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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000684 | Controlled-access (Type I) | 2024/04/03 |
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MOLECULAR DATA
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Gene-specific somatic epigenetic mosaicism of FDFT1 underlies a non-hereditary localized form of porokeratosis | JGAD000817 | |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
