Validation of K-cell versus Bulk Tissue

  • LIWEN’s K-Cell technology could offer comparable and stable NGS data quality to traditional bulk tissue sample in a low-input system.
  • QC Statistics of K-Cell vs Bulk tissue DNA-seq (WES)
    QC Statistics A
    ( bulk tissues)
    B
    ( ~2000 Cells )
    C
    ( ~5000 Cells )
    High quality reads percentage 96.04% 96.57% 96.66%
    Mapping rate 99.99% 99.94% 99.98%
    Duplicate rate 10.71% 20.77% 12.84%
    Fraction region covered >10X* 94.47% 94.12% 94.19%
    *After adjusted to mean coverage of 90X
    - When compared with bulk tissue sample, 2 K cells and 5 K cells input both have equivalent QC statistics (High quality reads percentage, Mapping rate, and Fraction region covered > 10X), only Duplication rate is affected by the ultra-low input, which could be compensated by increased sequencing depth.

     
  • Replication performance of K-Cell DNA-seq (WES)
    Sample ID Mapping rate Properly paired mapping rate Mean coverage sequencing depth on official target Fraction of official target covered with at least 200X
    T3909799 99.84% 97.08% 752.33 95.58%
    T3912759 99.81% 96.54% 750.87 93.70%
    T3116689 99.81% 95.44% 761.87 96.93%
    T3128859 99.80% 95.61% 590.19 94.64%
    T3619619 99.80% 95.03% 751.92 95.99%
    T3324899 99.89% 92.90% 804.99 95.89%

    - To remove the effect of duplication rate and increase the discovery of low frequency somatic mutations, increased sequencing depth strategy were tested with replication. Result shows low variability, high-performance of LIWEN’s K-Cell technology, and may improve the capture of tumor heterogeneity.

  • QC Statistics of K-Cell RNA-seq

    QC Statistics Test Sample
    Aligned_reads(%) 75.08
    mRNA_bases(%) 95.87
    Ribosomal_bases(%) <0.01
    Coding_bases(%) 58.16
    UTR_bases(%) 37.72
    Intronic_bases(%) 2.24
    Intergenic_bases(%) 1.88
    -K-Cell RNA-seq result shows high quality and suitable for subsequent analyses.
     
  • EML4-ALK fusion example detected by K-Cell RNA-seq
    EML4-ALK fusion