Implementing Massive Parallel Sequencing into Biliary Samples Obtained through Endoscopic Retrograde Cholangiopancreatography for Diagnosing Malignant Bile Duct Strictures
Abstract
:1. Introduction
2. Results
2.1. Clinicopathological Findings of the Study Population
2.2. Mutation Analysis of Biliary Brush Cytology and Bile Fluid
2.3. Mutations in Biliary Brush Cytology Compared with Bile Fluid Samples
3. Discussion
4. Materials and Methods
4.1. Sample Collection
4.2. Massively Parallel Sequencing with Oncomine Comprehensive Assay
4.3. Massively Parallel Sequencing with Oncomine Pan-Cancer Cell-Free Assay
4.4. Classification of Genomic Alterations
4.5. Statistical Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Case | Diagnosis | Pathology | Cytology | Treatment | Prognosis | OS (Day) | |
---|---|---|---|---|---|---|---|
Initial | Confirmed | ||||||
cc06 | eCCA | dBDC | AC | Positive * | PPPD, Adjuvant ChT | death | 622 |
cc08 | eCCA | pCCA | AC | Negative † | ConserTx | death | 239 |
dc09 | eCCA | pCCA | AC | Positive | ConserTx | F/U loss | 325 |
cc10 | eCCA | pCCA | AC | Suspicious ‡ | ConserTx | F/U loss | 120 |
cc11 | eCCA | SC | SC, IgG4-related | Negative | ConserTx | alive | 2284 |
cc13 | eCCA | dBDC | AC | Positive | ConserTx | death | 267 |
cc14 | eCCA | pCCA | AC | Positive | PPPD | F/U loss | 408 |
cc15 | eCCA | dBDC | AC | Negative | PPPD | alive | 2001 |
cc16 | eCCA | dBDC | AC with SRC | Negative | ConserTx | death | 303 |
Case | S/A (y) | Gene | Mutation | Mutation Change | Depth | VAF | rsID | Class | OPCCFA |
---|---|---|---|---|---|---|---|---|---|
Type | (×) | (%) | (%) | ||||||
cc06 | M/61 | TP53 | missense | c.832C>G/p.P278A | 1965 | 64 | rs17849781 | tier 2 | 3.7 |
ERBB2 | amplification (8 copies) | tier 2 | 1.8 | ||||||
cc08 | M/72 | TP53 | missense | c.1039G>A/p.A347T | 2000 | 46 | rs1597349147 | tier 2 | 3.7 |
BRAF | missense | c.1397G>A/p.G466E | 1999 | 6 | rs121913351 | tier 2 | 0.8 | ||
cc09 | F/79 | TP53 | missense | c.535C>T/p.H179Y | 1694 | 70 | rs587780070 | tier 2 | 3.1 |
CTNNB1 | missense | c.134C>G/p.S45C | 2000 | 14 | rs121913409 | tier 2 | 0.6 | ||
SMAD4 | missense | c.1051G>A/p.D351N | 2000 | 15 | rs1057519739 | tier 2 | 0.3 | ||
NRAS | missense | c.182A>T/p.Q61L | 2000 | 43 | rs11554290 | tier 2 | 2.6 | ||
cc10 | M/58 | MDM2 | amplification (6 copies) | tier 2 | N.A. | ||||
cc11 | M/64 | Not Detected | N.D. | ||||||
cc13 | M/76 | TP53 | missense | c.707A>G/p.236C | 1970 | 62 | rs730882026 | tier 2 | 2.9 |
FGFR2 | missense | c.1144T>C/p.C382R | 1885 | 36 | rs121913474 | tier 1 | 1.4 | ||
cc14 | F/76 | TP53 | missense | c.523C>T/p.R175C | 1222 | 45 | rs138729528 | tier 2 | 3.9 |
BRAF | missense | c.1781A>G/p.D594G | 1022 | 28 | rs121913338 | tier 2 | 2.6 | ||
CTNNB1 | missense | c.134C>G/p.S45C | 1999 | 67 | rs121913409 | tier 2 | 2.5 | ||
SMAD4 | missense | c.1081C>T/p.R361C | 2000 | 30 | rs80338963 | tier 2 | 0.7 | ||
PIK3CA | missense | c.1624G>A/p.E542K | 1963 | 37 | rs121913273 | tier 2 | 0.3 | ||
cc15 | M/71 | TP53 | missense | c.817C>T/p.R273C | 2000 | 31 | rs121913343 | tier 2 | 3.4 |
BRAF | missense | c.1780G>A/p.D594N | 2000 | 16 | rs397516896 | tier 2 | 0.3 | ||
CDKN2A | nonsense | c.205G>T/p.E69* | 1434 | 47 | rs121913383 | tier 2 | N.A. | ||
FBXW7 | frameshift | c.58delA/p.R20Efs*9 | 1981 | 15 | N.A. | tier 2 | 2.2 | ||
FBXW7 | frameshift | c.1218delG/p.W406Cfs*9 | 1994 | 13 | N.A. | tier 2 | 3.1 | ||
cc16 | F/90 | KRAS | missense | c.182A>T/p.Q61L | 2000 | 26 | rs121913240 | tier 2 | 4.3 |
Case | S/A (y) | Gene | Mutation | Mutation Change | Depth | VAF | rsID | Class | OPCCFA |
---|---|---|---|---|---|---|---|---|---|
Type | (×) | (%) | |||||||
gs03 | F/34 | Not Detected | N.D. | ||||||
gs06 | F/62 | TET2 | missense | c.4076G>A/p.R1359H | 1999 | 29 | rs775677220 | tier 3 | N.A. |
gs08 | M/57 | Not Detected | N.D. | ||||||
gs13 | F/59 | Not Detected | N.D. | ||||||
gs14 | F/64 | Not Detected | N.D. | ||||||
gs17 | M/47 | Not Detected | N.D. | ||||||
gs29 | M/55 | ATM | missense | c.7328G>A/p.R2443 | 2000 | 13 | rs587782310 | tier 3 | N.A. |
gs32 | M/42 | Not Detected | N.D. | ||||||
gs49 | F/43 | Not Detected | N.D. | ||||||
gs51 | M/56 | Not Detected | N.D. |
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Park, W.; Gwack, J.; Park, J. Implementing Massive Parallel Sequencing into Biliary Samples Obtained through Endoscopic Retrograde Cholangiopancreatography for Diagnosing Malignant Bile Duct Strictures. Int. J. Mol. Sci. 2024, 25, 9461. https://doi.org/10.3390/ijms25179461
Park W, Gwack J, Park J. Implementing Massive Parallel Sequencing into Biliary Samples Obtained through Endoscopic Retrograde Cholangiopancreatography for Diagnosing Malignant Bile Duct Strictures. International Journal of Molecular Sciences. 2024; 25(17):9461. https://doi.org/10.3390/ijms25179461
Chicago/Turabian StylePark, Wonsuk, Jin Gwack, and Joonhong Park. 2024. "Implementing Massive Parallel Sequencing into Biliary Samples Obtained through Endoscopic Retrograde Cholangiopancreatography for Diagnosing Malignant Bile Duct Strictures" International Journal of Molecular Sciences 25, no. 17: 9461. https://doi.org/10.3390/ijms25179461