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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000985

Type of data
NGS (Exome, RNA-seq)
Access criteria
Controlled-access (Type I)
Total data volume
654 GB
File formats
  • BAM
  • BAI
  • CSV
Research
hum0533
Date published
2025-10-17
Date modified
2025-10-17
DDBJ Search
JGAD000985 (opens in a new tab)
JGA Study
JGAS000843 (opens in a new tab)

Analysis method

WES

Materials and participants
GAPPS (ICD10: D139): 7 cases
61 samples (14 gastric carcinoma, 13 gastric polyp, 27 normal gastric mucosa, 7 peripheral blood)
  • Health status
    Affected
  • Subject count
    7 (Individual)
Disease
GAPPS (D139)
Sample description
DNA extracted from tumor tissues or non-tumor tissues
  • Tissue
    Peripheral blood, Stomach
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
SureSelect Human All Exon V6
Fragmentation
Enzymatic fragmentation
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh38
Mapping quality
Median MAPQ ≥ 60
QC and filtering
FastQC (v0.11.9)
Hard-filter (GATK recommendation)
SNP: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0
INDEL: QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0
Analysis method
GATK (v4.2.6.1), Picard MarkDuplicates (v2.27.5), Samtools (v1.14), ANNOVAR (2020-06-08 release)
Coverage (depth)
175x
144–236x (Range)
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
GAPPS (ICD10: D139): 7 cases
53 samples (13 gastric carcinoma, 13 gastric polyp, 27 normal gastric mucosa)
  • Health status
    Affected
  • Subject count
    7 (Individual)
Disease
GAPPS (D139)
Sample description
RNA extracted from tumor tissues or non-tumor tissues
  • Tissue
    Stomach
  • Tumor / normal
    Mixed
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
NEBNext Ultra II RNA Library Prep Kit for Illumina
Fragmentation
Enzymatic fragmentation
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh38
Mapping quality
Median MAPQ ≥ 60
QC and filtering
FastQC (v0.11.9)
Hard-filter (GATK recommendation)
SNP: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0
INDEL: QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0
Analysis method
STAR (v2.7.10a), RSEM (v1.3.3), Samtools (v1.14), DESeq2 (v1.38.3)
Data use policy
NBDC data sharing policy (JGAP000001)