NBDC Research ID: hum0444.v1

 

SUMMARY

Aims: In patients diagnosed with a single-gene disease, those considered to have a genetic background or predisposition influencing their disease's pathogenesis, those with diseases believed to involve acquired genetic changes contributing to their development, or those with an undiagnosed disease resembling a genetic predisposition but not matching any known diseases, we analyze both congenital and acquired genetic changes, as well as genetic or expression changes in the diseased tissue, using various multi-omics techniques (whole-exome, whole-genome, targeted-exome, transcriptome, ATAC sequencing, SNP-chip, EPIC array, etc.). The primary objective is to identify the genetic changes contributing to the pathogenesis.

Methods: WGS, WES, long-read WGS, Amplicon-seq, RNA-seq, SNP-chip and methylation array analysis

Participants/Materials: 8 porokeratosis patients

 

Dataset IDType of DataCriteriaRelease Date
JGAS000684

NGS (WGS)

NGS (Exome)

NGS (Long-read WGS)

NGS (Amplicon-seq)

NGS (RNA-seq)

SNP-chip

Methylation array

Controlled-access (Type I) 2024/04/03

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MOLECULAR DATA

WGS

Participants/Materials

porokeratosis (ICD10: Q82.8): 4 cases

    skin: 5 samples (lesion: 4 samples, non-lesion: 1 sample)

    peripheral blood: 3 samples

Targets WGS
Target Loci for Capture Methods -
Platform MGI [DNBSEQ-T7]
Library Source DNAs extracted from skin and peripheral blood
Cell Lines -
Library Construction (kit name) TruSeq Nano DNA Sample Preparation Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Mapping Methods BWA
Mapping Quality >99% mapped to the reference genome (median)
Reference Genome Sequence GRCh37
Coverage (Depth) 30
Japanese Genotype-phenotype Archive Dataset ID JGAD000817
Total Data Volume 850.9 GB (bam)
Comments (Policies) NBDC policy

 

Exome

Participants/Materials

porokeratosis (ICD10: Q82.8): 7 cases

    skin: 12 samples (lesion: 8 samples, non-lesion: 4 samples)

    peripheral blood: 6 samples

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source DNAs extracted from skin and peripheral blood
Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V6 Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Mapping Methods BWA
Mapping Quality >99% mapped to the reference genome (median)
Reference Genome Sequence GRCh37
Coverage (Depth) 140
Japanese Genotype-phenotype Archive Dataset ID JGAD000817
Total Data Volume 850.9 GB (bam)
Comments (Policies) NBDC policy

 

Long-read WGS

Participants/Materials

porokeratosis (ICD10: Q82.8): 1 cases

    peripheral blood: 1 sample

Targets Long-read WGS
Target Loci for Capture Methods -
Platform PacBio [Sequel II]
Library Source DNAs extracted from peripheral blood
Cell Lines -
Library Construction (kit name) SMRTbell Express Template Prep Kit 3.0
Fragmentation Methods -
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 15,000 bp on average
Mapping Methods pbmm2
Mapping Quality 100% mapped to the reference genome
Reference Genome Sequence GRCh37
Coverage (Depth) 4M reads/sample
Japanese Genotype-phenotype Archive Dataset ID JGAD000817
Total Data Volume 850.9 GB (bam)
Comments (Policies) NBDC policy

 

Amplicon-seq

Participants/Materials

porokeratosis (ICD10: Q82.8): 7 cases

    skin: 20 samples (lesion: 16 samples, non-lesion: 4 samples)

    peripheral blood: 4 samples

Targets Amplicon-seq
Target Loci for Capture Methods known causative genes for porokeratosis (Supplementary Table1)
Platform Illumina [MiSeq]
Library Source DNAs extracted from skin and peripheral blood
Cell Lines -
Library Construction (kit name) HaloPlex Target Enrichment System
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 250 bp
Mapping Methods BWA
Mapping Quality >99% mapped to the reference genome (median)
Reference Genome Sequence GRCh37
Coverage (Depth) 982
Japanese Genotype-phenotype Archive Dataset ID JGAD000817
Total Data Volume 850.9 GB (bam)
Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

porokeratosis (ICD10: Q82.8): 1 case

    cultured cell: 6 samples (lesion: 3 samples, non-lesion: 3 samples)

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source RNAs extracted from cultured cell
Cell Lines -
Library Construction (kit name) TruSeq Stranded Total RNA Library Prep kit with Ribo-Zero Human/Mouse/Rat
Fragmentation Methods Divalent cations
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 50 bp
Mapping Methods STAR
Mapping Quality Uniquely mapped reads (STAR) 84-86%
Reference Genome Sequence GRCh37
Coverage (Depth) Number of input reads (STAR) 25-30M reads/sample
Japanese Genotype-phenotype Archive Dataset ID JGAD000817
Total Data Volume 802 GB (bam)
Comments (Policies) NBDC policy

 

SNP-chip

Participants/Materials

porokeratosis (ICD10: Q82.8): 8 cases

    skin: 28 samples (lesion: 21 samples, non-lesion: 5 samples)

    peripheral blood: 7 samples

Targets SNP-chip
Target Loci for Capture Methods -
Platform Illumina [Infinium Asian Screening Array-24 v1.0 BeadChip]
Source DNAs extracted from skin and peripheral blood
Cell Lines -
Reagents (Kit, Version) Infinium Asian Screening Array-24 v1.0 BeadChip
Genotype Call Methods (software) GenomeStudio
Association Analysis (software) -
Marker Number 659,184
Japanese Genotype-phenotype Archive Dataset ID JGAD000817
Total Data Volume 850.9 GB (idat)
Comments (Policies) NBDC policy

 

 

Methylation array

Participants/Materials

porokeratosis (ICD10: Q82.8): 8 cases

    skin: 28 samples (lesion: 21 samples, non-lesion: 7 samples)

    peripheral cultured cell: 2 samples (lesion: 1 sample, non-lesion: 1 sample)

Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina [Infinium MethylationEPIC BeadChip]
Source DNAs extracted from skin and cultured cell
Cell Lines -
Reagents (Kit, Version) Infinium MethylationEPIC BeadChip Kit
Probe Number 862,927
Japanese Genotype-phenotype Archive Dataset ID JGAD000817
Total Data Volume 850.9 GB (idat)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Akiharu Kubo

Affiliation: Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (B) Understanding the mechanism of cell competition/clonal expansion and developing new therapies by elucidating the pathomechanism of porokeratosis JP23H02931
KAKENHI Grant-in-Aid for Scientific Research (B) Understanding cell competition in humans by elucidating the pathomechanism of porokeratosis JP20H03704
Practical Research Project for Rare/Intractable Diseases, Japan Agency for Medical Research and Development (AMED) Diagnosis of rare diseases and elucidation of molecular pathological states by using epigenetic information JP22ek0109489
Practical Research Project for Rare/Intractable Diseases, Japan Agency for Medical Research and Development (AMED) Innovative detection systems for structural, splicing, and methylation aberrations to improve the diagnostic rate of undiagnosed patients: early diagnosis and preparation for N-of-1 drug development JP23ek0109672
Precursory Research for Innovative Medical care (PRIME), Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED) Elucidating the developing factors and expanding mechanisms of juvenile somatic mosaicism to establish novel therapeutic strategies JP21gm6310026

 

PUBLICATIONS

TitleDOIDataset ID
1 Gene-specific somatic epigenetic mosaicism of FDFT1 underlies a non-hereditary localized form of porokeratosis JGAD000817
2

 

USRES (Controlled-access Data)

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