2022
Centers for Mendelian Genomics: A decade of facilitating gene discovery
Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Consortium C, Adams M, Aguet F, Akay G, Anderson P, Antonescu C, Arachchi H, Atik M, Austin-Tse C, Babb L, Bacus T, Bahrambeigi V, Balasubramanian S, Bayram Y, Beaudet A, Beck C, Belmont J, Below J, Bilguvar K, Boehm C, Boerwinkle E, Boone P, Bowne S, Brand H, Buckingham K, Byrne A, Calame D, Campbell I, Cao X, Carvalho C, Chander V, Chang J, Chao K, Chinn I, Clarke D, Collins R, Cummings B, Dardas Z, Dawood M, Delano K, DiTroia S, Doddapaneni H, Du H, Du R, Duan R, Eldomery M, Eng C, England E, Evangelista E, Everett S, Fatih J, Felsenfeld A, Francioli L, Frazar C, Fu J, Gamarra E, Gambin T, Gan W, Gandhi M, Ganesh V, Garimella K, Gauthier L, Giroux D, Gonzaga-Jauregui C, Goodrich J, Gordon W, Griffith S, Grochowski C, Gu S, Gudmundsson S, Hall S, Hansen A, Harel T, Harmanci A, Herman I, Hetrick K, Hijazi H, Horike-Pyne M, Hsu E, Hu J, Huang Y, Hurless J, Jahl S, Jarvik G, Jiang Y, Johanson E, Jolly A, Karaca E, Khayat M, Knight J, Kolar J, Kumar S, Lalani S, Laricchia K, Larkin K, Leal S, Lemire G, Lewis R, Li H, Ling H, Lipson R, Liu P, Lovgren A, López-Giráldez F, MacMillan M, Mangilog B, Mano S, Marafi D, Marosy B, Marshall J, Martin R, Marvin C, Mawhinney M, McGee S, McGoldrick D, Mehaffey M, Mekonnen B, Meng X, Mitani T, Miyake C, Mohr D, Morris S, Mullen T, Murdock D, Murugan M, Muzny D, Myers B, Neira J, Nguyen K, Nielsen P, Nudelman N, O’Heir E, O’Leary M, Ongaco C, Orange J, Osei-Owusu I, Paine I, Pais L, Paschall J, Patterson K, Pehlivan D, Pelle B, Penney S, Chavez J, Pierce-Hoffman E, Poli C, Punetha J, Radhakrishnan A, Richardson M, Rodrigues E, Roote G, Rosenfeld J, Ryke E, Sabo A, Sanchez A, Schrauwen I, Scott D, Sedlazeck F, Serrano J, Shaw C, Shelford T, Shively K, Singer-Berk M, Smith J, Snow H, Snyder G, Solomonson M, Son R, Song X, Stankiewicz P, Stephan T, Sutton V, Sveden A, Sánchez D, Tackett M, Talkowski M, Threlkeld M, Tiao G, Udler M, Vail L, Valivullah Z, Valkanas E, VanNoy G, Wang Q, Wang G, Wang L, Wangler M, Watts N, Weisburd B, Weiss J, Wheeler M, White J, Williamson C, Wilson M, Wiszniewski W, Withers M, Witmer D, Witzgall L, Wohler E, Wojcik M, Wong I, Wood J, Wu N, Xing J, Yang Y, Yi Q, Yuan B, Zeiger J, Zhang C, Zhang P, Zhang Y, Zhang X, Zhang Y, Zhang S, Zoghbi H, van den Veyver I, Rehm H, O’Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genetics In Medicine 2022, 24: 784-797. PMID: 35148959, PMCID: PMC9119004, DOI: 10.1016/j.gim.2021.12.005.Peer-Reviewed Original ResearchConceptsGene discoveryMendelian GenomicsUnderstanding of genesGene-phenotype relationshipsGenome variationWorldwide data sharingCandidate genesMendelian phenotypesGenomic researchGenome sequencingMatchmaker ExchangeGenomicsGenesSequencingBiomedical researchMajor roleDiscoveryExomePhenotypeRoleGenotypesCommunityImplications of Selection Bias Due to Delayed Study Entry in Clinical Genomic Studies
