Revolutionary OncoVee™ K-Cell Kit: Small Sample, Big Results

Effective transcription level analysis usually requires a large sample of tissue, about a yellow bean size. This requirement eliminates early-stage tumors or biopsy-challenged cases from possibly benefiting from sequencing analysis. LIDE has solved this issue with its OncoVee™ K-cell Kit.

“K” referencing the ~1,000’s of cells needed for transcription, instead of the 10-100’s of thousands of cells usually needed for RNA and DNA sequencing. By only requiring a small sample size, this technology expands the patient base and scenarios that can benefit from genomics, transcriptomics and even proteomics analysis.
Quality scores have been validated and similar to bulk tissue samples.


Fig. OncoVee™ K Cell DNASeq and RNASeq Assay Kits from LIWEN, a subsidiary of LIDE.
Fig. OncoVee™ K Cell DNASeq and RNASeq Assay Kits from LIWEN, a subsidiary of LIDE.

LIDE K-Cell Kits have enabled several key services:


Validation vs. Larger Bulk Tissue Sample:
A valid concern of starting with a small sample size is the quality of the reads. LIDE has validated inputs of 2,000 cells and 5,000 cells against bulk tissue samples, demonstrating K-Cell Kits can offer comparable and stable NGS data quality compared to bulk tissue samples. 

DNAseq A(Bulk tissues) B(~2000 Cells) C(~5000 Cells)
Primary target region size 36,035,818 36,035,818 36,035,818
High Quality reads rate 96.04% 96.57% 96.66%
Duplication rate 10.71% 20.77% 12.84%
Mapping rate 99.99% 99.94% 99.98%
Aligned reads 73,131,449 163,320,248 261,473,812
Mean insert size 202.96694 172.11678 158.913807
Average coverage 81.332987 152.565749 255.76497
Fraction region covered >10X*
*after adjusted to mean coverage of 90X
94.47% 94.12% 94.19%

Table: QC statistics of K-Cell vs bulk tissue DNA-seq (WES)

Even with lower input samples, K-Cell Kits can deliver equivalent QC statistics (high quality reads rate, mapping rate and fraction region covered > 10X). Only duplication rate is affected by the ultra-low input, but this can be minimized by increased sequencing depth. Below are results from increasing sequencing depth with replication. Results demonstrate low variability, high-performance of K-Cell technology, and may improve the capture of tumor heterogeneity and increase the discovery of low frequency somatic mutations.

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%

Table: Replication performance of K-Cell DNA-seq (WES)


Additionally, K-Cell RNA-seq results also demonstrate high quality reads suitable for subsequent analyses.

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

Table: QC Statistics of K-Cell RNA-seq


Fig. EML4-ALK fusion example detected by K-Cell RNA-seq
Fig. EML4-ALK fusion example detected by K-Cell RNA-seq