Cross-platform comparison of next-generation sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for detecting KRAS/NRAS/BRAF/PIK3CA mutations in cfDNA from metastatic colorectal cancer patients.

Abstract

BACKGROUND:

Examining tumor KRAS/NRAS/BRAF/PIK3CA status in metastatic colorectal cancer (mCRC) is essential for treatment selection and prognosis evaluation. Cell-free DNA (cfDNA) in plasma is a feasible source for tumor gene analysis.

METHODS:

In this study, we recruited mCRC patients and analyzed their KRAS/NRAS/BRAF/PIK3CA status in cfDNA using two platforms, next-generation sequencing (NGS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). The performance between the two platforms and the concordance rate between cfDNA and tissue were analyzed. The relationship between cfDNA-related variables and clinical variables was also assessed. Tumor mutations in cfDNA from patients receiving continuous treatments were monitored in the follow-ups.

RESULTS:

Next-generation sequencing and MALDI-TOF had similar specificity (100.0% vs. 99.3%) and negative predictive value (99.9% vs. 99.4%), whereas NGS had higher sensitivity (97.1% vs. 85.3% of MALDI-TOF) and positive predictive value (100% vs. 82.9% of MALDI-TOF). The overall concordance rate of NGS and MALDI-TOF was 98.6%. For the reportable types of mutations in both cfDNA and tissue, the concordance rate was 96.1%. Among 28 tissue-positive patients, the allele frequencies of tumor mutations in cfDNA were higher in patients with primary tumor burden (p = 0.0141). Both CEA and CA 19-9 were positively correlated with cfDNA concentration (r = 0.3278 and r = 0.3992). The allele frequencies of tumor mutations changed with disease progression.

CONCLUSIONS:

Next-generation sequencing showed slightly better performance in detecting cfDNA mutations and was more suitable for clinical practice. cfDNA-related variables reflected the tumor status and showed a promising potential in monitoring disease progression.

• Authors: Xiaojing Xu, Fei Huang, Minlu Cao, Xinning Chen, Hao Wang, Huiqin Jiang, Yiyi Yu, Minna Shen, Yihui Yang, Beili Wang, Tianshu Liu, Wei Guo
• Journal: Journal of clinical laboratory analysis (J Clin Lab Anal) Vol. 35 Issue 9 Pg. e23818 (Sep 2021) ISSN: 1098-2825 [Electronic] United States
• PMID: 34403504 (Publication Type: Comparative Study, Journal Article)
• Copyright: © 2021 The Authors. Journal of Clinical Laboratory Analysis published by Wiley Periodicals LLC.

Chemical References

• Biomarkers, Tumor
• Cell-Free Nucleic Acids
• KRAS protein, human
• Membrane Proteins
• Class I Phosphatidylinositol 3-Kinases
• PIK3CA protein, human
• BRAF protein, human
• Proto-Oncogene Proteins B-raf
• GTP Phosphohydrolases
• NRAS protein, human
• Proto-Oncogene Proteins p21(ras)

Topics

• Aged
• Biomarkers, Tumor (genetics)
• Cell-Free Nucleic Acids (analysis, genetics)
• Class I Phosphatidylinositol 3-Kinases (genetics)
• Colorectal Neoplasms (genetics, pathology)
• Female
• Follow-Up Studies
• GTP Phosphohydrolases (genetics)
• High-Throughput Nucleotide Sequencing (methods)
• Humans
• Liver Neoplasms (genetics, secondary)
• Lung Neoplasms (genetics, secondary)
• Male
• Membrane Proteins (genetics)
• Middle Aged
• Mutation
• Prognosis
• Prospective Studies
• Proto-Oncogene Proteins B-raf (genetics)
• Proto-Oncogene Proteins p21(ras) (genetics)
• Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization (methods)