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CancerRadar

CancerRadar – accurate and sensitive detection and localization of cancer

CancerRadar

Early cancer detection by cell-free DNA (cfDNA) faces multiple challenges: the low fraction of tumor DNA in cfDNA, the molecular heterogeneity of cancer, and sample sizes that are too small to reflect the diverse patient population. We have developed an integrated cancer detection system that addresses all three challenges. It consists of (1) a cost-effective experimental assay, cfMethyl-Seq, for genome-wide methylation profiling of cfDNA, which provides >12-fold enrichment over Whole Genome Bisulfite Sequencing in CpG islands; and (2) a computational platform to extract multiple types of methylation information from cfMethyl-Seq data and diagnose the patient.

Applying our system to 408 colon, liver, lung, and stomach cancer patients and controls, at the specificity of 97.9% we achieve a sensitivity of 85.9% in detecting all-stage cancer and a sensitivity of 81.4% in detecting early-stage (I and II) cancers, and an accuracy of 89.6% for locating the Tissue-Of-Origin (TOO) of all-stage cancer and of 84.4% for early-stage cancer.

References:

  1. Stackpole ML*, Zeng W*, Li S*, Liu CC, Zhou Y, He S, Yeh A, Wang Z, Sun F, Li Q, Yuan Z, Yildirim A, Chen PJ, Winograd P, Tran B, Li PS, Noor Z, Garon EB, French S, Magyar CE, Dry S, Lajonchere C, Geschwind D, Choi G, Saab S, Alber F, Wong WH, Dubinett SM, Aberle D, Agopian VG#, Han SHB#, Ni X#, Li W#, Zhou XJ# (2022). Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.
    Submitted.
  2. Li W*, Li Q*, Kang S, Same M, Zhou Y, Sun C, Liu CC, Matsuoka L, Sher L, Wong WH, Alber F and Zhou XJ (2018). CancerDetector: Ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data
    Nucleic Acid Research, 2018 Sep;46(15):e89.
  1. Kang S, Li Q, Chen Q, Zhou Y, Park S, Lee G, Grimes, B, Krysan K, Yu M, Wang W, Alber F, Sun F, Dubinett SM#, Li W#, Zhou XJ#(2017). CancerLocator: Non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA
    Genome Biology, 2017 Mar 24;18(1):53.