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NanOnCT Panel

NanOnCT Panel

Catalog Number:
#1001902 (16 rxn)
#1001901 (96 rxn)

NanOnCT Panel v1.0 is a compactable panel designed for analysis of solid tumors and liquid biopsy. This panel involves a total number of 69 genes with selected regions covered. With an optimized probe design, this panel offers a highly uniform coverage over targeted regions for both FFPE and cell-free DNA.


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Gene List

Genes with coding regions covered

AKT1 ALK APC AR ARAF ATM BRAF BRCA1 BRCA2 CCND1
CDH1 CDK12 CDK4 CDK6 CDKN2A CTNNB1 DDR2 EGFR ERBB2  ERCC2
ESR1 EZH2 FGFR1 FGFR2 FGFR3 GNA11 GNAQ GNAS HRAS IDH1
IDH2 JAK2 JAK3 KDM6A KIT KRAS MAP2K1 MAP2K2 MDM2 MET
MLH1 MPL MSH2 MSH6 MTOR MYC NF1 NPM1 NRAS NTRK1
NTRK2 NTRK3 PDGFRA PIK3CA PMS2 PTCH1 PTEN PTPN11 RAF1 RB1
RET ROS1 SMARCB1 SMO STK11 TERT TP53 TSC1 TSC2
Genes with full coding regions shown in bold.


Genes with selected introns covered

ALK

BRAF

EGFR

FGFR2

FGFR3

MET

NTRK1

NTRK2

PDGFRA

RET

ROS1


Microsatellite Markers

BAT-25

BAT-26

BAT-40

BAT-RII

NR-21

NR-22

NR-24

NR-27

MONO-27

D2S123

D5S346

D17S261

D17S520

D18S34

 

 

 

 


Performance

Table 1. On-target rate for gDNA and cfDNA samples

Platforms

gDNA

On-target rate (%)

cfDNA

On-target rate (%)

HiSeq X Ten, PE150

87.02

87.35

DNBSEQ-G400, PE100

85.47

87.00

The DNA libraries were prepared using NadPrep library kits with 50 ng of human genomic DNA (Promega, G1512) and 10 ng of plasma cfDNA from a healthy donor, respectively. 1 M read pairs were subsampled for the analysis. On-target rates were calculated as the percentage of mapped read pairs that overlap with probe regions.


Coverage Uniformity

OnCT Research Panel Pic1

Fig 1. Improved design cfDNA capture. The optimized design of NanOnCT Panel v1.0 showed improved coverage uniformity for cfDNA libraries on both Illumina®️ and MGI platforms.

Variant Analysis

OnCT Research Panel Pic2

Fig 2. Evaluation of NanOnCT Panel v1.0 on the analysis of SNVs and indels. DNA libraries were prepared from Onco SNV Multiplex 1-25% gDNA (Genewell, GW-OGTM004) using NadPrep library kits. The enriched libraries were sequenced either on HiSeq X Ten (PE150) or DNBSEQ-G400 (PE100).

OnCT Research Panel Pic3

Fig 3. Evaluation of NanOnCT Panel v1.0 on the analysis of structural variations. A. & B. Gene amplification; C. SNVs with regions of high or low GC content and long insertion / deletion. The DNA libraries were prepared from Onco Structural Multiplex 5% gDNA (GeneWell, GW- OGTM001) using NadPrep library kits. The libraries were enriched using the NanOnCT Panel v1.0. The enriched libraries were sequenced either on HiSeq X Ten (PE150) or DNBSEQ-G400 (PE100).

Coverage Over Selected Microsatellite Markers

OnCT Research Panel Pic4

Fig 4. Effective coverage over microsatellite markers. The enriched libraries were sequenced on a HiSeq X Ten platform (PE150). Only reads spanning full-length of microsatellite markers were counted as effective reads.

OnCT Research Panel Pic5

Fig 5. Length distribution of microsatellite site in a sample with microsatellite instability (MSI) for A. BAT-25 and B. NR-27.


For research use only. Not for use in diagnostic procedures.

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