KDR Mutation: A High-Frequency Rare Mutation and its Correlation with other Somatic Mutations in Indian Colorectal Cancer Patients

Background: The KRAS mutations are high-frequency somatic mutations found in colorectal cancer patients from Western and Asian countries however, with the exception of exon 2 of KRAS, other prevalence and prognostic values have not been adequately assessed in Asian patients. The aim of this study was to determine the mutation frequencies of whole exon mutations of KRAS in Chinese colorectal cancer patients and to investigate their impact on prognosis. Methods: A total of 7189 tumor tissue samples (iCohort) were subjected to next-generation sequencing for detection of KRAS mutations. All pathologic or likely pathologic mutations of KRAS were considered. In addition, clinical features and prognostic dates were collected from 145 patients at The Third Affiliated Hospital of Soochow University, China (sCohort) and used droplet digital™ polymerase chain reaction to detect KRAS mutations. Results: In the iCohort, 2706 patients (37.6%) were confirmed harboring KRAS mutations. The most frequent of these mutations were G12D (32.19%), G12V (17.96%), and G13D (17.59%). In the sCohort, 51 colorectal cancer patients (35.17%) had KRAS mutations, among which KRAS G12D (64.71%), G13D (29.41%), and G14D (3.92%) were high-frequency. The KRAS mutations were associated with shorter median overall survival than wild-type tumors (69 vs. 55 months; HR 1.80; 95% Cl 1.22, 2.64; P=0.0003). In the Cox multivariate analysis, age (HR 1.562; 95% Cl 1.10, 2.22; P=0.013), tumor differentiation (HR 0.417; 95% Cl 0.19, 0.90; P=0.026), and KRAS mutation (HR 1.897; 95% Cl 0.19, 0.90; P=0.001) remained independent predictors of shorter overall survival. Among the common KRAS mutations, G12D was significantly associated with shorter overall survival (HR 2.17; 95% Cl 1.31, 3.58; P < 0.0001) compared with KRAS wild-type patients. Conclusions: Our findings indicate that KRAS genes are frequently mutated, and over 30% harbored the KRAS G12D mutation subtype. We found that the KRAS G12D mutation is associated with inferior survival and is a biomarker of poor prognosis in Chinese patients. Our data emphasize the importance of molecular features in colorectal cancer patients, which could potentially be improved by G12D-specific related inhibitors.

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INFLUENCE OF SOMATIC MUTATIONS OF KRAS, NRAS, BRAF AND MICROSATELLITE INSTABILITY STATUS ON SURVIVAL OF COLORECTAL CANCER PATIENTS WITH PERITONAL CARCINO

Siberian Journal of Oncology ◽

10.21294/1814-4861-2020-19-5-61-67 ◽

2020 ◽

Vol 19 (5) ◽

pp. 61-67

Author(s):

V. P. Shubin ◽

Yu. A. Shelygin ◽

S. I. Achkasov ◽

O. I. Sushkov ◽

A. A. Ponomarenko ◽

...

Keyword(s):

Colorectal Cancer ◽

Microsatellite Instability ◽

Peritoneal Carcinomatosis ◽

Cancer Patients ◽

Somatic Mutations ◽

Disease Free Survival ◽

Free Survival ◽

The Status ◽

Colorectal Cancer Patients ◽

Disease Free

Purpose: to evaluate the effect of somatic mutations of the KRAS, NRAS, BRAF genes and the status of microsatellite instability on the overall and disease-free survival of patients undergoing cytoreductive surgery with hyperthermic intraperitoneal chemotherapy.Material and Methods. From 2012 to 2018, the study included 45 patients who underwent surgery for synchronous peritoneal carcinomatosis with colorectal cancer. In all patients, mutations of the KRAS, NRAS, BRAF genes and MSI status of the tumor and peritoneum metastases were determined using Sanger sequencing, fragment analysis and digital droplet polymerase chain reaction. The effect of mutations on patient survival was evaluated.Results. The prevalence of somatic mutations was 69 % of patients. The discordance between the tumor and peritoneum metastases was 9 %. All tumors and peritoneum metastases were microsatellite stable. KRAS, NRAS, BRAF mutations did not affect the overall and disease-free survival (p=0.87 and p=0.85, respectively).Conclusion. Somatic mutations in the KRAS, NRAS, or BRAF genes are not a prognostic factor affecting the overall and relapse-free survival of colorectal cancer patients with peritoneal carcinomatosis. The molecular status of primary tumor may differ from the status of peritoneal metastasis. It should be taken into account when prescribing targeted drugs.

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Highly multiplexed quantifications of 299 somatic mutations in colorectal cancer patients by automated MALDI-TOF mass spectrometry

10.21203/rs.2.12726/v4 ◽

2020 ◽

Author(s):

Chang Xu ◽

Danli Peng ◽

Jialu Li ◽

Meihua Chen ◽

Yujie Hu ◽

...

