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Next-generation Sequencing in Gastrointestinal Cancer

The safety and scientific validity of this study is the responsibility of the study sponsor and investigators. Listing a study does not mean it has been evaluated by the U.S. Federal Government. Know the risks and potential benefits of clinical studies and talk to your health care provider before participating. Read our disclaimer for details. Identifier: NCT03476057
Recruitment Status : Not yet recruiting
First Posted : March 23, 2018
Last Update Posted : July 2, 2018
Information provided by (Responsible Party):
Fujian Cancer Hospital

Brief Summary:
Liquid biopsy has been successfully applied to the treatment and diagnosis of cancer. cfDNA has been paid more and more attention in liquid biopsy. Previous studies have shown that cfDNA can be used for predicting the efficacy of radiotherapy or chemotherapy for lung cancer, rectal cancer and esophageal cancer. It is also reported that cfDNA can be used for the evaluation of postoperative recurrence of advanced gastric cancer. However, the use of NGS to detect cfDNA in gastrointestinal tumors has not been reported. The purpose of this study is to investigate the correlation between cfDNA, cfDNA tumor buden with advanced gastrointestinal tract tumor patients, and find out prognosis gene of advanced gastrointestinal tract tumor.

Condition or disease Intervention/treatment
Gastrointestinal Cancer Diagnostic Test: Device: NGS sequencing cfDNA

Detailed Description:

Sample DNA handling: Peripheral blood lymphocytes (PBLs), and plasma were collected for analysis for each patient. 10mL tubes containing blood samples with EDTA added were centrifuged at 1000g for 10min. The cell pellets containing peripheral blood lymphocytes were stored at -20 °C. The supernatants were centrifuged again at 10,000 g for 10 min, and plasma was collected and stored at -80°C.Tiangen whole blood DNA Kit (Tiangen, Beijing, PRC) were used to extracted DNA from peripheral blood lymphocytes, respectively. QIAamp Circulating Nucleic Acid Kit (Qiagen, German) was used to extract cfDNA form plasma. All kits were used according to the manufacturers' instructions.

Library preparation and sequencing: For each sample, DNA was quantified with the Qubit dsDNA HS Assay kit (Life Technologies,USA) as manufacturer's recommended protocol. Targeted amplification and Illumina adapter-ligated library preparation was performed using Amplicon Sequencing-Illumina Compatible Kit following manufacturer's instructions (Questgenomics, Nanjing, PRC). All samples were subjected to Illumina HiSeq X-Ten for paired-end sequencing (150bp each end). The AmpliSeq Cancer Panel covers 1406 cancer-associated genes which developed by Co. Roche.

Variant calling: Initial data from HiSeq X-Ten were evaluated by using fastQC (v0.11.3). Raw reads were mapped to reference genome hg19 by using BWA (0.7.12-r1039). Program Samtools and VarScan (v2.4.1) was used for variant calling: (1) the average total coverage depth was defined as >1000 and each variant coverage as >10; for called variant, at least one sample with variant frequency >1%, variant frequency of each sample >0.5%, and P value <0.01; (2) visual examination of the mutations was performed using Samtools software ( and possible errors specific to one DNA strand were filtered out. Software ANNOVAR (v2015-06-17) and snpEff (v4.2) was used for variant annotation

Statistical analysis: For variant frequency less than 0.5%, 0 was replaced. R (hclust, v3.2.4) was used for variant frequency clustering analysis to show what types of samples from cancer patients are more similar. Student's T test was applied for comparison of cfDNA concentration and p<0.05 was considered statistically significant.

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Study Type : Observational
Estimated Enrollment : 200 participants
Observational Model: Cohort
Time Perspective: Prospective
Official Title: Next-generation Sequencing in Gastrointestinal Cancer
Estimated Study Start Date : July 1, 2018
Estimated Primary Completion Date : December 31, 2020
Estimated Study Completion Date : December 31, 2020

Group/Cohort Intervention/treatment
Advanced gastrointestinal tumor
200 patients with pathologically confirmed Advanced gastrointestinal tumor who never treated with chemotherapy at Fujian Cancer Hospital
Diagnostic Test: Device: NGS sequencing cfDNA
NGS sequencing cfDNA and Tumor Burden

Primary Outcome Measures :
  1. cfDNA [ Time Frame: 6 months ]
    demonstrates the spectrum of cfDNA alterations/ profiling

Secondary Outcome Measures :
  1. Tumor mutation burden [ Time Frame: 6 months ]
    demonstrates the tumor mutation burden alterations/ profiling

Biospecimen Retention:   Samples With DNA
whole blood, FFPE

Information from the National Library of Medicine

Choosing to participate in a study is an important personal decision. Talk with your doctor and family members or friends about deciding to join a study. To learn more about this study, you or your doctor may contact the study research staff using the contacts provided below. For general information, Learn About Clinical Studies.

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Ages Eligible for Study:   Child, Adult, Older Adult
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   No
Sampling Method:   Probability Sample
Study Population
Stage III/ IV gastrointestinal cancer

Inclusion Criteria:

  • patients with pathologically confirmed Stage III/ IV gastrointestinal cancer
  • all patients had not received chemotherapy

Exclusion Criteria:


Information from the National Library of Medicine

To learn more about this study, you or your doctor may contact the study research staff using the contact information provided by the sponsor.

Please refer to this study by its identifier (NCT number): NCT03476057

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Contact: Lin Rongbo, Doctor +8613705919382

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China, Fujian
Rongbo Lin
Fuzhou, Fujian, China, 350014
Contact: Rongbo Lin, MD    86+13705919382   
Sponsors and Collaborators
Fujian Cancer Hospital

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Responsible Party: Fujian Cancer Hospital Identifier: NCT03476057    
Other Study ID Numbers: FNF-009
First Posted: March 23, 2018    Key Record Dates
Last Update Posted: July 2, 2018
Last Verified: June 2018

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Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: No
Product Manufactured in and Exported from the U.S.: No
Keywords provided by Fujian Cancer Hospital:
Tumor Burden
Additional relevant MeSH terms:
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Gastrointestinal Neoplasms
Digestive System Neoplasms
Neoplasms by Site
Digestive System Diseases
Gastrointestinal Diseases