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Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma
- Source :
- Clinical Chemistry. 61:1408-1416
- Publication Year :
- 2015
- Publisher :
- Oxford University Press (OUP), 2015.
-
Abstract
- BACKGROUNDPancreatic ductal adenocarcinoma (PDAC) has a poor prognosis. Variant profiling is crucial for developing personalized treatment and elucidating the etiology of this disease.METHODSPatients with PDAC undergoing surgery from 2007 to 2012 (n = 73) were followed from diagnosis until death or the end of the study. We applied an anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) method to a panel of 65 selected genes and assessed analytical performance by sequencing a quantitative multiplex DNA reference standard. In clinical PDAC samples, detection of low-level KRAS (Kirsten rat sarcoma viral oncogene homolog) mutations was validated by allele-specific PCR and digital PCR. We compared overall survival of patients according to KRAS mutation status by log-rank test and applied logistic regression to evaluate the association between smoking and tumor variant types.RESULTSThe AMP-based NGS method could detect variants with allele frequencies as low as 1% given sufficient sequencing depth (>1500×). Low-frequency KRAS G12 mutations (allele frequency 1%–5%) were all confirmed by allele-specific PCR and digital PCR. The most prevalent genetic alterations were in KRAS (78% of patients), TP53 (tumor protein p53) (25%), and SMAD4 (SMAD family member 4) (8%). Overall survival in T3-stage PDAC patients differed among KRAS mutation subtypes (P = 0.019). Transversion variants were more common in ever-smokers than in never-smokers (odds ratio 5.7; 95% CI 1.2–27.8).CONCLUSIONSThe AMP-based NGS method is applicable for profiling tumor variants. Using this approach, we demonstrated that in PDAC patients, KRAS mutant subtype G12V is associated with poorer survival, and that transversion variants are more common among smokers.
- Subjects :
- Male
Candidate gene
medicine.medical_specialty
DNA Mutational Analysis
Clinical Biochemistry
Biology
medicine.disease_cause
Deep sequencing
Proto-Oncogene Proteins p21(ras)
Gene Frequency
Proto-Oncogene Proteins
Molecular genetics
Multiplex polymerase chain reaction
medicine
Humans
Digital polymerase chain reaction
Transversion
Allele frequency
Aged
Smad4 Protein
Aged, 80 and over
Smoking
Biochemistry (medical)
Pancreatic Ducts
Middle Aged
Survival Analysis
Molecular biology
Pancreatic Neoplasms
Mutation
ras Proteins
Cancer research
Female
KRAS
Tumor Suppressor Protein p53
Carcinoma, Pancreatic Ductal
Subjects
Details
- ISSN :
- 15308561 and 00099147
- Volume :
- 61
- Database :
- OpenAIRE
- Journal :
- Clinical Chemistry
- Accession number :
- edsair.doi.dedup.....8060a9cceb5ddf75f7afa24299213349