Keyword(s):

Colorectal Cancer ◽

Mass Spectrometry ◽

Cancer Patients ◽

Clinical Significance ◽

Somatic Mutations ◽

Cost Effective ◽

Maldi Tof ◽

Targeted Ngs ◽

Colorectal Cancer Patients ◽

Tof Ms

Abstract Background: Detection of somatic mutations in tumor tissues helps to understand tumor biology and guide treatment selection. Methods such as quantitative PCR can analyze a few mutations with high efficiency, while next generation sequencing (NGS) based methods can analyze hundreds to thousands of mutations. However, there is a lack of cost-effective method for quantitatively analyzing tens to a few hundred mutations of potential biological and clinical significance. Methods: Through a comprehensive database and literature review we selected 299 mutations associated with colorectal cancer. We then designed a highly multiplexed assay panel (8-wells covering 299 mutations in 109 genes) based on an automated MADLI-TOF mass spectrometry (MS) platform. The multiplex panel was tested with a total of 319 freshly frozen tissues and 92 FFPE samples from 229 colorectal cancer patients, with 13 samples also analyzed by a targeted NGS method covering 532 genes. Results: Multiplex somatic mutation panel based on MALDI-TOF MS detected and quantified at least one somatic mutation in 142 patients, with KRAS, TP53 and APC being the most frequently mutated genes. Extensive validation by both capillary sequencing and targeted NGS demonstrated high accuracy of the multiplex MS assay. Out of 35 mutations tested with plasmid constructs, sensitivities of 5% and 10% mutant allele frequency were achieved for 19 and 16 mutations, respectively. Conclusions: Automated MALDI-TOF MS offers an efficient and cost-effective platform for highly multiplexed quantitation of 299 somatic mutations, which may be useful in studying the biological and clinical significance of somatic mutations with large numbers of cancer tissues.

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Uncovering the landscape of somatic mutations in Malaysian colorectal cancer patients via whole genome sequencing

Frontiers in Pharmacology ◽

10.3389/conf.fphar.2018.63.00133 ◽

2018 ◽

Vol 9 ◽

Author(s):

Ryia Illani Mohd Yunos ◽

Nurul-Syakima Ab Mutalib ◽

Jia-Shiun Khoo ◽

Sazuita Saidin ◽

Muhiddin Ishak ◽

...

Keyword(s):

Colorectal Cancer ◽

Whole Genome Sequencing ◽

Cancer Patients ◽

Genome Sequencing ◽

Somatic Mutations ◽

Whole Genome ◽

Colorectal Cancer Patients

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Highly multiplexed quantifications of 299 somatic mutations in colorectal cancer patients by automated MALDI-TOF mass spectrometry

10.21203/rs.2.12726/v3 ◽

2020 ◽

Author(s):

Chang Xu ◽

Danli Peng ◽

Jialu Li ◽

Meihua Chen ◽

Yujie Hu ◽

...

Keyword(s):

Colorectal Cancer ◽

Mass Spectrometry ◽

Cancer Patients ◽

Clinical Significance ◽

Somatic Mutations ◽

Cost Effective ◽

Maldi Tof ◽

Targeted Ngs ◽

Colorectal Cancer Patients ◽

Tof Ms

Abstract Background: Detection of somatic mutations in tumor tissues helps to understand tumor biology and guide treatment selection. Methods such as quantitative PCR can analyze a few mutations with high efficiency, while next generation sequencing (NGS) based methods can analyze hundreds to thousands of mutations. However, there is a lack of cost-effective method for quantitatively analyzing tens to a few hundred mutations of potential biological and clinical significance. Methods: Through a comprehensive database and literature review we selected 299 mutations associated with colorectal cancer. We then designed a highly multiplexed assay panel (8-wells covering 299 mutations in 109 genes) based on an automated MADLI-TOF mass spectrometry (MS) platform. The multiplex panel was tested with a total of 319 freshly frozen tissues and 92 FFPE samples from 229 colorectal cancer patients, with 13 samples also analyzed by a targeted NGS method covering 532 genes. Results: Multiplex somatic mutation panel based on MALDI-TOF MS detected and quantified at least one somatic mutation in 142 patients, with KRAS, TP53 and APC being the most frequently mutated genes. Extensive validation by both capillary sequencing and targeted NGS demonstrated high accuracy of the multiplex MS assay. Out of 35 mutations tested with plasmid constructs, sensitivities of 5% and 10% mutant allele frequency were achieved for 19 and 16 mutations, respectively. Conclusions: Automated MALDI-TOF MS offers an efficient and cost-effective platform for highly multiplexed quantitation of 299 somatic mutations, which may be useful in studying the biological and clinical significance of somatic mutations with large numbers of cancer tissues.

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