Abstract 1303P
Background
Since most pancreatic cancers are diagnosed at unresectable stage, endoscopic ultrasound guided fine-needle biopsy (EUS-FNB) is the main method to acquire tissue for diagnosis and molecular profiling. We aimed to report the feasibility of whole exome sequencing (WES) with FNB samples and to find factors related with successful WES.
Methods
Between February 2018 and June 2021, tissues were acquired by EUS-FNB. WES was conducted and its feasibility was analyzed. First, genomic DNA from fresh frozen tissues was extracted using QIAamp DNA mini kit and samples satisfying the standard of DNA quantity and purity were proceeded to further library preparation and sequencing. Second, Phred quality score and GC contents were analyzed for sequencing quality. Thrid, mutational profile was compared with the previous TCGA data. In addition, we analyzed factors associated with successful WES; tumor, technical and pathological factors.
Results
A total of 218 pancreatic cancer tissues were collected. Eleven failed to satisfy DNA quantity standard and 207 samples performed further library preparation. All sequenced samples showed high rate of Q30 rate with the median (range) of 92.5% (88.6-93.6) and GC contents were well-balanced. The mutation count and distribution of common recurrent mutations in this cohort were similar with those in TCGA. Accordingly, the success rate of WES with FNB samples was 207/218 (95.0%). There was no significant difference in success rate according to tumor and technical factors but, high tumor cellularity on pathology was associated with successful WES (97.0% vs 88.8%, p=0.029).
Conclusions
Our data showed that FNB samples in pancreatic cancer were feasible for WES and tumor cellularity on pathology might be a predictor of successful WES. This genomic study with FNB samples, which can reflect real-world pancreatic cancer stage prevalence, is expected to give more sensitive insight on genomic landscape of pancreatic cancer. Table: 1303P
| Success (N=207) | Fail (N=11) | P-value | |||
| Sample quailty | DNA quantity (ug) | 0.896 (0.215-6.840) | 0.127 (0.004-0.189) | NA | |
| A260/280 | 1.84 (1.57-2.01) | 1.87 (0.40-2.09) | NA | ||
| Sequencing quality | GC rate | 49.6 (46.0-53.6) | NA | NA | |
| Q30 rate | 92.5 (88.6-93.6) | NA | NA | ||
| Factors related with successful WES | Storage date | 2018-2019 | 111 (53.6) | 6 (46.4) | 0.952 |
| 2020- | 96 (46.4) | 5 (45.5) | |||
| Location of mass | Head | 84 (40.6) | 5 (45.5) | 0.762 | |
| Body/Tail | 123 (59.4) | 6 (54) | |||
| Diameter of mass (cm) | 4.3 (1.9) | 4.3 (2.2) | 0.782 | ||
| Needle gauge | 20G | 10 (4.8) | 1 (9.1) | 0.442 | |
| 22G | 197 (95.2) | 9 (81.8) | |||
| 25G | 0 | 1 (9.1) | |||
| Route | Transgastric | 135 (65.2) | 9 (81.8) | 0.518 | |
| Transduodenal | 70 (33.8) | 2 (18.2) | |||
| Both | 2 (0.9) | 2 (0.9) | |||
| Cellularity | Low | 48 (23.2) | 6 (54.5) | 0.029 | |
| High | 159 (76.8) | 5 (45.5) |
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.