Brown S, Lavery J, Shen R, Martin A, Kehl K, Sweeney S, Lepisto E, Rizvi H, McCarthy C, Schultz N, Warner J, Park B, Bedard P, Riely G, Schrag D, Panageas K, Sweeney S, Foti M, Khotskaya Y, Fiandalo M, Gross B, Schultz N, Mastrogiacomo B, Sarmardy M, Li M, Resnick A, Waanders A, Lilly J, Carvajal R, Rabadan R, Ingham M, Hsaio S, Abraham J, Brenton J, Rueda O, Caldas C, Valgañón M, Silva D, Boursnell C, Garcia R, Rodriguez E, Nimmervoll B, Cerami E, Ducar M, Kumari P, Lindeman N, MacConnaill L, Orechia J, Schrag D, Shivdasani P, Van Allen E, Johnson J, Jänne P, Lepisto E, Hassett M, Pimentel S, Sripakdeevong P, Janeway K, Johnson J, Meyerson M, Quinn D, Cushing O, Haigis K, Miller D, Kehl K, Gustav A, Tramontano A, Baquero S, Bell J, Green M, McCall S, Datto M, Calvo F, Andre F, Guillaume M, Dogan S, Ludovic L, Scoazec J, Ardenos M, Vassal G, Michels S, Velculescu V, Baras A, Gocke C, Brahmer J, Sawyers C, Solit D, Gardos S, Berger M, Ladanyi M, Riely G, Sirintrapun J, Panageas K, Caroline A, Thomas S, Zarski A, Zehir A, Iasonosa A, Philip J, Brown S, Kung A, Kundra R, Rudolph J, Lavery J, Rivzi H, Schwartz J, McCarthy C, Bhuiya M, Martin A, Chu C, DuBois R, van de Velde T, Meijer G, Horlings H, van Tinteren H, Lolkema M, Nijman L, Bierkens M, Hoeve J, Voest E, Hiemstra A, Sonke G, Craenmehr J, Hudecek J, Monkhorst K, Urba W, Bernard B, Piening B, Bifulco C, Tittel P, Cramer J, Guinney J, Yu T, Guo X, Acebedo A, Gold P, Bailey N, Kadri S, Segal J, Pankhuri W, Wang P, George S, Christine M, Van't Veer L, Talevich E, Wren A, Sweet-Cordero A, Turski M, Bedard P, KamelReid S, Lu Z, Pugh T, Siu L, Watt S, Leighl N, Yu C, Ahmed L, Krishna G, Virtaenen C, Chow H, Plagianakos D, Del Rossi S, Singaravelan N, Hakgor S, Qazi N, Nguyen A, Stickle N, Stricker T, Micheel C, Anderson I, Jones L, Wang L, Lovly C, LeNoue Newton M, Park B, Warner J, Fabbri D, Coco J, Ye C, Chaugai S, Mishra S, Yang Y, Wen L, Dienstmann R, Aguilar Izquierdo S, Viaplana Donato C, Mancuso F, Topaloglu U, Liu L, Guan M, Zhang W, Jin G, Knight J, D'Eletto M, Ormay E, Mane S, Bilguvar K, Zenta W, Dykas D. Implications of Selection Bias Due to Delayed Study Entry in Clinical Genomic Studies. JAMA Oncology 2022, 8: 287-291. PMID: 34734967, PMCID: PMC9190030, DOI: 10.1001/jamaoncol.2021.5153.Peer-Reviewed Original ResearchConceptsOverall survivalStage IV non-small cell lung cancerNon-small cell lung cancerStage IV colorectal cancerUnadjusted median survivalCell lung cancerMedian survivalStudy entryCancer outcomesColorectal cancerLung cancerMolecular testingSurvival analysisGeneralizable research findingsClinical genomic studiesSurvivalCancerSelection biasAppropriate statistical methodsDiagnosisAmerican Association
2021
Correlation Between Surrogate End Points and Overall Survival in a Multi-institutional Clinicogenomic Cohort of Patients With Non–Small Cell Lung or Colorectal Cancer
Kehl K, Riely G, Lepisto E, Lavery J, Warner J, LeNoue-Newton M, Sweeney S, Rudolph J, Brown S, Yu C, Bedard P, Schrag D, Panageas K, Sweeney S, Foti M, Khotskaya Y, Fiandalo M, Gross B, Schultz N, Mastrogiacomo B, Sarmardy M, Li M, Resnick A, Waanders A, Lilly J, Carvajal R, Rabadan R, Ingham M, Hsaio S, Abraham J, Brenton J, Rueda O, Caldas C, Valgañón M, Silva D, Boursnell C, Garcia R, Rodriguez E, Nimmervoll B, Cerami E, Ducar M, Kumari P, Lindeman N, MacConnaill L, Orechia J, Schrag D, Shivdasani P, Van Allen E, Johnson J, Jänne P, Lepisto E, Hassett M, Pimentel S, Sripakdeevong P, Janeway K, Johnson J, Meyerson M, Quinn D, Cushing O, Haigis K, Miller D, Kehl K, Gustav A, Tramontano A, Baquero S, Bell