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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

JGAD000817

Type of data
NGS (WGS)
NGS (Exome)
NGS (Long-read WGS)
NGS (Amplicon-seq)
NGS (RNA-seq)
SNP-chip
Methylation array
Access criteria
Controlled-access (Type I)
Total data volume
851 GB
File formats
  • BAM
  • IDAT
Research
hum0444
Date published
2024-04-04
Date modified
2025-12-11
DDBJ Search
JGAD000817 (opens in a new tab)
JGA Study
JGAS000684 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0444_Supplementary_Table1.xlsxSupplementary Table110.1 KB

Analysis method

WGS

Materials and participants
porokeratosis (ICD10: Q82.8): 4 cases
skin: 5 samples (lesion: 4 samples, non-lesion: 1 sample)
peripheral blood: 3 samples
  • Health status
    Affected
  • Subject count
    4 (Individual)
Disease
porokeratosis (Q828)
Sample description
DNAs extracted from skin and peripheral blood
  • Tissue
    Peripheral blood, Skin
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
TruSeq Nano DNA Library Prep Kit
Fragmentation
Ultrasonic fragmentation
Platform
MGI DNBSEQ-T7
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh37
Mapping
BWA
Mapping quality
>99% mapped to the reference genome (median)
Coverage (depth)
30x
Data use policy
NBDC data sharing policy (JGAP000001)

WES

Materials and participants
porokeratosis (ICD10: Q82.8): 7 cases
skin: 12 samples (lesion: 8 samples, non-lesion: 4 samples)
peripheral blood: 6 samples
  • Health status
    Affected
  • Subject count
    7 (Individual)
Disease
porokeratosis (Q828)
Sample description
DNAs extracted from skin and peripheral blood
  • Tissue
    Peripheral blood, Skin
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WES
Target
N/A
Reagent kit
SureSelect Human All Exon V6
Fragmentation
Ultrasonic fragmentation
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
150 bp
Reference genome
GRCh37
Mapping
BWA
Mapping quality
>99% mapped to the reference genome (median)
Coverage (depth)
140x
Data use policy
NBDC data sharing policy (JGAP000001)

Long-read WGS

Materials and participants
porokeratosis (ICD10: Q82.8): 1 cases
peripheral blood: 1 sample
  • Health status
    Affected
  • Subject count
    1 (Individual)
Disease
porokeratosis (Q828)
Sample description
DNAs extracted from peripheral blood
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
WGS
Target
N/A
Reagent kit
SMRTbell Express Template Prep Kit 3.0
Fragmentation
N/A
Platform
PacBio Sequel II
Read type
Single-end
Read length
15,000 bp (Approx. mean)
Reference genome
GRCh37
Mapping
pbmm2
Mapping quality
100% mapped to the reference genome
Data use policy
NBDC data sharing policy (JGAP000001)

Amplicon-seq

Materials and participants
porokeratosis (ICD10: Q82.8): 7 cases
skin: 20 samples (lesion: 16 samples, non-lesion: 4 samples)
peripheral blood: 4 samples
  • Health status
    Affected
  • Subject count
    7 (Individual)
Disease
porokeratosis (Q828)
Sample description
DNAs extracted from skin and peripheral blood
  • Tissue
    Peripheral blood, Skin
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Amplicon-seq
Target
known causative genes for porokeratosis (Supplementary Table1)
Reagent kit
HaloPlex Target Enrichment
Fragmentation
N/A
Platform
Illumina MiSeq
Read type
Paired-end
Read length
250 bp
Reference genome
GRCh37
Mapping
BWA
Mapping quality
>99% mapped to the reference genome (median)
Coverage (depth)
982x
Data use policy
NBDC data sharing policy (JGAP000001)

RNA-seq

Materials and participants
porokeratosis (ICD10: Q82.8): 1 case
cultured cell: 6 samples (lesion: 3 samples, non-lesion: 3 samples)
  • Health status
    Affected
  • Subject count
    6 (Mixed)
Disease
porokeratosis (Q828)
Sample description
RNAs extracted from cultured cell
  • Tissue
    Cultured cell
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
RNA-seq
Target
N/A
Reagent kit
TruSeq Stranded Total RNA Library Prep Kit
Fragmentation
Divalent cations
Platform
Illumina NovaSeq 6000
Read type
Paired-end
Read length
50 bp
Reference genome
GRCh37
Mapping
STAR
Mapping quality
Uniquely mapped reads (STAR) 84-86%
Data use policy
NBDC data sharing policy (JGAP000001)

genome wide SNPs

Materials and participants
porokeratosis (ICD10: Q82.8): 8 cases
skin: 28 samples (lesion: 21 samples, non-lesion: 5 samples)
peripheral blood: 7 samples
  • Health status
    Affected
  • Subject count
    43 (Mixed)
Disease
porokeratosis (Q828)
Sample description
DNAs extracted from skin and peripheral blood
  • Tissue
    Peripheral blood, Skin
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
Infinium Asian Screening Array Kit
Platform
Illumina Infinium Asian Screening Array
Analysis method
GenomeStudio
Variant count
659,184
Data use policy
NBDC data sharing policy (JGAP000001)

Methylation Array

Materials and participants
porokeratosis (ICD10: Q82.8): 8 cases
skin: 28 samples (lesion: 21 samples, non-lesion: 7 samples)
cultured cell: 2 samples (lesion: 1 sample, non-lesion: 1 sample)
  • Health status
    Affected
  • Subject count
    38 (Mixed)
Disease
porokeratosis (Q828)
Sample description
DNAs extracted from skin and cultured cell
  • Tissue
    Cultured cell, Skin
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Methylation array
Target
N/A
Reagent kit
Infinium MethylationEPIC BeadChip Kit
Platform
Illumina Infinium MethylationEPIC
Probe count
862,927
Data use policy
NBDC data sharing policy (JGAP000001)