NBDC Research ID: hum0242.v1



Aims: To evaluate clinical validity of circulating tumor DNA (ctDNA) of tumor-unique mutations identified from colorectal cancer tissues, as a personalized tumor marker.

Methods: Pre- and post-operational plasma, primary tumor, and peripheral blood mononuclear cells (PBMCs) were collected from 12 enrolled patients. Among these patients, two patients had two separate colorectal tumors. The primary tumor specimens were taken from three regions immediately after the operation, and the cellularity of all specimens was microscopically confirmed to be >30%. DNA was extracted from 42 primary tumor specimens and 12 PBMCs, and target sequencing using a HiSeq 2000 System (Illumina) conducted for 151 genes that have been implicated in a wide range of cancers was performed.

Participants/Materials: Colorectal cancer patients with preoperative diagnosis of Stage III or higher. Individual written consent was obtained from each participant.

URL: https://nishizukalab.org/en/index.html


Dataset IDType of DataCriteriaRelease Date
JGAS000243 NGS (Target Capture) Controlled-access (Type I) 2021/01/05

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Colorectal cancer (ICD10: C189): 12 cases

    primary tumor tissue: 42 samples

    PBMC: 12 samples

Targets Target Capture
Target Loci for Capture Methods

Coding regions of the 151 disease-associated genes

ClearSeq SS Comprehensive Cancer kits

Platform Illumina [HiSeq 2000]
Library Source DNAs extracted from primary tumor tissues and PBMC
Cell Lines -
Library Construction (kit name) ClearSeq SS Comprehensive Cancer kits
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000343
Total Data Volume 119 GB (fastq, bam [ref: GRCh37])
Comments (Policies) NBDC policy



Principal Investigator: Satsoshi Nishizuka

Affiliation: Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences

Project / Group Name: -

URL: https://nishizukalab.org/en/index.html

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area) Establishment of selection process of molecular targeting drugs in response to biological heterogeneity in drug-resistant cancer cells 16H01578
KAKENHI Fund for the Promotion of Joint International Research (Fostering Joint International Research) Identification of compounds that potentially lead to the cancer relapse suppression on the basis of drug-resistant cancer subpopulation model (original) 15KK0317
KAKENHI Grant-in-Aid for Scientific Research (C) Circumvent practical issues for introducing ctDNA into daily practice 19K09224
KAKENHI Grant-in-Aid for Scientific Research (C) Effect of immune response to Helicobacter pylori on adjuvant chemotherapy for gastric cancer 19K09130
KAKENHI Grant-in-Aid for Scientific Research (C) Development of monitoring system for esophageal cancer by quantifying circulating tumor DNA 17K10605
KAKENHI Grant-in-Aid for Young Scientists (B) Development of longitudinal monitoring system for gastrointestinal cancer using circulating tumor DNA 18K15326
KAKENHI Grant-in-Aid for Young Scientists (B) The new estimation method of recurrence and metastasis on circulating tumor DNA detection in colorectal cancer patients 16K19951
JSPS Fujita Memorial Fund for Medical Research Impact of intratumor heterogeneity for ctDNA of colon cancer -
Keiryoukai Research Grant Development of precision medicine for esophageal cancer patients using circulating tumor mutational DNA 136
Iwate Prefectural Regional Innovation Grant Development of high-sensitive individualized tumor markers for quantitative evaluation of advanced cancer -



TitleDOIDataset ID


USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use