All Publications

  • Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing. Genome medicine Lau, B. T., Almeda, A., Schauer, M., McNamara, M., Bai, X., Meng, Q., Partha, M., Grimes, S. M., Lee, H., Heestand, G. M., Ji, H. P. 2023; 15 (1): 33


    Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This approach generated up to 200 million reads for a single cfDNA sample from cancer patients, an order of magnitude improvement over existing nanopore sequencing methods. We developed a single-molecule classifier to determine whether individual reads originated from a tumor or immune cells. Leveraging methylomes of matched tumors and immune cells, we characterized cfDNA methylomes of cancer patients for longitudinal monitoring during treatment.

    View details for DOI 10.1186/s13073-023-01178-3

    View details for PubMedID 37138315

    View details for PubMedCentralID 1283450

  • Tumor-associated microbiome features of metastatic colorectal cancer and clinical implications. Frontiers in oncology An, H. J., Partha, M. A., Lee, H., Lau, B. T., Pavlichin, D. S., Almeda, A., Hooker, A. C., Shin, G., Ji, H. P. 2023; 13: 1310054


    Colon microbiome composition contributes to the pathogenesis of colorectal cancer (CRC) and prognosis. We analyzed 16S rRNA sequencing data from tumor samples of patients with metastatic CRC and determined the clinical implications.We enrolled 133 patients with metastatic CRC at St. Vincent Hospital in Korea. The V3-V4 regions of the 16S rRNA gene from the tumor DNA were amplified, sequenced on an Illumina MiSeq, and analyzed using the DADA2 package.After excluding samples that retained <5% of the total reads after merging, 120 samples were analyzed. The median age of patients was 63 years (range, 34-82 years), and 76 patients (63.3%) were male. The primary cancer sites were the right colon (27.5%), left colon (30.8%), and rectum (41.7%). All subjects received 5-fluouracil-based systemic chemotherapy. After removing genera with <1% of the total reads in each patient, 523 genera were identified. Rectal origin, high CEA level (≥10 ng/mL), and presence of lung metastasis showed higher richness. Survival analysis revealed that the presence of Prevotella (p = 0.052), Fusobacterium (p = 0.002), Selenomonas (p<0.001), Fretibacterium (p = 0.001), Porphyromonas (p = 0.007), Peptostreptococcus (p = 0.002), and Leptotrichia (p = 0.003) were associated with short overall survival (OS, <24 months), while the presence of Sphingomonas was associated with long OS (p = 0.070). From the multivariate analysis, the presence of Selenomonas (hazard ratio [HR], 6.35; 95% confidence interval [CI], 2.38-16.97; p<0.001) was associated with poor prognosis along with high CEA level.Tumor microbiome features may be useful prognostic biomarkers for metastatic CRC.

    View details for DOI 10.3389/fonc.2023.1310054

    View details for PubMedID 38304032

    View details for PubMedCentralID PMC10833227

  • Analysis of 16S rRNA sequencing in advanced colorectal cancer tissue samples An, H., Partha, M. A., Lee, H., Lau, B., Shin, G., Almeda, A., Ji, H. P. LIPPINCOTT WILLIAMS & WILKINS. 2022