J, Green M, McCall S, Datto M, Calvo F, Andre F, Guillaume M, Dogan S, Ludovic L, Scoazec J, Ardenos M, Vassal G, Michels S, Velculescu V, Baras A, Gocke C, Brahmer J, Sawyers C, Solit D, Gardos S, Berger M, Ladanyi M, Riely G, Sirintrapun J, Caroline A, Thomas S, Zarski A, Zehir A, Iasonosa A, Philip J, Brown S, Kung A, Kundra R, Rudolph J, Lavery J, Rivzi H, Schwartz J, McCarthy C, Bhuiya M, Martin A, Chu C, DuBois R, van de Velde T, Meijer G, Horlings H, van Tinteren H, Lolkema M, Nijman L, Bierkens M, Hoeve J, Voest E, Hiemstra A, Sonke G, Craenmehr J, Hudecek J, Monkhorst K, Urba W, Bernard B, Piening B, Bifulco C, Tittel P, Cramer J, Guinney J, Yu T, Guo X, Acebedo A, Gold P, Bailey N, Kadri S, Segal J, Pankhuri W, Wang P, George S, Christine M, Van't Veer L, Talevich E, Wren A, Sweet-Cordero A, Turski M, Bedard P, KamelReid S, Lu Z, Pugh T, Siu L, Watt S, Leighl N, Yu C, Ahmed L, Krishna G, Virtaenen C, Chow H, Plagianakos D, Del Rossi S, Singaravelan N, Hakgor S, Qazi N, Nguyen A, Stickle N, Stricker T, Micheel C, Anderson I, Jones L, Wang L, Lovly C, LeNoue Newton M, Park B, Warner J, Fabbri D, Coco J, Ye C, Chaugai S, Mishra S, Yang Y, Wen L, Dienstmann R, Aguilar Izquierdo S, Viaplana Donato C, Mancuso F, Topaloglu U, Liu L, Guan M, Zhang W, Jin G, Knight J, D'Eletto M, Ormay E, Mane S, Bilguvar K, Zenta W, Dykas D. Correlation Between Surrogate End Points and Overall Survival in a Multi-institutional Clinicogenomic Cohort of Patients With Non–Small Cell Lung or Colorectal Cancer. JAMA Network Open 2021, 4: e2117547. PMID: 34309669, PMCID: PMC8314138, DOI: 10.1001/jamanetworkopen.2021.17547.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerCandidate surrogate end pointsProgression-free survivalSurrogate end pointsOverall survivalTreatment discontinuationColorectal cancerEnd pointCohort studyNext treatmentNon-small cell lungRetrospective cohort studyAlternative end pointsCell lung cancerKey end pointsAdvanced diseasePrimary outcomeSystemic therapyCell lungLung cancerProlonged survivalMAIN OUTCOMEProgression eventsAcademic centersPatients
2013
Genomic Analysis of Non-NF2 Meningiomas Reveals Mutations in TRAF7, KLF4, AKT1, and SMO
Clark VE, Erson-Omay EZ, Serin A, Yin J, Cotney J, Özduman K, Avşar T, Li J, Murray PB, Henegariu O, Yilmaz S, Günel JM, Carrión-Grant G, Yılmaz B, Grady C, Tanrıkulu B, Bakırcıoğlu M, Kaymakçalan H, Caglayan AO, Sencar L, Ceyhun E, Atik AF, Bayri Y, Bai H, Kolb LE, Hebert RM, Omay SB, Mishra-Gorur K, Choi M, Overton JD, Holland EC, Mane S, State MW, Bilgüvar K, Baehring JM, Gutin PH, Piepmeier JM, Vortmeyer A, Brennan CW, Pamir MN, Kılıç T, Lifton RP, Noonan JP, Yasuno K, Günel M. Genomic Analysis of Non-NF2 Meningiomas Reveals Mutations in TRAF7, KLF4, AKT1, and SMO. Science 2013, 339: 1077-1080. PMID: 23348505, PMCID: PMC4808587, DOI: 10.1126/science.1233009.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBrain NeoplasmsChromosomes, Human, Pair 22DNA Mutational AnalysisFemaleGenes, Neurofibromatosis 2Genomic InstabilityGenomicsHumansKruppel-Like Factor 4Kruppel-Like Transcription FactorsMaleMeningeal NeoplasmsMeningiomaMiddle AgedMutationNeoplasm GradingProto-Oncogene Proteins c-aktReceptors, G-Protein-CoupledSmoothened ReceptorTumor Necrosis Factor Receptor-Associated Peptides and Proteins