; Miotke, Laura L; Suarez, Carlos C; Almeda, Alison F AF; Haraldsdottir, Sigurdis S; Ji, Hanlee P HP
Targeted mutation detection in breast cancer using MammaSeq™.
Breast Cancer Research : Bcr
Smith, Nicholas G NG; Gyanchandani, Rekha R; Shah, Osama S OS; Gurda, Grzegorz T GT; Lucas, Peter C PC; Hartmaier, Ryan J RJ; Brufsky, Adam M AM; Puhalla, Shannon S; Bahreini, Amir A; Kota, Karthik K; Wald, Abigail I AI; Nikiforov, Yuri E YE; Nikiforova, Marina N MN; Oesterreich, Steffi S; Lee, Adrian V AV
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
Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.
Genetics In Medicine : Official Journal Of The American College Of Medical Genetics
Robbe, Pauline P; Popitsch, Niko N; Knight, Samantha J L SJL; Antoniou, Pavlos P; Becq, Jennifer J; He, Miao M; Kanapin, Alexander A; Samsonova, Anastasia A; Vavoulis, Dimitrios V DV; Ross, Mark T MT; Kingsbury, Zoya Z; Cabes, Maite M; Ramos, Sara D C SDC; Page, Suzanne S; Dreau, Helene H; Ridout, Kate K; Jones, Louise J LJ; Tuff-Lacey, Alice A; Henderson, Shirley S; Mason, Joanne J; Buffa, Francesca M FM; Verrill, Clare C; Maldonado-Perez, David D; Roxanis, Ioannis I; Collantes, Elena E; Browning, Lisa L; Dhar, Sunanda S; Damato, Stephen S; Davies, Susan S; Caulfield, Mark M; Bentley, David R DR; Taylor, Jenny C JC; Turnbull, Clare C; Schuh, Anna A; ,
VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.
Nucleic Acids Research
Lai, Zhongwu Z; Markovets, Aleksandra A; Ahdesmaki, Miika M; Chapman, Brad B; Hofmann, Oliver O; McEwen, Robert R; Johnson, Justin J; Dougherty, Brian B; Barrett, J Carl JC; Dry, Jonathan R JR
Epidermal growth factor receptor (EGFR) high gene copy number and activating mutations in lung adenocarcinomas are not consistently accompanied by positivity for EGFR protein by standard immunohistochemistry.
The Journal Of Molecular Diagnostics : Jmd
Pinter, Ferenc F; Papay, Judit J; Almasi, Andrea A; Sapi, Zoltan Z; Szabo, Edit E; Kanya, Melinda M; Tamasi, Anna A; Jori, Balazs B; Varkondi, Edit E; Moldvay, Judit J; Szondy, Klara K; Keri, Gyorgy G; Dominici, Massimo M; Conte, Pierfranco P; Eckhardt, Sandor S; Kopper, Laszlo L; Schwab, Richard R; Petak, Istvan I