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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.
Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth GP, Abaan OD, Talsania K, Lack J, Shen TW, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Tezak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Shi L, Wang C, Xiao W; Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium. Fang LT, et al. Among authors: ren l. Nat Biotechnol. 2021 Sep;39(9):1151-1160. doi: 10.1038/s41587-021-00993-6. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504347 Free PMC article.
Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies.
Jiang YZ, Ma D, Suo C, Shi J, Xue M, Hu X, Xiao Y, Yu KD, Liu YR, Yu Y, Zheng Y, Li X, Zhang C, Hu P, Zhang J, Hua Q, Zhang J, Hou W, Ren L, Bao D, Li B, Yang J, Yao L, Zuo WJ, Zhao S, Gong Y, Ren YX, Zhao YX, Yang YS, Niu Z, Cao ZG, Stover DG, Verschraegen C, Kaklamani V, Daemen A, Benson JR, Takabe K, Bai F, Li DQ, Wang P, Shi L, Huang W, Shao ZM. Jiang YZ, et al. Among authors: ren l, ren yx. Cancer Cell. 2019 Mar 18;35(3):428-440.e5. doi: 10.1016/j.ccell.2019.02.001. Epub 2019 Mar 7. Cancer Cell. 2019. PMID: 30853353 Free article.
Functional consequences of a rare missense BARD1 c.403G>A germline mutation identified in a triple-negative breast cancer patient.
Zheng Y, Li B, Pan D, Cao J, Zhang J, Wang X, Li X, Hou W, Bao D, Ren L, Yang J, Wang S, Qiu Y, Zhou F, Liu Z, Zhu S, Zhang L, Qing T, Wang Y, Yu Y, Wu J, Hu X, Shi L. Zheng Y, et al. Among authors: ren l. Breast Cancer Res. 2021 May 1;23(1):53. doi: 10.1186/s13058-021-01428-5. Breast Cancer Res. 2021. PMID: 33933153 Free PMC article.
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.
Xiao W, Ren L, Chen Z, Fang LT, Zhao Y, Lack J, Guan M, Zhu B, Jaeger E, Kerrigan L, Blomquist TM, Hung T, Sultan M, Idler K, Lu C, Scherer A, Kusko R, Moos M, Xiao C, Sherry ST, Abaan OD, Chen W, Chen X, Nordlund J, Liljedahl U, Maestro R, Polano M, Drabek J, Vojta P, Kõks S, Reimann E, Madala BS, Mercer T, Miller C, Jacob H, Truong T, Moshrefi A, Natarajan A, Granat A, Schroth GP, Kalamegham R, Peters E, Petitjean V, Walton A, Shen TW, Talsania K, Vera CJ, Langenbach K, de Mars M, Hipp JA, Willey JC, Wang J, Shetty J, Kriga Y, Raziuddin A, Tran B, Zheng Y, Yu Y, Cam M, Jailwala P, Nguyen C, Meerzaman D, Chen Q, Yan C, Ernest B, Mehra U, Jensen RV, Jones W, Li JL, Papas BN, Pirooznia M, Chen YC, Seifuddin F, Li Z, Liu X, Resch W, Wang J, Wu L, Yavas G, Miles C, Ning B, Tong W, Mason CE, Donaldson E, Lababidi S, Staudt LM, Tezak Z, Hong H, Wang C, Shi L. Xiao W, et al. Among authors: ren l. Nat Biotechnol. 2021 Sep;39(9):1141-1150. doi: 10.1038/s41587-021-00994-5. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504346 Free PMC article.
Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.
Zhao Y, Fang LT, Shen TW, Choudhari S, Talsania K, Chen X, Shetty J, Kriga Y, Tran B, Zhu B, Chen Z, Chen W, Wang C, Jaeger E, Meerzaman D, Lu C, Idler K, Ren L, Zheng Y, Shi L, Petitjean V, Sultan M, Hung T, Peters E, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Foox J, Mason CE, Xiao C, Hong H, Xiao W. Zhao Y, et al. Among authors: ren l. Sci Data. 2021 Nov 9;8(1):296. doi: 10.1038/s41597-021-01077-5. Sci Data. 2021. PMID: 34753956 Free PMC article.
Assessing reproducibility of inherited variants detected with short-read whole genome sequencing.
Pan B, Ren L, Onuchic V, Guan M, Kusko R, Bruinsma S, Trigg L, Scherer A, Ning B, Zhang C, Glidewell-Kenney C, Xiao C, Donaldson E, Sedlazeck FJ, Schroth G, Yavas G, Grunenwald H, Chen H, Meinholz H, Meehan J, Wang J, Yang J, Foox J, Shang J, Miclaus K, Dong L, Shi L, Mohiyuddin M, Pirooznia M, Gong P, Golshani R, Wolfinger R, Lababidi S, Sahraeian SME, Sherry S, Han T, Chen T, Shi T, Hou W, Ge W, Zou W, Guo W, Bao W, Xiao W, Fan X, Gondo Y, Yu Y, Zhao Y, Su Z, Liu Z, Tong W, Xiao W, Zook JM, Zheng Y, Hong H. Pan B, et al. Among authors: ren l. Genome Biol. 2022 Jan 3;23(1):2. doi: 10.1186/s13059-021-02569-8. Genome Biol. 2022. PMID: 34980216 Free PMC article.
Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials.
Zheng Y, Liu Y, Yang J, Dong L, Zhang R, Tian S, Yu Y, Ren L, Hou W, Zhu F, Mai Y, Han J, Zhang L, Jiang H, Lin L, Lou J, Li R, Lin J, Liu H, Kong Z, Wang D, Dai F, Bao D, Cao Z, Chen Q, Chen Q, Chen X, Gao Y, Jiang H, Li B, Li B, Li J, Liu R, Qing T, Shang E, Shang J, Sun S, Wang H, Wang X, Zhang N, Zhang P, Zhang R, Zhu S, Scherer A, Wang J, Wang J, Huo Y, Liu G, Cao C, Shao L, Xu J, Hong H, Xiao W, Liang X, Lu D, Jin L, Tong W, Ding C, Li J, Fang X, Shi L. Zheng Y, et al. Among authors: ren l. Nat Biotechnol. 2023 Sep 7. doi: 10.1038/s41587-023-01934-1. Online ahead of print. Nat Biotechnol. 2023. PMID: 37679543
6,713 results