BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

137 related articles for article (PubMed ID: 38229122)

  • 1. A benchmarking framework for the accurate and cost-effective detection of clinically-relevant structural variants for cancer target identification and diagnosis.
    Zhuang G; Zhang X; Du W; Xu L; Ma J; Luo H; Tang H; Wang W; Wang P; Li M; Yang X; Wu D; Fang S
    J Transl Med; 2024 Jan; 22(1):65. PubMed ID: 38229122
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.
    Talsania K; Shen TW; Chen X; Jaeger E; Li Z; Chen Z; Chen W; Tran B; Kusko R; Wang L; Pang AWC; Yang Z; Choudhari S; Colgan M; Fang LT; Carroll A; Shetty J; Kriga Y; German O; Smirnova T; Liu T; Li J; Kellman B; Hong K; Hastie AR; Natarajan A; Moshrefi A; Granat A; Truong T; Bombardi R; Mankinen V; Meerzaman D; Mason CE; Collins J; Stahlberg E; Xiao C; Wang C; Xiao W; Zhao Y
    Genome Biol; 2022 Dec; 23(1):255. PubMed ID: 36514120
    [TBL] [Abstract][Full Text] [Related]  

  • 3. A comprehensive benchmarking of WGS-based deletion structural variant callers.
    Sarwal V; Niehus S; Ayyala R; Kim M; Sarkar A; Chang S; Lu A; Rajkumar N; Darfci-Maher N; Littman R; Chhugani K; Soylev A; Comarova Z; Wesel E; Castellanos J; Chikka R; Distler MG; Eskin E; Flint J; Mangul S
    Brief Bioinform; 2022 Jul; 23(4):. PubMed ID: 35753701
    [TBL] [Abstract][Full Text] [Related]  

  • 4. svclassify: a method to establish benchmark structural variant calls.
    Parikh H; Mohiyuddin M; Lam HY; Iyer H; Chen D; Pratt M; Bartha G; Spies N; Losert W; Zook JM; Salit M
    BMC Genomics; 2016 Jan; 17():64. PubMed ID: 26772178
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
    Lee AY; Ewing AD; Ellrott K; Hu Y; Houlahan KE; Bare JC; Espiritu SMG; Huang V; Dang K; Chong Z; Caloian C; Yamaguchi TN; ; Kellen MR; Chen K; Norman TC; Friend SH; Guinney J; Stolovitzky G; Haussler D; Margolin AA; Stuart JM; Boutros PC
    Genome Biol; 2018 Nov; 19(1):188. PubMed ID: 30400818
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods.
    Mu JC; Tootoonchi Afshar P; Mohiyuddin M; Chen X; Li J; Bani Asadi N; Gerstein MB; Wong WH; Lam HY
    Sci Rep; 2015 Sep; 5():14493. PubMed ID: 26412485
    [TBL] [Abstract][Full Text] [Related]  

  • 7. PerSVade: personalized structural variant detection in any species of interest.
    Schikora-Tamarit MÀ; Gabaldón T
    Genome Biol; 2022 Aug; 23(1):175. PubMed ID: 35974382
    [TBL] [Abstract][Full Text] [Related]  

  • 8. SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines.
    Leung WY; Marschall T; Paudel Y; Falquet L; Mei H; Schönhuth A; Maoz Moss TY
    BMC Genomics; 2015 Mar; 16(1):238. PubMed ID: 25887570
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Structural Variant Detection from Long-Read Sequencing Data with cuteSV.
    Jiang T; Liu S; Cao S; Wang Y
    Methods Mol Biol; 2022; 2493():137-151. PubMed ID: 35751813
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Detection of structural variation using target captured next-generation sequencing data for genetic diagnostic testing.
    Mu W; Li B; Wu S; Chen J; Sain D; Xu D; Black MH; Karam R; Gillespie K; Farwell Hagman KD; Guidugli L; Pronold M; Elliott A; Lu HM
    Genet Med; 2019 Jul; 21(7):1603-1610. PubMed ID: 30563988
    [TBL] [Abstract][Full Text] [Related]  

  • 11. SMaSH: a benchmarking toolkit for human genome variant calling.
    Talwalkar A; Liptrap J; Newcomb J; Hartl C; Terhorst J; Curtis K; Bresler M; Song YS; Jordan MI; Patterson D
    Bioinformatics; 2014 Oct; 30(19):2787-95. PubMed ID: 24894505
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data.
    Karimnezhad A; Palidwor GA; Thavorn K; Stewart DJ; Campbell PA; Lo B; Perkins TJ
    BMC Med Genomics; 2020 Oct; 13(1):156. PubMed ID: 33059707
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Comparison and benchmark of structural variants detected from long read and long-read assembly.
    Lin J; Jia P; Wang S; Kosters W; Ye K
    Brief Bioinform; 2023 Jul; 24(4):. PubMed ID: 37200087
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A multi-platform reference for somatic structural variation detection.
    Espejo Valle-Inclan J; Besselink NJM; de Bruijn E; Cameron DL; Ebler J; Kutzera J; van Lieshout S; Marschall T; Nelen M; Priestley P; Renkens I; Roemer MGM; van Roosmalen MJ; Wenger AM; Ylstra B; Fijneman RJA; Kloosterman WP; Cuppen E
    Cell Genom; 2022 Jun; 2(6):100139. PubMed ID: 36778136
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing.
    Kosugi S; Momozawa Y; Liu X; Terao C; Kubo M; Kamatani Y
    Genome Biol; 2019 Jun; 20(1):117. PubMed ID: 31159850
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools.
    Garcia-Prieto CA; Martínez-Jiménez F; Valencia A; Porta-Pardo E
    Bioinformatics; 2022 Jun; 38(12):3181-3191. PubMed ID: 35512388
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Comparison of multiple algorithms to reliably detect structural variants in pears.
    Liu Y; Zhang M; Sun J; Chang W; Sun M; Zhang S; Wu J
    BMC Genomics; 2020 Jan; 21(1):61. PubMed ID: 31959124
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies.
    Du X; Li L; Liang F; Liu S; Zhang W; Sun S; Sun Y; Fan F; Wang L; Liang X; Qiu W; Fan G; Wang O; Yang W; Zhang J; Xiao Y; Wang Y; Wang D; Qu S; Chen F; Huang J
    Genomics Proteomics Bioinformatics; 2022 Feb; 20(1):192-204. PubMed ID: 33662625
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Truvari: refined structural variant comparison preserves allelic diversity.
    English AC; Menon VK; Gibbs RA; Metcalf GA; Sedlazeck FJ
    Genome Biol; 2022 Dec; 23(1):271. PubMed ID: 36575487
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Best practices for benchmarking germline small-variant calls in human genomes.
    Krusche P; Trigg L; Boutros PC; Mason CE; De La Vega FM; Moore BL; Gonzalez-Porta M; Eberle MA; Tezak Z; Lababidi S; Truty R; Asimenos G; Funke B; Fleharty M; Chapman BA; Salit M; Zook JM;
    Nat Biotechnol; 2019 May; 37(5):555-560. PubMed ID: 30858580
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.