TAILIEUCHUNG - Whole exome sequencing pipeline evaluation and mutation detection in esophageal cancer patients

This study provides a comparison of software pipelines to identify potential mutations by analyzing whole exome sequencing data from cancer patients, which can lead to early detection and prevention of cancer. This information may be useful to other research related to cancer diagnosis using molecular biology and bioinformatics | Journal of military pharmaco-medicine no1-2019 WHOLE EXOME SEQUENCING PIPELINE EVALUATION AND MUTATION DETECTION IN ESOPHAGEAL CANCER PATIENTS Tran Thi Bich Ngoc1; Ho Viet Hoanh2; Vu Phuong Nhung1; Nguyen Hai Ha1 Nguyen Van Ba2; Nguyen Dang Ton1; Tran Viet Tien2 SUMMARY Background: Esophageal cancer is the eighth most common cancer in global scale with over 400,000 new cases arising during the year. Generally, the early diagnosis of this cancer remains limited, resulting to approximately 15% five year survival rate. Next generation sequencing technologies have revolutionized cancer genomics by providing a holistic approach for detecting somatic mutations. Hereby, we describe a genomic analysis of 30 esophageal cancer patients using whole exome sequencing. Subjects and methods: 10 sequencing datasets were analyzed through 3 different pipelines. Fastq2vcf modified to use MuTect2 proved to be the most optimal pipeline for esophageal cancer WES data analysis over SeqMule and IMPACT. The selected pipeline was used to analyze the remaining 20 datasets. Results and conclusion: Among 30 patient samples, variants found by Fastq2vcf restricted mostly in chr17 followed by chr9 and were very rare in chr21. Most variants found were SNVs (1,034/1,200 variants) and present in all samples; out of which 841 were non-synonymous. 4 types of damaging mutations causing changes to protein sequences and gene functions were found in exome regions as well as splicing regions. This study provides a comparison of software pipelines to identify potential mutations by analyzing whole exome sequencing data from cancer patients, which can lead to early detection and prevention of cancer. This information may be useful to other research related to cancer diagnosis using molecular biology and bioinformatics. * Keywords: Esophageal cancer; Whole exome sequencing; Fastq2vcf; MuTect2. INTRODUCTION In Vietnam, esophageal squamous cell carcinoma (ESCC) has been the most prevalent type of esophageal .

• Y khoa - Dược
• Esophageal cancer patients
• Whole exome sequencing
• Fastq2vcf modified
• Esophageal squamous cell carcinoma
• Whole exome sequencing
• Generation sequencing
• BMC Cancer
• Esophageal cancer
• Neoadjuvant therapy
• Cyclooxygenase 2 inhibition
• Humans suggest
• Esophageal cancer risk
• 18FDG PET CT simulation
• 3D conformal radiotherapy
• CT simulation in 3D conformal
• Chemo radiotherapy for esophageal cancer
• Definitive chemoradiation
• Acute toxicity
• Irresectable esophageal cancer
• Mental disorder
• Gastric cancer
• Cohort study
• Cancer treatment
• Waiting time
• Narrow band imaging
• Head and neck cancer
• Second primary cancer
• Squamous cell carcinoma
• Prognostic factor
• Controlling nutritional status
• DNA damage repair genes JWA
• Cisplatin based therapy
• Elevated serum YKL 40 levels
• Diagnostic performance
• X ray computed
• Comprehensive positive score
• Upper third esophageal cancer
• Concurrent chemoradiotherapy
• Intensity modulated radiation therapy
• Intensitymodulated radiation
• Gastroesophageal cancer
• Na K 2Cl transporter
• Calculate hazard ratios
• Cancer specific survival
• Extent of lymphadenectomy
• Cutoff value
• Negative lymph nodes
• Cancer specific survival probability
• Elderly patients
• Quality of life
• Clinical trial
• Esophageal carcinoma
• Cancer patients’ outcomes
• Chronic comorbidities
• Angiotensin converting enzyme inhibitors
• Angiotensin receptor blockers
• Survival analysis
• Tumor suppressor candidate 3
• Overall survival
• Human malignancies
• Esophageal neoplasm
• Salvage treatment
• Optimal salvage regimen
• Thoracic esophageal squamous cell carcinoma
• Dietary intake
• Systematic review
• Meta analysis
• Magnetic resonance imaging
• Treatment outcome
• Circulating tumor cells
• Chemotherapeutic efficacy
• Non triploid patient
• Intraoperative ultrasonography
• Recurrent laryngeal nerve nodal metastases
• RLN lymph node dissection
• Steroid therapy
• C reactive protein
• Enhanced recovery after surgery care
• Serum C reactive protein
• Esophageal squamous cell cancer
• Comprehensive geriatric assessment
• Checkpoint inhibitors
• Personalized medicine
• Geriatric oncology
• Risk prediction
• Locoregional recurrence
• Distant metastases