Browsing by Subject "Precision medicine"

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  • Gong, BS; Li, D; Kusko, R; Novoradovskaya, N; Zhang, YF; Wang, SZ; Pabon-Pena, C; Zhang, ZH; Lai, K; Cai, WS; LoCoco, JS; Lader, E; Richmond, TA; Mittal, VK; Liu, LC; Johann, DJ; Willey, JC; Bushel, PR; Yu, Y; Xu, C; Chen, GC; Burgess, D; Cawley, S; Giorda, K; Haseley, N; Qiu, FJ; Wilkins, K; Arib, H; Attwooll, C; Babson, K; Bao, LL; Bao, WJ; Lucas, AB; Best, H; Bhandari, A; Bisgin, H; Blackburn, J; Blomquist, TM; Boardman, L; Burgher, B; Butler, DJ; Chang, CJ; Chaubey, A; Chen, T; Chierici, M; Chin, CR; Close, D; Conroy, J; Coleman, JC; Craig, DJ; Crawford, E; del Pozo, A; Deveson, IW; Duncan, D; Eterovic, AK; Fan, XH; Foox, J; Furlanello, C; Ghosal, A; Glenn, S; Guan, MJ; Haag, C; Hang, XY; Happe, S; Hennigan, B; Hipp, J; Hong, HX; Horvath, K; Hu, JH; Hung, LY; Jarosz, M; Kerkhof, J; Kipp, B; Kreil, DP; Lapunzina, P; Li, P; Li, QZ; Li, WH; Li, ZG; Liang, Y; Liu, SQ; Liu, ZC; Ma, C; Marella, N; Martin-Arenas, R; Megherbi, DB; Meng, QC; Mieczkowski, PA; Morrison, T; Muzny, D; Ning, BT; Parsons, BL; Paweletz, CP; Pirooznia, M; Qu, WB; Raymond, A; Rindler, P; Ringler, R; Sadikovic, B; Scherer, A; Schulze, E; Sebra, R; Shaknovich, R; Shi, Q; Shi, TL; Silla-Castro, JC; Smith, M; Lopez, MS; Song, P; Stetson, D; Strahl, M; Stuart, A; Supplee, J; Szankasi, P; Tan, HW; Tang, LY; Tao, YH; Thakkar, S; Thierry-Mieg, D; Thierry-Mieg, J; Thodima, VJ; Thomas, D; Tichy, B; Tom, N; Garcia, EV; Verma, S; Walker, K; Wang, C; Wang, JW; Wang, YX; Wen, ZN; Wirta, V; Wu, LH; Xiao, CL; Xiao, WZ; Xu, SB; Yang, M; Ying, JM; Yip, SH; Zhang, GL; Zhang, S; Zhao, MR; Zheng, YT; Zhou, XY; Mason, CE; Mercer, T; Tong, WD; Shi, LM; Jones, W; Xu, JS (2021)
    BackgroundTargeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.ResultsAll panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.ConclusionThis comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.
  • Alligier, Maud; Barres, Romain; Blaak, Ellen E.; Boirie, Yves; Bouwman, Jildau; Brunault, Paul; Campbell, Kristina; Clement, Karine; Farooqi, I. Sadaf; Farpour-Lambert, Nathalie J.; Fruhbeck, Gema; Goossens, Gijs H.; Hager, Jorg; Halford, Jason C. G.; Hauner, Hans; Jacobi, David; Julia, Chantal; Langin, Dominique; Natali, Andrea; Neovius, Martin; Oppert, Jean Michel; Pagotto, Uberto; Palmeira, Antonio L.; Roche, Helen; Ryden, Mikael; Scheen, Andre J.; Simon, Chantal; Sorensen, Thorkild I. A.; Tappy, Luc; Yki-Järvinen, Hannele; Ziegler, Olivier; Laville, Martine (2020)
    Heterogeneity of interindividual and intraindividual responses to interventions is often observed in randomized, controlled trials for obesity. To address the global epidemic of obesity and move toward more personalized treatment regimens, the global research community must come together to identify factors that may drive these heterogeneous responses to interventions. This project, called OBEDIS (OBEsity Diverse Interventions Sharing - focusing on dietary and other interventions), provides a set of European guidelines for a minimal set of variables to include in future clinical trials on obesity, regardless of the specific endpoints. Broad adoption of these guidelines will enable researchers to harmonize and merge data from multiple intervention studies, allowing stratification of patients according to precise phenotyping criteria which are measured using standardized methods. In this way, studies across Europe may be pooled for better prediction of individuals' responses to an intervention for obesity - ultimately leading to better patient care and improved obesity outcomes.
  • Santos-Cortez, R.L.P.; Bhutta, M.F.; Earl, J.P.; Hafrén, Lena; Jennings, M.; Mell, J.C.; Pichichero, M.E.; Ryan, A.F.; Tateossian, Hilda; Ehrlich, G.D. (2020)
    Objective: To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media. Data sources: PubMed articles published since the last meeting in June 2015 up to June 2019. Review methods: A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. Conclusion: Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media. Implications for practice: In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics. © 2020 Elsevier B.V.